Ciriello, G.
Magnani, L.
Aitken, S.J.
Akkari, L.
Behjati, S.
Hanahan, D.
Landau, D.A.
Lopez-Bigas, N.
Lupiáñez, D.G.
Marine, J.-.
Martin-Villalba, A.
Natoli, G.
Obenauf, A.C.
Oricchio, E.
Scaffidi, P.
Sottoriva, A.
Swarbrick, A.
Tonon, G.
Vanharanta, S.
Zuber, J.
(2024). Cancer Evolution: A Multifaceted Affair. Cancer discov,
Vol.14
(1),
pp. 36-48.
show abstract
full text
UNLABELLED: Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery. SIGNIFICANCE: Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution..
Rosano, D.
Sofyali, E.
Dhiman, H.
Ghirardi, C.
Ivanoiu, D.
Heide, T.
Vingiani, A.
Bertolotti, A.
Pruneri, G.
Canale, E.
Dewhurst, H.F.
Saha, D.
Slaven, N.
Barozzi, I.
Li, T.
Zemlyanskiy, G.
Phillips, H.
James, C.
Győrffy, B.
Lynn, C.
Cresswell, G.D.
Rehman, F.
Noberini, R.
Bonaldi, T.
Sottoriva, A.
Magnani, L.
(2024). Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer discov,
,
pp. OF1-OF24.
show abstract
UNLABELLED: Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE: This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs..
Zapata, L.
Caravagna, G.
Williams, M.J.
Lakatos, E.
AbdulJabbar, K.
Werner, B.
Chowell, D.
James, C.
Gourmet, L.
Milite, S.
Acar, A.
Riaz, N.
Chan, T.A.
Graham, T.A.
Sottoriva, A.
(2023). Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nat genet,
Vol.55
(3),
pp. 451-460.
show abstract
full text
In cancer, evolutionary forces select for clones that evade the immune system. Here we analyzed >10,000 primary tumors and 356 immune-checkpoint-treated metastases using immune dN/dS, the ratio of nonsynonymous to synonymous mutations in the immunopeptidome, to measure immune selection in cohorts and individuals. We classified tumors as immune edited when antigenic mutations were removed by negative selection and immune escaped when antigenicity was covered up by aberrant immune modulation. Only in immune-edited tumors was immune predation linked to CD8 T cell infiltration. Immune-escaped metastases experienced the best response to immunotherapy, whereas immune-edited patients did not benefit, suggesting a preexisting resistance mechanism. Similarly, in a longitudinal cohort, nivolumab treatment removes neoantigens exclusively in the immunopeptidome of nonimmune-edited patients, the group with the best overall survival response. Our work uses dN/dS to differentiate between immune-edited and immune-escaped tumors, measuring potential antigenicity and ultimately helping predict response to treatment..
Chen, B.
Ramazzotti, D.
Heide, T.
Spiteri, I.
Fernandez-Mateos, J.
James, C.
Magnani, L.
Graham, T.A.
Sottoriva, A.
(2023). Contribution of pks+ E coli mutations to colorectal carcinogenesis. Nat commun,
Vol.14
(1),
p. 7827.
show abstract
The dominant mutational signature in colorectal cancer genomes is C > T deamination (COSMIC Signature 1) and, in a small subgroup, mismatch repair signature (COSMIC signatures 6 and 44). Mutations in common colorectal cancer driver genes are often not consistent with those signatures. Here we perform whole-genome sequencing of normal colon crypts from cancer patients, matched to a previous multi-omic tumour dataset. We analyse normal crypts that were distant vs adjacent to the cancer. In contrast to healthy individuals, normal crypts of colon cancer patients have a high incidence of pks + (polyketide synthases) E.coli (Escherichia coli) mutational and indel signatures, and this is confirmed by metagenomics. These signatures are compatible with many clonal driver mutations detected in the corresponding cancer samples, including in chromatin modifier genes, supporting their role in early tumourigenesis. These results provide evidence that pks + E.coli is a potential driver of carcinogenesis in the human gut..
Stankunaite, R.
George, S.L.
Gallagher, L.
Jamal, S.
Shaikh, R.
Yuan, L.
Hughes, D.
Proszek, P.Z.
Carter, P.
Pietka, G.
Heide, T.
James, C.
Tari, H.
Lynn, C.
Jain, N.
Portela, L.R.
Rogers, T.
Vaidya, S.J.
Chisholm, J.C.
Carceller, F.
Szychot, E.
Mandeville, H.
Angelini, P.
Jesudason, A.B.
Jackson, M.
Marshall, L.V.
Gatz, S.A.
Anderson, J.
Sottoriva, A.
Chesler, L.
Hubank, M.
(2022). Circulating tumour DNA sequencing to determine therapeutic response and identify tumour heterogeneity in patients with paediatric solid tumours. Eur j cancer,
Vol.162,
pp. 209-220.
show abstract
full text
OBJECTIVE: Clinical diagnostic sequencing of circulating tumour DNA (ctDNA) is well advanced for adult patients, but application to paediatric cancer patients lags behind. METHODS: To address this, we have developed a clinically relevant (67 gene) NGS capture panel and accompanying workflow that enables sensitive and reliable detection of low-frequency genetic variants in cell-free DNA (cfDNA) from children with solid tumours. We combined gene panel sequencing with low pass whole-genome sequencing of the same library to inform on genome-wide copy number changes in the blood. RESULTS: Analytical validity was evaluated using control materials, and the method was found to be highly sensitive (0.96 for SNVs and 0.97 for INDEL), specific (0.82 for SNVs and 0.978 for INDEL), repeatable (>0.93 [95% CI: 0.89-0.95]) and reproducible (>0.87 [95% CI: 0.87-0.95]). Potential for clinical application was demonstrated in 39 childhood cancer patients with a spectrum of solid tumours in which the single nucleotide variants expected from tumour sequencing were detected in cfDNA in 94.4% (17/18) of cases with active extracranial disease. In 13 patients, where serial samples were available, we show a close correlation between events detected in cfDNA and treatment response, demonstrate that cfDNA analysis could be a useful tool to monitor disease progression, and show cfDNA sequencing has the potential to identify targetable variants that were not detected in tumour samples. CONCLUSIONS: This is the first pan-cancer DNA sequencing panel that we know to be optimised for cfDNA in children for blood-based molecular diagnostics in paediatric solid tumours..
Reijns, M.A.
Parry, D.A.
Williams, T.C.
Nadeu, F.
Hindshaw, R.L.
Rios Szwed, D.O.
Nicholson, M.D.
Carroll, P.
Boyle, S.
Royo, R.
Cornish, A.J.
Xiang, H.
Ridout, K.
Genomics England Research Consortium,
Colorectal Cancer Domain UK 100,000 Genomes Project,
Schuh, A.
Aden, K.
Palles, C.
Campo, E.
Stankovic, T.
Taylor, M.S.
Jackson, A.P.
(2022). Signatures of TOP1 transcription-associated mutagenesis in cancer and germline. Nature,
Vol.602
(7898),
pp. 623-631.
show abstract
full text
The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair1. In microorganisms, transcription has been demonstrated to be mutagenic2,3; however, the impact of transcription-associated mutagenesis remains to be established in higher eukaryotes4. Here we show that ID4-a cancer insertion-deletion (indel) mutation signature of unknown aetiology5 characterized by short (2 to 5 base pair) deletions -is due to a transcription-associated mutagenesis process. We demonstrate that defective ribonucleotide excision repair in mammals is associated with the ID4 signature, with mutations occurring at a TNT sequence motif, implicating topoisomerase 1 (TOP1) activity at sites of genome-embedded ribonucleotides as a mechanistic basis. Such TOP1-mediated deletions occur somatically in cancer, and the ID-TOP1 signature is also found in physiological settings, contributing to genic de novo indel mutations in the germline. Thus, although topoisomerases protect against genome instability by relieving topological stress6, their activity may also be an important source of mutations in the human genome..
Gatenbee, C.D.
Baker, A.-.
Schenck, R.O.
Strobl, M.
West, J.
Neves, M.P.
Hasan, S.Y.
Lakatos, E.
Martinez, P.
Cross, W.C.
Jansen, M.
Rodriguez-Justo, M.
Whelan, C.J.
Sottoriva, A.
Leedham, S.
Robertson-Tessi, M.
Graham, T.A.
Anderson, A.R.
(2022). Immunosuppressive niche engineering at the onset of human colorectal cancer. Nat commun,
Vol.13
(1),
p. 1798.
show abstract
full text
The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune "cold" ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC..
Palles, C.
West, H.D.
Chew, E.
Galavotti, S.
Flensburg, C.
Grolleman, J.E.
Jansen, E.A.
Curley, H.
Chegwidden, L.
Arbe-Barnes, E.H.
Lander, N.
Truscott, R.
Pagan, J.
Bajel, A.
Sherwood, K.
Martin, L.
Thomas, H.
Georgiou, D.
Fostira, F.
Goldberg, Y.
Adams, D.J.
van der Biezen, S.A.
Christie, M.
Clendenning, M.
Thomas, L.E.
Deltas, C.
Dimovski, A.J.
Dymerska, D.
Lubinski, J.
Mahmood, K.
van der Post, R.S.
Sanders, M.
Weitz, J.
Taylor, J.C.
Turnbull, C.
Vreede, L.
van Wezel, T.
Whalley, C.
Arnedo-Pac, C.
Caravagna, G.
Cross, W.
Chubb, D.
Frangou, A.
Gruber, A.J.
Kinnersley, B.
Noyvert, B.
Church, D.
Graham, T.
Houlston, R.
Lopez-Bigas, N.
Sottoriva, A.
Wedge, D.
Genomics England Research Consortium,
CORGI Consortium,
WGS500 Consortium,
Jenkins, M.A.
Kuiper, R.P.
Roberts, A.W.
Cheadle, J.P.
Ligtenberg, M.J.
Hoogerbrugge, N.
Koelzer, V.H.
Rivas, A.D.
Winship, I.M.
Ponte, C.R.
Buchanan, D.D.
Power, D.G.
Green, A.
Tomlinson, I.P.
Sampson, J.R.
Majewski, I.J.
de Voer, R.M.
(2022). Germline MBD4 deficiency causes a multi-tumor predisposition syndrome. Am j hum genet,
Vol.109
(5),
pp. 953-960.
show abstract
full text
We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management..
Heide, T.
Househam, J.
Cresswell, G.D.
Spiteri, I.
Lynn, C.
Mossner, M.
Kimberley, C.
