Publications

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August 2024, Nature, DOI: 10.1038/s41586-024-07747-9, Licence CC BY 4.0

Alex J. Cornish, Andreas J. Gruber, Ben Kinnersley, Daniel Chubb, Anna Frangou, Giulio Caravagna, Luis Zapata, Show all 36 authors. Richard S. Houlston.

Colorectal carcinoma (CRC) is a common cause of mortality¹, but a comprehensive description of its genomic landscape is lacking2–9. Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichiacolipks+ colibactin in rectal cancers¹⁰ and the importance of the SBS93 signature11–13, which suggests that diet or smoking is a risk factor. Immune-escape driver mutations¹⁴ are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care.

June 2024, Genome Biology 25(1), DOI: 10.1186/s13059-024-03302-x, License CC BY 4.0 

Lucie Gourmet, Andrea Sottoriva, Simon Walker-Samuel, Maria Secrier and Luis Zapata.

Background Carcinogenesis is driven by interactions between genetic mutations and the local tumor microenvironment. Recent research has identified hundreds of cancer driver genes; however, these studies often include a mixture of different molecular subtypes and ecological niches and ignore the impact of the immune system. Results In this study, we compare the landscape of driver genes in tumors that escaped the immune system (escape +) versus those that did not (escape −). We analyze 9896 primary tumors from The Cancer Genome Atlas using the ratio of non-synonymous to synonymous mutations (dN/dS) and find 85 driver genes, including 27 and 16 novel genes, in escape − and escape + tumors, respectively. The dN/dS of driver genes in immune escaped tumors is significantly lower and closer to neutrality than in non-escaped tumors, suggesting selection buffering in driver genes fueled by immune escape. Additionally, we find that immune evasion leads to more mutated sites, a diverse array of mutational signatures and is linked to tumor prognosis. Conclusions Our findings highlight the need for improved patient stratification to identify new therapeutic targets for cancer treatment.

March 2023 Nature Genetics 55(3):1-10 DOI: 10.1038/s41588-023-01313-1  License CC BY 4.0

Luis Zapata, Giulio Caravagna, Marc J. Williams Show all 15 authors Andrea Sottoriva

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.

July 2020, DOI: 10.1101/2020.07.21.215038

Luis Zapata, Giulio Caravagna, Marc J Williams, Show all 8 authors  , Andrea Sottoriva

Immunoediting is a major force during cancer evolution that selects for clones with low immunogenicity (adaptation), or clones with mechanisms of immune evasion (escape). However, quantifying immunogenicity in the cancer genome and how the tumour-immune coevolutionary dynamics impact patient outcomes remain unexplored. Here we show that the ratio of nonsynonymous to synonymous mutations (dN/dS) in the immunopeptidome quantifies tumor immunogenicity and differentiates between adaptation and escape. We analysed 8,543 primary tumors from TCGA and validated immune dN/dS as a measure of selection associated with immune infiltration in immune-adapted tumours. In a cohort of 308 metastatic patients that received immunotherapy, pre-treatment lesions in non-responders showed increased immune selection (dN/dS<1), whereas responders did not and instead harbour a higher proportion of genetic escape mechanisms. Ultimately, these findings highlight the potential of evolutionary genomic measures to predict clinical response to immunotherapy.

Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

Genome Biology 2018 May 31;19(1):67. doi: 10.1186/s13059-018-1434-0.

Luis Zapata, Oriol Pich , Luis Serrano , Fyodor A Kondrashov, Stephan Ossowski, Martin H Schaefer

Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic.

Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes.

Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.

Keywords: Cancer immunology; Cancer-essential genes; Negative selection; Neoepitopes; Tumor evolution.

Preprint, February 2024, DOI: 10.1101/2024.02.12.579956 ,License CC BY-NC 4.0

Eszter Lakatos, Vinaya Gunasri, Luis Zapata, Show all 22 authors, Trevor A. Graham

Immune system control is a major hurdle that cancer evolution must circumvent. Therelative timing and evolutionary dynamics of subclones that have escaped immunecontrol remain incompletely characterized, and how immune-mediated selectionshapes the epigenome has received little attention. Here, we infer the genome- andepigenome-driven evolutionary dynamics of tumour-immune coevolution withinprimary colorectal cancers (CRCs). We utilise our existing CRC multi-region multi-omic dataset that we supplement with high-resolution spatially-resolved neoantigensequencing data and highly multiplexed imaging of the tumour microenvironment(TME). Analysis of somatic chromatin accessibility alterations (SCAAs) revealsfrequent somatic loss of accessibility at antigen presenting genes, and that SCAAscontribute to silencing of neoantigens. We observe that strong immune escape andexclusion occur at the outset of CRC formation, and that within tumours, including atthe microscopic level of individual tumour glands, additional immune escapealterations have negligible consequences for the immunophenotype of cancer cells.Further minor immuno-editing occurs during local invasion and is associated with TMEreorganisation, but that evolutionary bottleneck is relatively weak. Collectively, weshow that immune evasion in CRC follows a “Big Bang” evolutionary pattern, wherebygenetic, epigenetic and TME-driven immune evasion acquired by the time oftransformation defines subsequent cancer-immune evolution
(PDF) Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer. Available from: https://www.researchgate.net/publication/378289109_Epigenome_and_early_selection_determine_the_tumour-immune_evolutionary_trajectory_of_colorectal_cancer.

Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms

Proc Natl Acad Sci USA. 2016 Jul 12;113(28):E4052-60. doi: 10.1073/pnas.1607532113. Epub 2016 Jun 27.

Luis Zapata, Jia Ding, Eva-Maria Willing, Benjamin Hartwig, Daniela Bezdan, Wen-Biao Jiao, Vipul Patel, Geo Velikkakam James, Maarten Koornneef, Stephan Ossowski , Korbinian Schneeberger 

Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.

Keywords: Arabidopsis; PacBio sequencing; de novo assembly; gene absence/presence polymorphisms; inversions.

Natl Sci Rev. 2022 Nov 11;9(12):nwac250. doi: 10.1093/nsr/nwac250. eCollection 2022 Dec.

Bingjie Chen 1 2 3, Xianrui Wu 4 5, Yongsen Ruan 1, Yulin Zhang 1, Qichun Cai 6, Luis Zapata 3, Chung-I Wu 1, Ping Lan, Haijun Wen 

Despite the concern of within-tumor genetic diversity, this diversity is in fact limited by the kinship among cells in the tumor. Indeed, genomic studies have amply supported the 'Nowell dogma' whereby cells of the same tumor descend from a single progenitor cell. In parallel, genomic data also suggest that the diversity could be >10-fold larger if tumor cells are of multiple origins. We develop an evolutionary hypothesis that a single tumor may often harbor multiple cell clones of independent origins, but only one would be large enough to be detected. To test the hypothesis, we search for independent tumors within a larger one (or tumors-in-tumor). Very high density sampling was done on two cases of colon tumors. Case 1 indeed has 13 independent clones of disparate sizes, many having heavy mutation burdens and potentially highly tumorigenic. In Case 2, despite a very intensive search, only two small independent clones could be found. The two cases show very similar movements and metastasis of the dominant clone. Cells initially move actively in the expanding tumor but become nearly immobile in late stages. In conclusion, tumors-in-tumor are plausible but could be very demanding to find. Despite their small sizes, they can enhance the within-tumor diversity by orders of magnitude. Such increases may contribute to the missing genetic diversity associated with the resistance to cancer therapy.

Keywords: cancer evolution; intratumoral heterogeneity; tumor origins; tumors-in-tumor.

© The Author(s) 2022. Published by Oxford University Press on behalf of China Science Publishing & Media

Nature 2022 Nov;611(7937):744-753. doi: 10.1038/s41586-022-05311-x. Epub 2022 Oct 26 

PMID: 36289336, PMCID: PMC9684078, DOI: 10.1038/s41586-022-05311-x

Jacob Househam, Timon Heide , George D Cresswell, Inmaculada Spiteri, Chris Kimberley, Luis Zapata , Claire Lynn, Chela James , Maximilian Mossner, Javier Fernandez-Mateos, Alessandro Vinceti, Ann-Marie Baker, Calum Gabbutt, Alison Berner, Melissa Schmidt, Bingjie Chen, Eszter Lakatos ,Vinay Gunasri, DanielNichol, HelenaCosta, Miriam Mitchinson, DanieleRamazzotti , Benjamin Werner, Francesco Iorio, Marnix Jansen, Giulio Caravagna , Chris P Barnes, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Andrea Sottoriva , Trevor A Graham

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.

Nature 2022 Nov;611(7937):733-743. doi: 10.1038/s41586-022-05202-1. Epub 2022 Oct 26.

PMID: 36289335, PMCID: PMC9684080, DOI: 10.1038/s41586-022-05202-1

Timon Heide, Jacob Househam, George D Cresswell, Inmaculada Spiteri, Claire Lynn, Maximilian Mossner, Chris Kimberley, Javier Fernandez-Mateos, Bingjie Chen, Luis Zapata, Chela James, Iros Barozzi, Ketevan Chkhaidze, Daniel Nichol, Vinaya Gunasri, Alison Berner, Melissa Schmidt, Eszter Lakatos, Ann-Marie Baker, Helena Costa, Miriam Mitchinson, Rocco Piazza, Marnix Jansen , Giulio Caravagna, DanieleRamazzotti, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Trevor A Graham, Andrea Sottoriva

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.

Nat Genet 2020 Oct;52(10):1057-1066. doi: 10.1038/s41588-020-0687-1. Epub 2020 Sep 14.

PMID: 32929288, PMCID: PMC7610467, DOI: 10.1038/s41588-020-0687-1

Eszter Lakatos, Marc J Williams, Ryan O Schenck, William C H Cross, Jacob Househam, Luis Zapata , Benjamin Werner, Chandler Gatenbee, Mark Robertson-Tessi, Chris P Barnes, Alexander R A Anderson, Andrea Sottoriva, Trevor A Graham.

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.

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