Fernandez-Mateos, J.
Chen, B.
Zapata, L.
James, C.
Barozzi, I.
Chkhaidze, K.
Nichol, D.
Gunasri, V.
Berner, A.
Schmidt, M.
Lakatos, E.
Baker, A.-.
Costa, H.
Mitchinson, M.
Piazza, R.
Jansen, M.
Caravagna, G.
Ramazzotti, D.
Shibata, D.
Bridgewater, J.
Rodriguez-Justo, M.
Magnani, L.
Graham, T.A.
Sottoriva, A.
(2022). The co-evolution of the genome and epigenome in colorectal cancer. Nature,
Vol.611
(7937),
pp. 733-743.
show abstract
full text
Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology..
Househam, J.
Heide, T.
Cresswell, G.D.
Spiteri, I.
Kimberley, C.
Zapata, L.
Lynn, C.
James, C.
Mossner, M.
Fernandez-Mateos, J.
Vinceti, A.
Baker, A.-.
Gabbutt, C.
Berner, A.
Schmidt, M.
Chen, B.
Lakatos, E.
Gunasri, V.
Nichol, D.
Costa, H.
Mitchinson, M.
Ramazzotti, D.
Werner, B.
Iorio, F.
Jansen, M.
Caravagna, G.
Barnes, C.P.
Shibata, D.
Bridgewater, J.
Rodriguez-Justo, M.
Magnani, L.
Sottoriva, A.
Graham, T.A.
(2022). Phenotypic plasticity and genetic control in colorectal cancer evolution. Nature,
Vol.611
(7937),
pp. 744-753.
show abstract
full text
Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour..
Tari, H.
Kessler, K.
Trahearn, N.
Werner, B.
Vinci, M.
Jones, C.
Sottoriva, A.
(2022). Quantification of spatial subclonal interactions enhancing the invasive phenotype of pediatric glioma. Cell rep,
Vol.40
(9),
p. 111283.
show abstract
full text
Diffuse midline gliomas (DMGs) are highly aggressive, incurable childhood brain tumors. They present a clinical challenge due to many factors, including heterogeneity and diffuse infiltration, complicating disease management. Recent studies have described the existence of subclonal populations that may co-operate to drive pro-tumorigenic processes such as cellular invasion. However, a precise quantification of subclonal interactions is lacking, a problem that extends to other cancers. In this study, we combine spatial computational modeling of cellular interactions during invasion with co-evolution experiments of clonally disassembled patient-derived DMG cells. We design a Bayesian inference framework to quantify spatial subclonal interactions between molecular and phenotypically distinct lineages with different patterns of invasion. We show how this approach could discriminate genuine interactions, where one clone enhanced the invasive phenotype of another, from those apparently only due to the complex dynamics of spatially restricted growth. This study provides a framework for the quantification of subclonal interactions in DMG..
Bollen, Y.
Stelloo, E.
van Leenen, P.
van den Bos, M.
Ponsioen, B.
Lu, B.
van Roosmalen, M.J.
Bolhaqueiro, A.C.
Kimberley, C.
Mossner, M.
Cross, W.C.
Besselink, N.J.
van der Roest, B.
Boymans, S.
Oost, K.C.
de Vries, S.G.
Rehmann, H.
Cuppen, E.
Lens, S.M.
Kops, G.J.
Kloosterman, W.P.
Terstappen, L.W.
Barnes, C.P.
Sottoriva, A.
Graham, T.A.
Snippert, H.J.
(2021). Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns. Nat genet,
Vol.53
(8),
pp. 1187-1195.
show abstract
full text
Central to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq-a protocol that integrates live-cell imaging of tumor organoid outgrowth and whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness..
Smyth, E.C.
Vlachogiannis, G.
Hedayat, S.
Harbery, A.
Hulkki-Wilson, S.
Salati, M.
Kouvelakis, K.
Fernandez-Mateos, J.
Cresswell, G.D.
Fontana, E.
Seidlitz, T.
Peckitt, C.
Hahne, J.C.
Lampis, A.
Begum, R.
Watkins, D.
Rao, S.
Starling, N.
Waddell, T.
Okines, A.
Crosby, T.
Mansoor, W.
Wadsley, J.
Middleton, G.
Fassan, M.
Wotherspoon, A.
Braconi, C.
Chau, I.
Vivanco, I.
Sottoriva, A.
Stange, D.E.
Cunningham, D.
Valeri, N.
(2021). EGFR amplification and outcome in a randomised phase III trial of chemotherapy alone or chemotherapy plus panitumumab for advanced gastro-oesophageal cancers. Gut,
Vol.70
(9),
pp. 1632-1641.
show abstract
full text
OBJECTIVE: Epidermal growth factor receptor (EGFR) inhibition may be effective in biomarker-selected populations of advanced gastro-oesophageal adenocarcinoma (aGEA) patients. Here, we tested the association between outcome and EGFR copy number (CN) in pretreatment tissue and plasma cell-free DNA (cfDNA) of patients enrolled in a randomised first-line phase III clinical trial of chemotherapy or chemotherapy plus the anti-EGFR monoclonal antibody panitumumab in aGEA (NCT00824785). DESIGN: EGFR CN by either fluorescence in situ hybridisation (n=114) or digital-droplet PCR in tissues (n=250) and plasma cfDNAs (n=354) was available for 474 (86%) patients in the intention-to-treat (ITT) population. Tissue and plasma low-pass whole-genome sequencing was used to screen for coamplifications in receptor tyrosine kinases. Interaction between chemotherapy and EGFR inhibitors was modelled in patient-derived organoids (PDOs) from aGEA patients. RESULTS: EGFR amplification in cfDNA correlated with poor survival in the ITT population and similar trends were observed when the analysis was conducted in tissue and plasma by treatment arm. EGFR inhibition in combination with chemotherapy did not correlate with improved survival, even in patients with significant EGFR CN gains. Addition of anti-EGFR inhibitors to the chemotherapy agent epirubicin in PDOs, resulted in a paradoxical increase in viability and accelerated progression through the cell cycle, associated with p21 and cyclin B1 downregulation and cyclin E1 upregulation, selectively in organoids from EGFR-amplified aGEA. CONCLUSION: EGFR CN can be accurately measured in tissue and liquid biopsies and may be used for the selection of aGEA patients. EGFR inhibitors may antagonise the antitumour effect of anthracyclines with important implications for the design of future combinatorial trials..
Sottoriva, A.
Heide, T.
Cresswell, G.
Spiteri, I.
Lynn, C.
Fernandez-Mateos, J.
Chen, B.
Zapata, L.
Chkhaidze, K.
Nichol, D.
Caravagna, G.
James, C.
Mossner, M.
Kimberley, C.
Househam, J.
Berner, A.
Schmidt, M.
Lakatos, E.
Baker, A.-.
Graham, T.
Barozzi, I.
Costa, H.
Mitchinson, M.
Jansen, M.
Bridgewater, J.
Rodriguez-Justo, M.
Magnani, L.
Ramazzotti, D.
Shibata, D.
(2021). The co-evolution of the genome and epigenome in colorectal cancer. ,
.
show abstract
Colorectal malignancies are a leading cause of cancer death. Despite large-scale genomic efforts, DNA mutations do not fully explain malignant evolution. Here we study the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,373 samples from 30 primary cancers and 9 concomitant adenomas and generated 1,212 chromatin accessibility profiles, 527 whole-genomes and 297 whole-transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent chromatin changes in regulatory regions of cancer drivers with otherwise no mutation. Genome-wide alterations in transcription factor binding accessibility involved CTCF, downregulation of interferon, and increased accessibility for SOX and HOX, indicating developmental genes reactivation. Epigenetic aberrations were heritable, distinguishing adenomas from cancers. Mutational signature analysis showed the epigenome influencing DNA mutation accumulation. This study provides a map of (epi)genetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology..
Lupo, B.
Sassi, F.
Pinnelli, M.
Galimi, F.
Zanella, E.R.
Vurchio, V.
Migliardi, G.
Gagliardi, P.A.
Puliafito, A.
Manganaro, D.
Luraghi, P.
Kragh, M.
Pedersen, M.W.
Horak, I.D.
Boccaccio, C.
Medico, E.
Primo, L.
Nichol, D.
Spiteri, I.
Heide, T.
Vatsiou, A.
Graham, T.A.
Élez, E.
Argiles, G.
Nuciforo, P.
Sottoriva, A.
Dienstmann, R.
Pasini, D.
Grassi, E.
Isella, C.
Bertotti, A.
Trusolino, L.
(2020). Colorectal cancer residual disease at maximal response to EGFR blockade displays a druggable Paneth cell-like phenotype. Sci transl med,
Vol.12
(555).
show abstract
full text
Blockade of epidermal growth factor receptor (EGFR) causes tumor regression in some patients with metastatic colorectal cancer (mCRC). However, residual disease reservoirs typically remain even after maximal response to therapy, leading to relapse. Using patient-derived xenografts (PDXs), we observed that mCRC cells surviving EGFR inhibition exhibited gene expression patterns similar to those of a quiescent subpopulation of normal intestinal secretory precursors with Paneth cell characteristics. Compared with untreated tumors, these pseudodifferentiated tumor remnants had reduced expression of genes encoding EGFR-activating ligands, enhanced activity of human epidermal growth factor receptor 2 (HER2) and HER3, and persistent signaling along the phosphatidylinositol 3-kinase (PI3K) pathway. Clinically, properties of residual disease cells from the PDX models were detected in lingering tumors of responsive patients and in tumors of individuals who had experienced early recurrence. Mechanistically, residual tumor reprogramming after EGFR neutralization was mediated by inactivation of Yes-associated protein (YAP), a master regulator of intestinal epithelium recovery from injury. In preclinical trials, Pan-HER antibodies minimized residual disease, blunted PI3K signaling, and induced long-term tumor control after treatment discontinuation. We found that tolerance to EGFR inhibition is characterized by inactivation of an intrinsic lineage program that drives both regenerative signaling during intestinal repair and EGFR-dependent tumorigenesis. Thus, our results shed light on CRC lineage plasticity as an adaptive escape mechanism from EGFR-targeted therapy and suggest opportunities to preemptively target residual disease..
Loupakis, F.
Depetris, I.
Biason, P.
Intini, R.
Prete, A.A.
Leone, F.
Lombardi, P.
Filippi, R.
Spallanzani, A.
Cascinu, S.
Bonetti, L.R.
Maddalena, G.
Valeri, N.
Sottoriva, A.
Zapata, L.
Salmaso, R.
Munari, G.
Rugge, M.
Dei Tos, A.P.
Golovato, J.
Sanborn, J.Z.
Nguyen, A.
Schirripa, M.
Zagonel, V.
Lonardi, S.
Fassan, M.
(2020). Prediction of Benefit from Checkpoint Inhibitors in Mismatch Repair Deficient Metastatic Colorectal Cancer: Role of Tumor Infiltrating Lymphocytes. Oncologist,
Vol.25
(6),
pp. 481-487.
show abstract
BACKGROUND: Immunotherapy with immune checkpoint inhibitors (ICIs) is highly effective in microsatellite instability-high (MSI-H) metastatic colorectal cancer (mCRC); however, specific predictive biomarkers are lacking. PATIENTS AND METHODS: Data and samples from 85 patients with MSI-H mCRC treated with ICIs were gathered. Tumor infiltrating lymphocytes (TILs) and tumor mutational burden (TMB) were analyzed in an exploratory cohort of "super" responders and "clearly" refractory patients; TILs were then evaluated in the whole cohort of patients. Primary objectives were the correlation between the number of TILs and TMB and their role as biomarkers of ICI efficacy. Main endpoints included response rate (RR), progression-free survival (PFS), and overall survival (OS). RESULTS: In the exploratory cohort, an increasing number of TILs correlated to higher TMB (Pearson's test, p = .0429). In the whole cohort, median number of TILs was 3.6 in responders compared with 1.8 in nonresponders (Mann-Whitney test, p = .0448). RR was 70.6% in patients with high number of TILs (TILs-H) compared with 42.9% in patients with low number of TILs (odds ratio = 3.20, p = .0291). Survival outcomes differed significantly in favor of TILs-H (PFS: hazard ratio [HR] = 0.42, p = .0278; OS: HR = 0.41, p = .0463). CONCLUSION: A significant correlation between higher TMB and increased number of TILs was shown. A significantly higher activity and better PFS and OS with ICI in MSI-H mCRC were reported in cases with high number of TILs, thus supporting further studies of TIL count as predictive biomarker of ICI efficacy. IMPLICATIONS FOR PRACTICE: Microsatellite instability is the result of mismatch repair protein deficiency, caused by germline mutations or somatic modifications in mismatch repair genes. In metastatic colorectal cancer (mCRC), immunotherapy (with immune checkpoint inhibitors [ICIs]) demonstrated remarkable clinical benefit in microsatellite instability-high (MSI-H) patients. ICI primary resistance has been observed in approximately 25% of patients with MSI-H mCRC, underlining the need for predictive biomarkers. In this study, tumor mutational burden (TMB) and tumor infiltrating lymphocyte (TIL) analyses were performed in an exploratory cohort of patients with MSI-H mCRC treated with ICIs, demonstrating a significant correlation between higher TMB and increased number of TILs. Results also demonstrated a significant correlation between high number of TILs and clinical responses and survival benefit in a large data set of patients with MSI-H mCRC treated with ICI. TMB and TILs could represent predictive biomarkers of ICI efficacy in MSI-H mCRC and should be incorporated in future trials testing checkpoint inhibitors in colorectal cancer..
Caravagna, G.
Heide, T.
Williams, M.J.
Zapata, L.
Nichol, D.
Chkhaidze, K.
Cross, W.
Cresswell, G.D.
Werner, B.
Acar, A.
Chesler, L.
Barnes, C.P.
Sanguinetti, G.
Graham, T.A.
Sottoriva, A.
(2020). Subclonal reconstruction of tumors by using machine learning and population genetics. Nat genet,
Vol.52
(9),
pp. 898-907.
show abstract
full text
Most cancer genomic data are generated from bulk samples composed of mixtures of cancer subpopulations, as well as normal cells. Subclonal reconstruction methods based on machine learning aim to separate those subpopulations in a sample and infer their evolutionary history. However, current approaches are entirely data driven and agnostic to evolutionary theory. We demonstrate that systematic errors occur in the analysis if evolution is not accounted for, and this is exacerbated with multi-sampling of the same tumor. We present a novel approach for model-based tumor subclonal reconstruction, called MOBSTER, which combines machine learning with theoretical population genetics. Using public whole-genome sequencing data from 2,606 samples from different cohorts, new data and synthetic validation, we show that this method is more robust and accurate than current techniques in single-sample, multiregion and longitudinal data. This approach minimizes the confounding factors of nonevolutionary methods, thus leading to more accurate recovery of the evolutionary history of human cancers..
Lakatos, E.
Williams, M.J.
Schenck, R.O.
Cross, W.C.
Househam, J.
Zapata, L.
Werner, B.
Gatenbee, C.
Robertson-Tessi, M.
Barnes, C.P.
Anderson, A.R.
Sottoriva, A.
Graham, T.A.
(2020). Evolutionary dynamics of neoantigens in growing tumors. Nat genet,
Vol.52
(10),
pp. 1057-1066.
show abstract
full text
Cancers accumulate mutations that lead to neoantigens, novel peptides that elicit an immune response, and consequently undergo evolutionary selection. Here we establish how negative selection shapes the clonality of neoantigens in a growing cancer by constructing a mathematical model of neoantigen evolution. The model predicts that, without immune escape, tumor neoantigens are either clonal or at low frequency; hypermutated tumors can only establish after the evolution of immune escape. Moreover, the site frequency spectrum of somatic variants under negative selection appears more neutral as the strength of negative selection increases, which is consistent with classical neutral theory. These predictions are corroborated by the analysis of neoantigen frequencies and immune escape in exome and RNA sequencing data from 879 colon, stomach and endometrial cancers..
Caravagna, G.
Sanguinetti, G.
Graham, T.A.
Sottoriva, A.
(2020). The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. Bmc bioinformatics,
Vol.21
(1),
p. 531.
show abstract
full text
BACKGROUND: The large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolution methods are used to determine the composition of cancer subpopulations in the biopsy sample, a fundamental step to determine clonal expansions and their evolutionary trajectories. RESULTS: In a recent work we have developed a new model-based approach to carry out subclonal deconvolution from the site frequency spectrum of somatic mutations. This new method integrates, for the first time, an explicit model for neutral evolutionary forces that participate in clonal expansions; in that work we have also shown that our method improves largely over competing data-driven methods. In this Software paper we present mobster, an open source R package built around our new deconvolution approach, which provides several functions to plot data and fit models, assess their confidence and compute further evolutionary analyses that relate to subclonal deconvolution. CONCLUSIONS: We present the mobster package for tumour subclonal deconvolution from bulk sequencing, the first approach to integrate Machine Learning and Population Genetics which can explicitly model co-existing neutral and positive selection in cancer. We showcase the analysis of two datasets, one simulated and one from a breast cancer patient, and overview all package functionalities..
Acar, A.
Nichol, D.
Fernandez-Mateos, J.
Cresswell, G.D.
Barozzi, I.
Hong, S.P.
Trahearn, N.
Spiteri, I.
Stubbs, M.
Burke, R.
Stewart, A.
Caravagna, G.
Werner, B.
Vlachogiannis, G.
Maley, C.C.
Magnani, L.
Valeri, N.
Banerji, U.
Sottoriva, A.
(2020). Exploiting evolutionary steering to induce collateral drug sensitivity in cancer. Nat commun,
Vol.11
(1),
p. 1923.
show abstract
full text
Drug resistance mediated by clonal evolution is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at a cost of decreased fecundity or increased sensitivity to another drug. These evolutionary trade-offs can be exploited using 'evolutionary steering' to control the tumour population and delay resistance. However, recapitulating cancer evolutionary dynamics experimentally remains challenging. Here, we present an approach for evolutionary steering based on a combination of single-cell barcoding, large populations of 108-109 cells grown without re-plating, longitudinal non-destructive monitoring of cancer clones, and mathematical modelling of tumour evolution. We demonstrate evolutionary steering in a lung cancer model, showing that it shifts the clonal composition of the tumour in our favour, leading to collateral sensitivity and proliferative costs. Genomic profiling revealed some of the mechanisms that drive evolved sensitivity. This approach allows modelling evolutionary steering strategies that can potentially control treatment resistance..
Werner, B.
Case, J.
Williams, M.J.
Chkhaidze, K.
Temko, D.
Fernández-Mateos, J.
Cresswell, G.D.
Nichol, D.
Cross, W.
Spiteri, I.
Huang, W.
Tomlinson, I.P.
Barnes, C.P.
Graham, T.A.
Sottoriva, A.
(2020). Measuring single cell divisions in human tissues from multi-region sequencing data. Nat commun,
Vol.11
(1),
p. 1035.
show abstract
full text
Both normal tissue development and cancer growth are driven by a branching process of cell division and mutation accumulation that leads to intra-tissue genetic heterogeneity. However, quantifying somatic evolution in humans remains challenging. Here, we show that multi-sample genomic data from a single time point of normal and cancer tissues contains information on single-cell divisions. We present a new theoretical framework that, applied to whole-genome sequencing data of healthy tissue and cancer, allows inferring the mutation rate and the cell survival/death rate per division. On average, we found that cells accumulate 1.14 mutations per cell division in healthy haematopoiesis and 1.37 mutations per division in brain development. In both tissues, cell survival was maximal during early development. Analysis of 131 biopsies from 16 tumours showed 4 to 100 times increased mutation rates compared to healthy development and substantial inter-patient variation of cell survival/death rates..
Cresswell, G.D.
Nichol, D.
Spiteri, I.
Tari, H.
Zapata, L.
Heide, T.
Maley, C.C.
Magnani, L.
Schiavon, G.
Ashworth, A.
Barry, P.
Sottoriva, A.
(2020). Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking. Nat commun,
Vol.11
(1),
p. 1446.
show abstract
full text
Circulating tumour DNA (ctDNA) allows tracking of the evolution of human cancers at high resolution, overcoming many limitations of tissue biopsies. However, exploiting ctDNA to determine how a patient's cancer is evolving in order to aid clinical decisions remains difficult. This is because ctDNA is a mix of fragmented alleles, and the contribution of different cancer deposits to ctDNA is largely unknown. Profiling ctDNA almost invariably requires prior knowledge of what genomic alterations to track. Here, we leverage on a rapid autopsy programme to demonstrate that unbiased genomic characterisation of several metastatic sites and concomitant ctDNA profiling at whole-genome resolution reveals the extent to which ctDNA is representative of widespread disease. We also present a methylation profiling method that allows tracking evolutionary changes in ctDNA at single-molecule resolution without prior knowledge. These results have critical implications for the use of liquid biopsies to monitor cancer evolution in humans and guide treatment..
Williams, M.J.
Zapata, L.
Werner, B.
Barnes, C.P.
Sottoriva, A.
Graham, T.A.
(2020). Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios. Elife,
Vol.9.
show abstract
full text
The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection in somatic cells. However the link, in somatic evolution, between dN/dS values and fitness coefficients is missing. Here we present a quantitative model of somatic evolutionary dynamics that determines the selective coefficients of individual driver mutations from dN/dS estimates. We then measure the DFE for somatic mutant clones in ostensibly normal oesophagus and skin. We reveal a broad distribution of fitness effects, with the largest fitness increases found for TP53 and NOTCH1 mutants (proliferative bias 1-5%). This study provides the theoretical link between dN/dS values and selective coefficients in somatic evolution, and measures the DFE of mutations in human tissues..
Spiteri, I.
Caravagna, G.
Cresswell, G.D.
Vatsiou, A.
Nichol, D.
Acar, A.
Ermini, L.
Chkhaidze, K.
Werner, B.
Mair, R.
Brognaro, E.
Verhaak, R.G.
Sanguinetti, G.
Piccirillo, S.G.
Watts, C.
Sottoriva, A.
(2019). Evolutionary dynamics of residual disease in human glioblastoma. Ann oncol,
Vol.30
(3),
pp. 456-463.
show abstract
full text
BACKGROUND: Glioblastoma is the most common and aggressive adult brain malignancy against which conventional surgery and chemoradiation provide limited benefit. Even when a good treatment response is obtained, recurrence inevitably occurs either locally (∼80%) or distally (∼20%), driven by cancer clones that are often genomically distinct from those in the primary tumour. Glioblastoma cells display a characteristic infiltrative phenotype, invading the surrounding tissue and often spreading across the whole brain. Cancer cells responsible for relapse can reside in two compartments of residual disease that are left behind after treatment: the infiltrated normal brain parenchyma and the sub-ventricular zone. However, these two sources of residual disease in glioblastoma are understudied because of the difficulty in sampling these regions during surgery. PATIENT AND METHODS: Here, we present the results of whole-exome sequencing of 69 multi-region samples collected using fluorescence-guided resection from 11 patients, including the infiltrating tumour margin and the sub-ventricular zone for each patient, as well as matched blood. We used a phylogenomic approach to dissect the spatio-temporal evolution of each tumour and unveil the relation between residual disease and the main tumour mass. We also analysed two patients with paired primary-recurrence samples with matched residual disease. RESULTS: Our results suggest that infiltrative subclones can arise early during tumour growth in a subset of patients. After treatment, the infiltrative subclones may seed the growth of a recurrent tumour, thus representing the 'missing link' between the primary tumour and recurrent disease. CONCLUSIONS: These results are consistent with recognised clinical phenotypic behaviour and suggest that more specific therapeutic targeting of cells in the infiltrated brain parenchyma may improve patient's outcome..
Turajlic, S.
Sottoriva, A.
Graham, T.
Swanton, C.
(2019). Resolving genetic heterogeneity in cancer. Nat rev genet,
Vol.20
(7),
pp. 404-416.
show abstract
full text
To a large extent, cancer conforms to evolutionary rules defined by the rates at which clones mutate, adapt and grow. Next-generation sequencing has provided a snapshot of the genetic landscape of most cancer types, and cancer genomics approaches are driving new insights into cancer evolutionary patterns in time and space. In contrast to species evolution, cancer is a particular case owing to the vast size of tumour cell populations, chromosomal instability and its potential for phenotypic plasticity. Nevertheless, an evolutionary framework is a powerful aid to understand cancer progression and therapy failure. Indeed, such a framework could be applied to predict individual tumour behaviour and support treatment strategies..
Chkhaidze, K.
Heide, T.
Werner, B.
Williams, M.J.
Huang, W.
Caravagna, G.
Graham, T.A.
Sottoriva, A.
(2019). Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. Plos comput biol,
Vol.15
(7),
p. e1007243.
show abstract
full text
Quantification of the effect of spatial tumour sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumour growth that accounts for somatic mutations, selection, drift and spatial constraints, to simulate multi-region sequencing data derived from spatial sampling of a neoplasm. We show that the spatial structure of a solid cancer has a major impact on the detection of clonal selection and genetic drift from both bulk and single-cell sequencing data. Our results indicate that spatial constrains can introduce significant sampling biases when performing multi-region bulk sampling and that such bias becomes a major confounding factor for the measurement of the evolutionary dynamics of human tumours. We also propose a statistical inference framework that incorporates spatial effects within a growing tumour and so represents a further step forwards in the inference of evolutionary dynamics from genomic data. Our analysis shows that measuring cancer evolution using next-generation sequencing while accounting for the numerous confounding factors remains challenging. However, mechanistic model-based approaches have the potential to capture the sources of noise and better interpret the data..
Nawaz, S.
Trahearn, N.A.
Heindl, A.
Banerjee, S.
Maley, C.C.
Sottoriva, A.
Yuan, Y.
(2019). Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer. Ebiomedicine,
Vol.48,
pp. 224-235.
show abstract
full text
BACKGROUND: Despite treatment advances, there remains a significant risk of recurrence in ovarian cancer, at which stage it is usually incurable. Consequently, there is a clear need for improved patient stratification. However, at present clinical prognosticators remain largely unchanged due to the lack of reproducible methods to identify high-risk patients. METHODS: In high-grade serous ovarian cancer patients with advanced disease, we spatially define a tumour ecological balance of stromal resource and immune hazard using high-throughput image and spatial analysis of routine histology slides. On this basis an EcoScore is developed to classify tumours by a shift in this balance towards cancer-favouring or inhibiting conditions. FINDINGS: The EcoScore provides prognostic value stronger than, and independent of, known risk factors. Crucially, the clinical relevance of mutational burden and genomic instability differ under different stromal resource conditions, suggesting that the selective advantage of these cancer hallmarks is dependent on the context of stromal spatial structure. Under a high resource condition defined by a high level of geographical intermixing of cancer and stromal cells, selection appears to be driven by point mutations; whereas, in low resource tumours featured with high hypoxia and low cancer-immune co-localization, selection is fuelled by aneuploidy. INTERPRETATION: Our study offers empirical evidence that cancer fitness depends on tumour spatial constraints, and presents a biological basis for developing better assessments of tumour adaptive strategies in overcoming ecological constraints including immune surveillance and hypoxia..
Williams, M.J.
Sottoriva, A.
Graham, T.A.
(2019). Measuring Clonal Evolution in Cancer with Genomics. Annu rev genomics hum genet,
Vol.20,
pp. 309-329.
show abstract
Cancers originate from somatic cells in the human body that have accumulated genetic alterations. These mutations modify the phenotype of the cells, allowing them to escape the homeostatic regulation that maintains normal cell number. Viewed through the lens of evolutionary biology, the transformation of normal cells into malignant cells is evolution in action. Evolution continues throughout cancer growth, progression, treatment resistance, and disease relapse, driven by adaptation to changes in the cancer's environment, and intratumor heterogeneity is an inevitable consequence of this evolutionary process. Genomics provides a powerful means to characterize tumor evolution, enabling quantitative measurement of evolving clones across space and time. In this review, we discuss concepts and approaches to quantify and measure this evolutionary process in cancer using genomics..
Sottoriva, A.
(2018). Divergent adaptation in thyroid cancers. Ann oncol,
Vol.29
(6),
pp. 1353-1353.
full text
Barry, P.
Vatsiou, A.
Spiteri, I.
Nichol, D.
Cresswell, G.D.
Acar, A.
Trahearn, N.
Hrebien, S.
Garcia-Murillas, I.
Chkhaidze, K.
Ermini, L.
Huntingford, I.S.
Cottom, H.
Zabaglo, L.
Koelble, K.
Khalique, S.
Rusby, J.E.
Muscara, F.
Dowsett, M.
Maley, C.C.
Natrajan, R.
Yuan, Y.
Schiavon, G.
Turner, N.
Sottoriva, A.
(2018). The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer. Clin cancer res,
Vol.24
(19),
pp. 4763-4770.
show abstract
full text
Purpose: The most significant prognostic factor in early breast cancer is lymph node involvement. This stage between localized and systemic disease is key to understanding breast cancer progression; however, our knowledge of the evolution of lymph node malignant invasion remains limited, as most currently available data are derived from primary tumors.Experimental Design: In 11 patients with treatment-naïve node-positive early breast cancer without clinical evidence of distant metastasis, we investigated lymph node evolution using spatial multiregion sequencing (n = 78 samples) of primary and lymph node deposits and genomic profiling of matched longitudinal circulating tumor DNA (ctDNA).Results: Linear evolution from primary to lymph node was rare (1/11), whereas the majority of cases displayed either early divergence between primary and nodes (4/11) or no detectable divergence (6/11), where both primary and nodal cells belonged to a single recent expansion of a metastatic clone. Divergence of metastatic subclones was driven in part by APOBEC. Longitudinal ctDNA samples from 2 of 7 subjects with evaluable plasma taken perioperatively reflected the two major evolutionary patterns and demonstrate that private mutations can be detected even from early metastatic nodal deposits. Moreover, node removal resulted in disappearance of private lymph node mutations in ctDNA.Conclusions: This study sheds new light on a crucial evolutionary step in the natural history of breast cancer, demonstrating early establishment of axillary lymph node metastasis in a substantial proportion of patients. Clin Cancer Res; 24(19); 4763-70. ©2018 AACR..
Williams, M.J.
Werner, B.
Heide, T.
Curtis, C.
Barnes, C.P.
Sottoriva, A.
Graham, T.A.
(2018). Quantification of subclonal selection in cancer from bulk sequencing data. Nat genet,
Vol.50
(6),
pp. 895-903.
show abstract
full text
Subclonal architectures are prevalent across cancer types. However, the temporal evolutionary dynamics that produce tumor subclones remain unknown. Here we measure clone dynamics in human cancers by using computational modeling of subclonal selection and theoretical population genetics applied to high-throughput sequencing data. Our method determined the detectable subclonal architecture of tumor samples and simultaneously measured the selective advantage and time of appearance of each subclone. We demonstrate the accuracy of our approach and the extent to which evolutionary dynamics are recorded in the genome. Application of our method to high-depth sequencing data from breast, gastric, blood, colon and lung cancer samples, as well as metastatic deposits, showed that detectable subclones under selection, when present, consistently emerged early during tumor growth and had a large fitness advantage (>20%). Our quantitative framework provides new insight into the evolutionary trajectories of human cancers and facilitates predictive measurements in individual tumors from widely available sequencing data..
Werner, B.
Sottoriva, A.
(2018). Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates. Plos comput biol,
Vol.14
(6),
p. e1006233.
show abstract
full text
The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand, thus avoiding accumulating somatic mutations. However, quantitating the extent of non-random DNA strand segregation in human stem cells remains difficult in vivo. Here we show that the change of the mean and variance of the mutational burden with age in healthy human tissues allows estimating strand segregation probabilities and somatic mutation rates. We analysed deep sequencing data from healthy human colon, small intestine, liver, skin and brain. We found highly effective non-random DNA strand segregation in all adult tissues (mean strand segregation probability: 0.98, standard error bounds (0.97,0.99)). In contrast, non-random strand segregation efficiency is reduced to 0.87 (0.78,0.88) in neural tissue during early development, suggesting stem cell pool expansions due to symmetric self-renewal. Healthy somatic mutation rates differed across tissue types, ranging from 3.5 × 10-9/bp/division in small intestine to 1.6 × 10-7/bp/division in skin..
Caravagna, G.
Giarratano, Y.
Ramazzotti, D.
Tomlinson, I.
Graham, T.A.
Sanguinetti, G.
Sottoriva, A.
(2018). Detecting repeated cancer evolution from multi-region tumor sequencing data. Nat methods,
Vol.15
(9),
pp. 707-714.
show abstract
full text
Recurrent successions of genomic changes, both within and between patients, reflect repeated evolutionary processes that are valuable for the anticipation of cancer progression. Multi-region sequencing allows the temporal order of some genomic changes in a tumor to be inferred, but the robust identification of repeated evolution across patients remains a challenge. We developed a machine-learning method based on transfer learning that allowed us to overcome the stochastic effects of cancer evolution and noise in data and identified hidden evolutionary patterns in cancer cohorts. When applied to multi-region sequencing datasets from lung, breast, renal, and colorectal cancer (768 samples from 178 patients), our method detected repeated evolutionary trajectories in subgroups of patients, which were reproduced in single-sample cohorts (n = 2,935). Our method provides a means of classifying patients on the basis of how their tumor evolved, with implications for the anticipation of disease progression..
Khan, K.H.
Cunningham, D.
Werner, B.
Vlachogiannis, G.
Spiteri, I.
Heide, T.
Mateos, J.F.
Vatsiou, A.
Lampis, A.
Damavandi, M.D.
Lote, H.
Huntingford, I.S.
Hedayat, S.
Chau, I.
Tunariu, N.
Mentrasti, G.
Trevisani, F.
Rao, S.
Anandappa, G.
Watkins, D.
Starling, N.
Thomas, J.
Peckitt, C.
Khan, N.
Rugge, M.
Begum, R.
Hezelova, B.
Bryant, A.
Jones, T.
Proszek, P.
Fassan, M.
Hahne, J.C.
Hubank, M.
Braconi, C.
Sottoriva, A.
Valeri, N.
(2018). Longitudinal Liquid Biopsy and Mathematical Modeling of Clonal Evolution Forecast Time to Treatment Failure in the PROSPECT-C Phase II Colorectal Cancer Clinical Trial. Cancer discov,
Vol.8
(10),
pp. 1270-1285.
show abstract
full text
Sequential profiling of plasma cell-free DNA (cfDNA) holds immense promise for early detection of patient progression. However, how to exploit the predictive power of cfDNA as a liquid biopsy in the clinic remains unclear. RAS pathway aberrations can be tracked in cfDNA to monitor resistance to anti-EGFR monoclonal antibodies in patients with metastatic colorectal cancer. In this prospective phase II clinical trial of single-agent cetuximab in RAS wild-type patients, we combine genomic profiling of serial cfDNA and matched sequential tissue biopsies with imaging and mathematical modeling of cancer evolution. We show that a significant proportion of patients defined as RAS wild-type based on diagnostic tissue analysis harbor aberrations in the RAS pathway in pretreatment cfDNA and, in fact, do not benefit from EGFR inhibition. We demonstrate that primary and acquired resistance to cetuximab are often of polyclonal nature, and these dynamics can be observed in tissue and plasma. Furthermore, evolutionary modeling combined with frequent serial sampling of cfDNA allows prediction of the expected time to treatment failure in individual patients. This study demonstrates how integrating frequently sampled longitudinal liquid biopsies with a mathematical framework of tumor evolution allows individualized quantitative forecasting of progression, providing novel opportunities for adaptive personalized therapies.Significance: Liquid biopsies capture spatial and temporal heterogeneity underpinning resistance to anti-EGFR monoclonal antibodies in colorectal cancer. Dense serial sampling is needed to predict the time to treatment failure and generate a window of opportunity for intervention. Cancer Discov; 8(10); 1270-85. ©2018 AACR. See related commentary by Siravegna and Corcoran, p. 1213 This article is highlighted in the In This Issue feature, p. 1195..
Cross, W.
Kovac, M.
Mustonen, V.
Temko, D.
Davis, H.
Baker, A.-.
Biswas, S.
Arnold, R.
Chegwidden, L.
Gatenbee, C.
Anderson, A.R.
Koelzer, V.H.
Martinez, P.
Jiang, X.
Domingo, E.
Woodcock, D.J.
Feng, Y.
Kovacova, M.
Maughan, T.
S:CORT Consortium,
Jansen, M.
Rodriguez-Justo, M.
Ashraf, S.
Guy, R.
Cunningham, C.
East, J.E.
Wedge, D.C.
Wang, L.M.
Palles, C.
Heinimann, K.
Sottoriva, A.
Leedham, S.J.
Graham, T.A.
Tomlinson, I.P.
(2018). The evolutionary landscape of colorectal tumorigenesis. Nat ecol evol,
Vol.2
(10),
pp. 1661-1672.
show abstract
full text
The evolutionary events that cause colorectal adenomas (benign) to progress to carcinomas (malignant) remain largely undetermined. Using multi-region genome and exome sequencing of 24 benign and malignant colorectal tumours, we investigate the evolutionary fitness landscape occupied by these neoplasms. Unlike carcinomas, advanced adenomas frequently harbour sub-clonal driver mutations-considered to be functionally important in the carcinogenic process-that have not swept to fixation, and have relatively high genetic heterogeneity. Carcinomas are distinguished from adenomas by widespread aneusomies that are usually clonal and often accrue in a 'punctuated' fashion. We conclude that adenomas evolve across an undulating fitness landscape, whereas carcinomas occupy a sharper fitness peak, probably owing to stabilizing selection..
Vlachogiannis, G.
Hedayat, S.
Vatsiou, A.
Jamin, Y.
Fernández-Mateos, J.
Khan, K.
Lampis, A.
Eason, K.
Huntingford, I.
Burke, R.
Rata, M.
Koh, D.-.
Tunariu, N.
Collins, D.
Hulkki-Wilson, S.
Ragulan, C.
Spiteri, I.
Moorcraft, S.Y.
Chau, I.
Rao, S.
Watkins, D.
Fotiadis, N.
Bali, M.
Darvish-Damavandi, M.
Lote, H.
Eltahir, Z.
Smyth, E.C.
Begum, R.
Clarke, P.A.
Hahne, J.C.
Dowsett, M.
de Bono, J.
Workman, P.
Sadanandam, A.
Fassan, M.
Sansom, O.J.
Eccles, S.
Starling, N.
Braconi, C.
Sottoriva, A.
Robinson, S.P.
Cunningham, D.
Valeri, N.
(2018). Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science,
Vol.359
(6378),
pp. 920-926.
show abstract
full text
Patient-derived organoids (PDOs) have recently emerged as robust preclinical models; however, their potential to predict clinical outcomes in patients has remained unclear. We report on a living biobank of PDOs from metastatic, heavily pretreated colorectal and gastroesophageal cancer patients recruited in phase 1/2 clinical trials. Phenotypic and genotypic profiling of PDOs showed a high degree of similarity to the original patient tumors. Molecular profiling of tumor organoids was matched to drug-screening results, suggesting that PDOs could complement existing approaches in defining cancer vulnerabilities and improving treatment responses. We compared responses to anticancer agents ex vivo in organoids and PDO-based orthotopic mouse tumor xenograft models with the responses of the patients in clinical trials. Our data suggest that PDOs can recapitulate patient responses in the clinic and could be implemented in personalized medicine programs..
Heindl, A.
Khan, A.M.
Rodrigues, D.N.
Eason, K.
Sadanandam, A.
Orbegoso, C.
Punta, M.
Sottoriva, A.
Lise, S.
Banerjee, S.
Yuan, Y.
(2018). Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. Nat commun,
Vol.9
(1),
p. 3917.
show abstract
full text
How tumor microenvironmental forces shape plasticity of cancer cell morphology is poorly understood. Here, we conduct automated histology image and spatial statistical analyses in 514 high grade serous ovarian samples to define cancer morphological diversification within the spatial context of the microenvironment. Tumor spatial zones, where cancer cell nuclei diversify in shape, are mapped in each tumor. Integration of this spatially explicit analysis with omics and clinical data reveals a relationship between morphological diversification and the dysregulation of DNA repair, loss of nuclear integrity, and increased disease mortality. Within the Immunoreactive subtype, spatial analysis further reveals significantly lower lymphocytic infiltration within diversified zones compared with other tumor zones, suggesting that even immune-hot tumors contain cells capable of immune escape. Our findings support a model whereby a subpopulation of morphologically plastic cancer cells with dysregulated DNA repair promotes ovarian cancer progression through positive selection by immune evasion..
Lote, H.
Spiteri, I.
Ermini, L.
Vatsiou, A.
Roy, A.
McDonald, A.
Maka, N.
Balsitis, M.
Bose, N.
Simbolo, M.
Mafficini, A.
Lampis, A.
Hahne, J.C.
Trevisani, F.
Eltahir, Z.
Mentrasti, G.
Findlay, C.
Kalkman, E.A.
Punta, M.
Werner, B.
Lise, S.
Aktipis, A.
Maley, C.
Greaves, M.
Braconi, C.
White, J.
Fassan, M.
Scarpa, A.
Sottoriva, A.
Valeri, N.
(2017). Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer. Ann oncol,
Vol.28
(6),
pp. 1243-1249.
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BACKGROUND: Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but lack of chronological references makes dating the exact onset of tumours very challenging. PATIENTS AND METHODS: Here, we describe the case of a colorectal cancer (CRC) patient presenting with synchronous lung metastasis and metachronous thyroid, chest wall and urinary tract metastases over the course of 5 years. The chest wall metastasis was caused by needle tract seeding, implying a known time of onset. Using whole genome sequencing data from primary and metastatic sites we inferred the complete chronology of the cancer by exploiting the time of needle tract seeding as an in vivo 'stopwatch'. This approach allowed us to follow the progression of the disease back in time, dating each ancestral node of the phylogenetic tree in the past history of the tumour. We used a Bayesian phylogenomic approach, which accounts for possible dynamic changes in mutational rate, to reconstruct the phylogenetic tree and effectively 'carbon date' the malignant progression. RESULTS: The primary colon cancer emerged between 5 and 8 years before the clinical diagnosis. The primary tumour metastasized to the lung and the thyroid within a year from its onset. The thyroid lesion presented as a tumour-to-tumour deposit within a benign Hurthle adenoma. Despite rapid metastatic progression from the primary tumour, the patient showed an indolent disease course. Primary cancer and metastases were microsatellite stable and displayed low chromosomal instability. Neo-antigen analysis suggested minimal immunogenicity. CONCLUSION: Our data provide the first in vivo experimental evidence documenting the timing of metastatic progression in CRC and suggest that genomic instability might be more important than the metastatic potential of the primary cancer in dictating CRC fate..
Graham, T.A.
Sottoriva, A.
(2017). Measuring cancer evolution from the genome. J pathol,
Vol.241
(2),
pp. 183-191.
show abstract
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The temporal dynamics of cancer evolution remain elusive, because it is impractical to longitudinally observe cancers unperturbed by treatment. Consequently, our knowledge of how cancers grow largely derives from inferences made from a single point in time - the endpoint in the cancer's evolution, when it is removed from the body and studied in the laboratory. Fortuitously however, the cancer genome, by virtue of ongoing mutations that uniquely mark clonal lineages within the tumour, provides a rich, yet surreptitious, record of cancer development. In this review, we describe how a cancer's genome can be analysed to reveal the temporal history of mutation and selection, and discuss why both selective and neutral evolution feature prominently in carcinogenesis. We argue that selection in cancer can only be properly studied once we have some understanding of what the absence of selection looks like. We review the data describing punctuated evolution in cancer, and reason that punctuated phenotype evolution is consistent with both gradual and punctuated genome evolution. We conclude that, to map and predict evolutionary trajectories during carcinogenesis, it is critical to better understand the relationship between genotype change and phenotype change. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd..
Sottoriva, A.
Barnes, C.P.
Graham, T.A.
(2017). Catch my drift? Making sense of genomic intra-tumour heterogeneity. Biochim biophys acta rev cancer,
Vol.1867
(2),
pp. 95-100.
show abstract
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The cancer genome is shaped by three components of the evolutionary process: mutation, selection and drift. While many studies have focused on the first two components, the role of drift in cancer evolution has received little attention. Drift occurs when all individuals in the population have the same likelihood of producing surviving offspring, and so by definition a drifting population is one that is evolving neutrally. Here we focus on how neutral evolution is manifested in the cancer genome. We discuss how neutral passenger mutations provide a magnifying glass that reveals the evolutionary dynamics underpinning cancer development, and outline how statistical inference can be used to quantify these dynamics from sequencing data. We argue that only after we understand the impact of neutral drift on the genome can we begin to make full sense of clonal selection. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer? Edited by Dr. Robert A. Gatenby..
Sun, R.
Hu, Z.
Sottoriva, A.
Graham, T.A.
Harpak, A.
Ma, Z.
Fischer, J.M.
Shibata, D.
Curtis, C.
(2017). Between-region genetic divergence reflects the mode and tempo of tumor evolution. Nat genet,
Vol.49
(7),
pp. 1015-1024.
show abstract
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Given the implications of tumor dynamics for precision medicine, there is a need to systematically characterize the mode of evolution across diverse solid tumor types. In particular, methods to infer the role of natural selection within established human tumors are lacking. By simulating spatial tumor growth under different evolutionary modes and examining patterns of between-region subclonal genetic divergence from multiregion sequencing (MRS) data, we demonstrate that it is feasible to distinguish tumors driven by strong positive subclonal selection from those evolving neutrally or under weak selection, as the latter fail to dramatically alter subclonal composition. We developed a classifier based on measures of between-region subclonal genetic divergence and projected patient data into model space, finding different modes of evolution both within and between solid tumor types. Our findings have broad implications for how human tumors progress, how they accumulate intratumoral heterogeneity, and ultimately how they may be more effectively treated..
Baker, A.-.
Huang, W.
Wang, X.-.
Jansen, M.
Ma, X.-.
Kim, J.
Anderson, C.M.
Wu, X.
Pan, L.
Su, N.
Luo, Y.
Domingo, E.
Heide, T.
Sottoriva, A.
Lewis, A.
Beggs, A.D.
Wright, N.A.
Rodriguez-Justo, M.
Park, E.
Tomlinson, I.
Graham, T.A.
(2017). Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution. Nat commun,
Vol.8
(1),
p. 1998.
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Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones. Computational modeling suggests that subclones must arise sufficiently early, or carry a considerable fitness advantage, to form large or spatially disparate subclones. Examples of putative treatment-resistant cells isolated in small topographical areas are observed. The BaseScope assay represents a significant technical advance for in situ mutation detection that provides new insight into tumor evolution, and could have ramifications for selecting patients for treatment..
Maley, C.C.
Aktipis, A.
Graham, T.A.
Sottoriva, A.
Boddy, A.M.
Janiszewska, M.
Silva, A.S.
Gerlinger, M.
Yuan, Y.
Pienta, K.J.
Anderson, K.S.
Gatenby, R.
Swanton, C.
Posada, D.
Wu, C.-.
Schiffman, J.D.
Hwang, E.S.
Polyak, K.
Anderson, A.R.
Brown, J.S.
Greaves, M.
Shibata, D.
(2017). Classifying the evolutionary and ecological features of neoplasms. Nat rev cancer,
Vol.17
(10),
pp. 605-619.
show abstract
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Neoplasms change over time through a process of cell-level evolution, driven by genetic and epigenetic alterations. However, the ecology of the microenvironment of a neoplastic cell determines which changes provide adaptive benefits. There is widespread recognition of the importance of these evolutionary and ecological processes in cancer, but to date, no system has been proposed for drawing clinically relevant distinctions between how different tumours are evolving. On the basis of a consensus conference of experts in the fields of cancer evolution and cancer ecology, we propose a framework for classifying tumours that is based on four relevant components. These are the diversity of neoplastic cells (intratumoural heterogeneity) and changes over time in that diversity, which make up an evolutionary index (Evo-index), as well as the hazards to neoplastic cell survival and the resources available to neoplastic cells, which make up an ecological index (Eco-index). We review evidence demonstrating the importance of each of these factors and describe multiple methods that can be used to measure them. Development of this classification system holds promise for enabling clinicians to personalize optimal interventions based on the evolvability of the patient's tumour. The Evo- and Eco-indices provide a common lexicon for communicating about how neoplasms change in response to interventions, with potential implications for clinical trials, personalized medicine and basic cancer research..
Werner, B.
Traulsen, A.
Sottoriva, A.
Dingli, D.
(2017). Detecting truly clonal alterations from multi-region profiling of tumours. Sci rep,
Vol.7,
p. 44991.
show abstract
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Modern cancer therapies aim at targeting tumour-specific alterations, such as mutations or neo-antigens, and maximal treatment efficacy requires that targeted alterations are present in all tumour cells. Currently, treatment decisions are based on one or a few samples per tumour, creating uncertainty on whether alterations found in those samples are actually present in all tumour cells. The probability of classifying clonal versus sub-clonal alterations from multi-region profiling of tumours depends on the earliest phylogenetic branching event during tumour growth. By analysing 181 samples from 10 renal carcinoma and 11 colorectal cancers we demonstrate that the information gain from additional sampling falls onto a simple universal curve. We found that in colorectal cancers, 30% of alterations identified as clonal with one biopsy proved sub-clonal when 8 samples were considered. The probability to overestimate clonal alterations fell below 1% in 7/11 patients with 8 samples per tumour. In renal cell carcinoma, 8 samples reduced the list of clonal alterations by 40% with respect to a single biopsy. The probability to overestimate clonal alterations remained as high as 92% in 7/10 renal cancer patients. Furthermore, treatment was associated with more unbalanced tumour phylogenetic trees, suggesting the need of denser sampling of tumours at relapse..
Lipinski, K.A.
Barber, L.J.
Davies, M.N.
Ashenden, M.
Sottoriva, A.
Gerlinger, M.
(2016). Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine. Trends cancer,
Vol.2
(1),
pp. 49-63.
show abstract
The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection, which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes, which have been extensively studied in evolutionary biology, limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes..
Werner, B.
Scott, J.G.
Sottoriva, A.
Anderson, A.R.
Traulsen, A.
Altrock, P.M.
(2016). The Cancer Stem Cell Fraction in Hierarchically Organized Tumors Can Be Estimated Using Mathematical Modeling and Patient-Specific Treatment Trajectories. Cancer res,
Vol.76
(7),
pp. 1705-1713.
show abstract
Many tumors are hierarchically organized and driven by a subpopulation of tumor-initiating cells (TIC), or cancer stem cells. TICs are uniquely capable of recapitulating the tumor and are thought to be highly resistant to radio- and chemotherapy. Macroscopic patterns of tumor expansion before treatment and tumor regression during treatment are tied to the dynamics of TICs. Until now, the quantitative information about the fraction of TICs from macroscopic tumor burden trajectories could not be inferred. In this study, we generated a quantitative method based on a mathematical model that describes hierarchically organized tumor dynamics and patient-derived tumor burden information. The method identifies two characteristic equilibrium TIC regimes during expansion and regression. We show that tumor expansion and regression curves can be leveraged to infer estimates of the TIC fraction in individual patients at detection and after continued therapy. Furthermore, our method is parameter-free; it solely requires the knowledge of a patient's tumor burden over multiple time points to reveal microscopic properties of the malignancy. We demonstrate proof of concept in the case of chronic myeloid leukemia (CML), wherein our model recapitulated the clinical history of the disease in two independent patient cohorts. On the basis of patient-specific treatment responses in CML, we predict that after one year of targeted treatment, the fraction of TICs increases 100-fold and continues to increase up to 1,000-fold after 5 years of treatment. Our novel framework may significantly influence the implementation of personalized treatment strategies and has the potential for rapid translation into the clinic. Cancer Res; 76(7); 1705-13. ©2016 AACR..
Williams, M.J.
Werner, B.
Barnes, C.P.
Graham, T.A.
Sottoriva, A.
(2016). Identification of neutral tumor evolution across cancer types. Nat genet,
Vol.48
(3),
pp. 238-244.
show abstract
full text
Despite extraordinary efforts to profile cancer genomes, interpreting the vast amount of genomic data in the light of cancer evolution remains challenging. Here we demonstrate that neutral tumor evolution results in a power-law distribution of the mutant allele frequencies reported by next-generation sequencing of tumor bulk samples. We find that the neutral power law fits with high precision 323 of 904 cancers from 14 types and from different cohorts. In malignancies identified as evolving neutrally, all clonal selection seemingly occurred before the onset of cancer growth and not in later-arising subclones, resulting in numerous passenger mutations that are responsible for intratumoral heterogeneity. Reanalyzing cancer sequencing data within the neutral framework allowed the measurement, in each patient, of both the in vivo mutation rate and the order and timing of mutations. This result provides a new way to interpret existing cancer genomic data and to discriminate between functional and non-functional intratumoral heterogeneity..
Eskilsson, E.
Rosland, G.V.
Talasila, K.M.
Knappskog, S.
Keunen, O.
Sottoriva, A.
Foerster, S.
Solecki, G.
Taxt, T.
Jirik, R.
Fritah, S.
Harter, P.N.
Välk, K.
Al Hossain, J.
Joseph, J.V.
Jahedi, R.
Saed, H.S.
Piccirillo, S.G.
Spiteri, I.
Leiss, L.
Euskirchen, P.
Graziani, G.
Daubon, T.
Lund-Johansen, M.
Enger, P.Ø.
Winkler, F.
Ritter, C.A.
Niclou, S.P.
Watts, C.
Bjerkvig, R.
Miletic, H.
(2016). EGFRvIII mutations can emerge as late and heterogenous events in glioblastoma development and promote angiogenesis through Src activation. Neuro oncol,
Vol.18
(12),
pp. 1644-1655.
show abstract
BACKGROUND: Amplification of the epidermal growth factor receptor (EGFR) and its mutant EGFRvIII are among the most common genetic alterations in glioblastoma (GBM), the most frequent and most aggressive primary brain tumor. METHODS: In the present work, we analyzed the clonal evolution of these major EGFR aberrations in a small cohort of GBM patients using a unique surgical multisampling technique. Furthermore, we overexpressed both receptors separately and together in 2 patient-derived GBM stem cell lines (GSCs) to analyze their functions in vivo in orthotopic xenograft models. RESULTS: In human GBM biopsies, we identified EGFR amplification as an early event because EGFRvIII mutations emerge from intratumoral heterogeneity later in tumor development. To investigate the biological relevance of this distinct developmental pattern, we established experimental model systems. In these models, EGFR+ tumor cells showed activation of classical downstream signaling pathways upon EGF stimulation and displayed enhanced invasive growth without evidence of angiogenesis in vivo. In contrast, EGFRvIII+ tumors were driven by activation of the prototypical Src family kinase c-Src that promoted VEGF secretion leading to angiogenic tumor growth. CONCLUSIONS: The presented work shows that sequential EGFR amplification and EGFRvIII mutations might represent concerted evolutionary events that drive the aggressive nature of GBM by promoting invasion and angiogenesis via distinct signaling pathways. In particular, c-SRC may be an attractive therapeutic target for tumors harboring EGFRvIII as we identified this protein specifically mediating angiogenic tumor growth downstream of EGFRvIII..
Piccirillo, S.G.
Spiteri, I.
Sottoriva, A.
Touloumis, A.
Ber, S.
Price, S.J.
Heywood, R.
Francis, N.-.
Howarth, K.D.
Collins, V.P.
Venkitaraman, A.R.
Curtis, C.
Marioni, J.C.
Tavaré, S.
Watts, C.
(2015). Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone. Cancer res,
Vol.75
(1),
pp. 194-202.
show abstract
full text
Glioblastoma, the most common and aggressive adult brain tumor, is characterized by extreme phenotypic diversity and treatment failure. Through fluorescence-guided resection, we identified fluorescent tissue in the sub-ependymal zone (SEZ) of patients with glioblastoma. Histologic analysis and genomic characterization revealed that the SEZ harbors malignant cells with tumor-initiating capacity, analogous to cells isolated from the fluorescent tumor mass (T). We observed resistance to supramaximal chemotherapy doses along with differential patterns of drug response between T and SEZ in the same tumor. Our results reveal novel insights into glioblastoma growth dynamics, with implications for understanding and limiting treatment resistance..
Sottoriva, A.
Kang, H.
Ma, Z.
Graham, T.A.
Salomon, M.P.
Zhao, J.
Marjoram, P.
Siegmund, K.
Press, M.F.
Shibata, D.
Curtis, C.
(2015). A Big Bang model of human colorectal tumor growth. Nat genet,
Vol.47
(3),
pp. 209-216.
show abstract
full text
What happens in early, still undetectable human malignancies is unknown because direct observations are impractical. Here we present and validate a 'Big Bang' model, whereby tumors grow predominantly as a single expansion producing numerous intermixed subclones that are not subject to stringent selection and where both public (clonal) and most detectable private (subclonal) alterations arise early during growth. Genomic profiling of 349 individual glands from 15 colorectal tumors showed an absence of selective sweeps, uniformly high intratumoral heterogeneity (ITH) and subclone mixing in distant regions, as postulated by our model. We also verified the prediction that most detectable ITH originates from early private alterations and not from later clonal expansions, thus exposing the profile of the primordial tumor. Moreover, some tumors appear 'born to be bad', with subclone mixing indicative of early malignant potential. This new model provides a quantitative framework to interpret tumor growth dynamics and the origins of ITH, with important clinical implications..
Gubernator, M.
Slater, S.C.
Spencer, H.L.
Spiteri, I.
Sottoriva, A.
Riu, F.
Rowlinson, J.
Avolio, E.
Katare, R.
Mangialardi, G.
Oikawa, A.
Reni, C.
Campagnolo, P.
Spinetti, G.
Touloumis, A.
Tavaré, S.
Prandi, F.
Pesce, M.
Hofner, M.
Klemens, V.
Emanueli, C.
Angelini, G.
Madeddu, P.
(2015). Epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia. Arterioscler thromb vasc biol,
Vol.35
(3),
pp. 675-688.
show abstract
OBJECTIVE: We investigated the association between the functional, epigenetic, and expressional profile of human adventitial progenitor cells (APCs) and therapeutic activity in a model of limb ischemia. APPROACH AND RESULTS: Antigenic and functional features were analyzed throughout passaging in 15 saphenous vein (SV)-derived APC lines, of which 10 from SV leftovers of coronary artery bypass graft surgery and 5 from varicose SV removal. Moreover, 5 SV-APC lines were transplanted (8×10(5) cells, IM) in mice with limb ischemia. Blood flow and capillary and arteriole density were correlated with functional characteristics and DNA methylation/expressional markers of transplanted cells. We report successful expansion of tested lines, which reached the therapeutic target of 30 to 50 million cells in ≈10 weeks. Typical antigenic profile, viability, and migratory and proangiogenic activities were conserved through passaging, with low levels of replicative senescence. In vivo, SV-APC transplantation improved blood flow recovery and revascularization of ischemic limbs. Whole genome screening showed an association between DNA methylation at the promoter or gene body level and microvascular density and to a lesser extent with blood flow recovery. Expressional studies highlighted the implication of an angiogenic network centered on the vascular endothelial growth factor receptor as a predictor of microvascular outcomes. FLT-1 gene silencing in SV-APCs remarkably reduced their ability to form tubes in vitro and support tube formation by human umbilical vein endothelial cells, thus confirming the importance of this signaling in SV-APC angiogenic function. CONCLUSIONS: DNA methylation landscape illustrates different therapeutic activities of human APCs. Epigenetic screening may help identify determinants of therapeutic vasculogenesis in ischemic disease..
Piccirillo, S.G.
Sottoriva, A.
Watts, C.
(2015). The role of sub-ventricular zone in gliomagenesis. Aging (albany ny),
Vol.7
(10),
pp. 738-739.
full text
Kang, H.
Salomon, M.P.
Sottoriva, A.
Zhao, J.
Toy, M.
Press, M.F.
Curtis, C.
Marjoram, P.
Siegmund, K.
Shibata, D.
(2015). Many private mutations originate from the first few divisions of a human colorectal adenoma. J pathol,
Vol.237
(3),
pp. 355-362.
show abstract
full text
Intratumoural mutational heterogeneity (ITH) or the presence of different private mutations in different parts of the same tumour is commonly observed in human tumours. The mechanisms generating such ITH are uncertain. Here we find that ITH can be remarkably well structured by measuring point mutations, chromosome copy numbers, and DNA passenger methylation from opposite sides and individual glands of a 6 cm human colorectal adenoma. ITH was present between tumour sides and individual glands, but the private mutations were side-specific and subdivided the adenoma into two major subclones. Furthermore, ITH disappeared within individual glands because the glands were clonal populations composed of cells with identical mutant genotypes. Despite mutation clonality, the glands were relatively old, diverse populations when their individual cells were compared for passenger methylation and by FISH. These observations can be organized into an expanding star-like ancestral tree with co-clonal expansion, where many private mutations and multiple related clones arise during the first few divisions. As a consequence, most detectable mutational ITH in the final tumour originates from the first few divisions. Much of the early history of a tumour, especially the first few divisions, may be embedded within the detectable ITH of tumour genomes..
Ellis, H.P.
Greenslade, M.
Powell, B.
Spiteri, I.
Sottoriva, A.
Kurian, K.M.
(2015). Current Challenges in Glioblastoma: Intratumour Heterogeneity, Residual Disease, and Models to Predict Disease Recurrence. Front oncol,
Vol.5,
p. 251.
show abstract
Glioblastoma (GB) is the most common primary malignant brain tumor, and despite the availability of chemotherapy and radiotherapy to combat the disease, overall survival remains low with a high incidence of tumor recurrence. Technological advances are continually improving our understanding of the disease, and in particular, our knowledge of clonal evolution, intratumor heterogeneity, and possible reservoirs of residual disease. These may inform how we approach clinical treatment and recurrence in GB. Mathematical modeling (including neural networks) and strategies such as multiple sampling during tumor resection and genetic analysis of circulating cancer cells, may be of great future benefit to help predict the nature of residual disease and resistance to standard and molecular therapies in GB..
Sottoriva, A.
Spiteri, I.
Shibata, D.
Curtis, C.
Tavaré, S.
(2013). Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization. Cancer res,
Vol.73
(1),
pp. 41-49.
show abstract
Substantial evidence supports the concept that cancers are organized in a cellular hierarchy with cancer stem cells (CSC) at the apex. To date, the primary evidence for CSCs derives from transplantation assays, which have known limitations. In particular, they are unable to report on the fate of cells within the original human tumor. Because of the difficulty in measuring tumor characteristics in patients, cellular organization and other aspects of cancer dynamics have not been quantified directly, although they likely play a fundamental role in tumor progression and therapy response. As such, new approaches to study CSCs in patient-derived tumor specimens are needed. In this study, we exploited ultradeep single-molecule genomic data derived from multiple microdissected colorectal cancer glands per tumor, along with a novel quantitative approach to measure tumor characteristics, define patient-specific tumor profiles, and infer tumor ancestral trees. We show that each cancer is unique in terms of its cellular organization, molecular heterogeneity, time from malignant transformation, and rate of mutation and apoptosis. Importantly, we estimate CSC fractions between 0.5% and 4%, indicative of a hierarchical organization responsible for long-lived CSC lineages, with variable rates of symmetric cell division. We also observed extensive molecular heterogeneity, both between and within individual cancer glands, suggesting a complex hierarchy of mitotic clones. Our framework enables the measurement of clinically relevant patient-specific characteristics in vivo, providing insight into the cellular organization and dynamics of tumor growth, with implications for personalized patient care..
Sottoriva, A.
Spiteri, I.
Piccirillo, S.G.
Touloumis, A.
Collins, V.P.
Marioni, J.C.
Curtis, C.
Watts, C.
Tavaré, S.
(2013). Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc natl acad sci u s a,
Vol.110
(10),
pp. 4009-4014.
show abstract
full text
Glioblastoma (GB) is the most common and aggressive primary brain malignancy, with poor prognosis and a lack of effective therapeutic options. Accumulating evidence suggests that intratumor heterogeneity likely is the key to understanding treatment failure. However, the extent of intratumor heterogeneity as a result of tumor evolution is still poorly understood. To address this, we developed a unique surgical multisampling scheme to collect spatially distinct tumor fragments from 11 GB patients. We present an integrated genomic analysis that uncovers extensive intratumor heterogeneity, with most patients displaying different GB subtypes within the same tumor. Moreover, we reconstructed the phylogeny of the fragments for each patient, identifying copy number alterations in EGFR and CDKN2A/B/p14ARF as early events, and aberrations in PDGFRA and PTEN as later events during cancer progression. We also characterized the clonal organization of each tumor fragment at the single-molecule level, detecting multiple coexisting cell lineages. Our results reveal the genome-wide architecture of intratumor variability in GB across multiple spatial scales and patient-specific patterns of cancer evolution, with consequences for treatment design..
Dvinge, H.
Git, A.
Gräf, S.
Salmon-Divon, M.
Curtis, C.
Sottoriva, A.
Zhao, Y.
Hirst, M.
Armisen, J.
Miska, E.A.
Chin, S.-.
Provenzano, E.
Turashvili, G.
Green, A.
Ellis, I.
Aparicio, S.
Caldas, C.
(2013). The shaping and functional consequences of the microRNA landscape in breast cancer. Nature,
Vol.497
(7449),
pp. 378-382.
show abstract
MicroRNAs (miRNAs) show differential expression across breast cancer subtypes, and have both oncogenic and tumour-suppressive roles. Here we report the miRNA expression profiles of 1,302 breast tumours with matching detailed clinical annotation, long-term follow-up and genomic and messenger RNA expression data. This provides a comprehensive overview of the quantity, distribution and variation of the miRNA population and provides information on the extent to which genomic, transcriptional and post-transcriptional events contribute to miRNA expression architecture, suggesting an important role for post-transcriptional regulation. The key clinical parameters and cellular pathways related to the miRNA landscape are characterized, revealing context-dependent interactions, for example with regards to cell adhesion and Wnt signalling. Notably, only prognostic miRNA signatures derived from breast tumours devoid of somatic copy-number aberrations (CNA-devoid) are consistently prognostic across several other subtypes and can be validated in external cohorts. We then use a data-driven approach to seek the effects of miRNAs associated with differential co-expression of mRNAs, and find that miRNAs act as modulators of mRNA-mRNA interactions rather than as on-off molecular switches. We demonstrate such an important modulatory role for miRNAs in the biology of CNA-devoid breast cancers, a common subtype in which the immune response is prominent. These findings represent a new framework for studying the biology of miRNAs in human breast cancer..
Vermeulen, L.
Morrissey, E.
van der Heijden, M.
Nicholson, A.M.
Sottoriva, A.
Buczacki, S.
Kemp, R.
Tavaré, S.
Winton, D.J.
(2013). Defining stem cell dynamics in models of intestinal tumor initiation. Science,
Vol.342
(6161),
pp. 995-998.
show abstract
Cancer is a disease in which cells accumulate genetic aberrations that are believed to confer a clonal advantage over cells in the surrounding tissue. However, the quantitative benefit of frequently occurring mutations during tumor development remains unknown. We quantified the competitive advantage of Apc loss, Kras activation, and P53 mutations in the mouse intestine. Our findings indicate that the fate conferred by these mutations is not deterministic, and many mutated stem cells are replaced by wild-type stem cells after biased, but still stochastic events. Furthermore, P53 mutations display a condition-dependent advantage, and especially in colitis-affected intestines, clones harboring mutations in this gene are favored. Our work confirms the previously theoretical notion that the tissue architecture of the intestine suppresses the accumulation of mutated lineages..
Ageron, M.
Aguilar, J.A.
Al Samarai, I.
Albert, A.
Ameli, F.
André, M.
Anghinolfi, M.
Anton, G.
Anvar, S.
Ardid, M.
Arnaud, K.
Aslanides, E.
Assis Jesus, A.C.
Astraatmadja, T.
Aubert, J.-.
Auer, R.
Barbarito, E.
Baret, B.
Basa, S.
Bazzotti, M.
Becherini, Y.
Beltramelli, J.
Bersani, A.
Bertin, V.
Beurthey, S.
Biagi, S.
Bigongiari, C.
Billault, M.
Blaes, R.
Bogazzi, C.
de Botton, N.
Bou-Cabo, M.
Boudahef, B.
Bouwhuis, M.C.
Brown, A.M.
Brunner, J.
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(2011). ANTARES: The first undersea neutrino telescope. Nuclear instruments and methods in physics research section a: accelerators, spectrometers, detectors and associated equipment,
Vol.656,
pp. 11-38.
show abstract
The ANTARES Neutrino Telescope was completed in May 2008 and is the first operational Neutrino Telescope in the Mediterranean Sea. The main purpose of the detector is to perform neutrino astronomy and the apparatus also offers facilities for marine and Earth sciences. This paper describes the design, the construction and the installation of the telescope in the deep sea, offshore from Toulon in France. An illustration of the detector performance is given..
Sottoriva, A.
Vermeulen, L.
Tavaré, S.
(2011). Modeling Evolutionary Dynamics of Epigenetic Mutations in Hierarchically Organized Tumors. Plos comput. biol.,
Vol.7.
full text
Sottoriva, A.
Verhoeff, J.J.
Borovski, T.
McWeeney, S.K.
Naumov, L.
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Sloot, P.M.
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(2010). Cancer stem cell tumor model reveals invasive morphology and increased phenotypical heterogeneity. Cancer res,
Vol.70
(1),
pp. 46-56.
show abstract
The recently developed concept of cancer stem cells (CSC) sheds new light on various aspects of tumor growth and progression. Here, we present a mathematical model of malignancies to investigate how a hierarchical organized cancer cell population affects the fundamental properties of solid malignancies. We establish that tumors modeled in a CSC context more faithfully resemble human malignancies and show invasive behavior, whereas tumors without a CSC hierarchy do not. These findings are corroborated by in vitro studies. In addition, we provide evidence that the CSC model is accompanied by highly altered evolutionary dynamics compared with the ones predicted to exist in a stochastic, nonhierarchical tumor model. Our main findings indicate that the CSC model allows for significantly higher tumor heterogeneity, which may affect therapy resistance. Moreover, we show that therapy which fails to target the CSC population is not only unsuccessful in curing the patient, but also promotes malignant features in the recurring tumor. These include rapid expansion, increased invasion, and enhanced heterogeneity..
Sottoriva, A.
Sloot, P.M.
Medema, J.P.
Vermeulen, L.
(2010). Exploring cancer stem cell niche directed tumor growth. Cell cycle,
Vol.9
(8),
pp. 1472-1479.
show abstract
The finding that only a sub-fraction of tumor cells, so called Cancer Stem Cells (CSC), is endowed with the capacity to initiate new tumors has important consequences for fundamental as well as clinical cancer research. Previously we established by computational modeling techniques that CSC driven tumor growth instigates infiltrative behavior, and perhaps most interesting, stimulates tumor cell heterogeneity. An important question that remains is to what extend CSC functions are intrinsically regulated or whether this capacity is orchestrated by the microenvironment, i.e. a putative CSC niche. Here we investigate how extrinsic regulation of CSC properties affects the characteristics of malignancies. We find that highly invasive growth in tumors dependent on a small subset of cells is not restricted to CSC-driven tumors, but is also observed in tumors where the CSC capacity of tumor cells is completely defined by the microenvironment. Importantly, also the high level of heterogeneity that was observed for CSC-driven tumors is preserved and partially even increased in malignancies with a microenvironmentally orchestrated CSC population. This indicates that invasive growth and high heterogeneity are fundamental properties of tumors fueled by a small population of tumor cells..
Sottoriva, A.
Tavaré, S.
(2010). Integrating approximate Bayesian computation with complex agent-based models for cancer research. Compstat 2010 - proceedings in computational statistics, eds. saporta g & lechevallier y. springer, physica verlag,
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(2009). A multiphysics and multiscale software environment for modeling astrophysical systems. New astronomy,
Vol.14,
pp. 369-378.
show abstract
We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a “Noah’s Ark” milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li..