Showing papers by "Gad Getz published in 2021"
TL;DR: This article identified key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors.
211 citations
Wellcome Trust Sanger Institute1, Francis Crick Institute2, University of Oxford3, Broad Institute4, University of Toronto5, University of Texas MD Anderson Cancer Center6, University of Cambridge7, Katholieke Universiteit Leuven8, Heidelberg University9, German Cancer Research Center10, Simon Fraser University11, Vancouver Prostate Centre12, NorthShore University HealthSystem13, Oregon Health & Science University14, University of Melbourne15, Walter and Eliza Hall Institute of Medical Research16, Cornell University17, University of California, Santa Cruz18, University College London19, University of California, Los Angeles20, Ontario Institute for Cancer Research21, Harvard University22, University of Chicago23, University of Cologne24, University of Helsinki25, University of Glasgow26, European Bioinformatics Institute27, University of Manchester28
TL;DR: In this article, the authors extensively characterize intra-tumor heterogeneity (ITH) across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations.
191 citations
TL;DR: In this paper, a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs) is presented.
136 citations
Johns Hopkins University1, Baylor College of Medicine2, Washington University in St. Louis3, Massachusetts Institute of Technology4, University of Michigan5, Princess Margaret Cancer Centre6, Mount Sinai Hospital7, University of Toronto8, Leidos9, Van Andel Institute10, Memorial Sloan Kettering Cancer Center11, University of Calgary12
TL;DR: In this article, a comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues was conducted to understand the underlying molecular alterations that drive PDAC oncogenesis.
135 citations
TL;DR: A high-throughput, droplet-based mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) is introduced, a method that combines high-confidence mtDNA mutation calling in thousands of single cells with their concomitant high-quality accessible chromatin profile, which enables the inference of mtDNA heteroplasmy, clonal relationships, cell state and accessible Chromatin variation in individual cells.
Abstract: Natural mitochondrial DNA (mtDNA) mutations enable the inference of clonal relationships among cells. mtDNA can be profiled along with measures of cell state, but has not yet been combined with the massively parallel approaches needed to tackle the complexity of human tissue. Here, we introduce a high-throughput, droplet-based mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), a method that combines high-confidence mtDNA mutation calling in thousands of single cells with their concomitant high-quality accessible chromatin profile. This enables the inference of mtDNA heteroplasmy, clonal relationships, cell state and accessible chromatin variation in individual cells. We reveal single-cell variation in heteroplasmy of a pathologic mtDNA variant, which we associate with intra-individual chromatin variability and clonal evolution. We clonally trace thousands of cells from cancers, linking epigenomic variability to subclonal evolution, and infer cellular dynamics of differentiating hematopoietic cells in vitro and in vivo. Taken together, our approach enables the study of cellular population dynamics and clonal properties in vivo.
122 citations
Shankha Satpathy1, Karsten Krug1, Pierre M. Jean Beltran1, Sara R. Savage2 +159 more•Institutions (13)
TL;DR: In this article, the authors characterized the proteogenomic landscape of LSCC and provided a deeper exposition of the LSCC biology with potential therapeutic implications, identifying NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin.
102 citations
TL;DR: It is shown that single CTCs from melanoma patients coordinately upregulate lipogenesis and iron homeostasis pathways, correlated with both intrinsic and acquired resistance to BRAF inhibitors across clonal cultures of BRAF-mutant C TCs.
Abstract: Circulating tumor cells (CTCs) are shed by cancer into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastasis. We show that single CTCs from melanoma patients coordinately upregulate lipogenesis and iron homeostasis pathways. These are correlated with both intrinsic and acquired resistance to BRAF inhibitors across clonal cultures of BRAF-mutant CTCs. The lipogenesis regulator SREBF2 directly induces transcription of the iron carrier Transferrin (TF), reducing intracellular iron pools, reactive oxygen species (ROS) and lipid peroxidation, thereby conferring resistance to inducers of ferroptosis. Knockdown of endogenous TF impairs tumor formation by melanoma CTCs, and their tumorigenic defects are partially rescued by the lipophilic anti-oxidants Ferrostatin-1 and Vitamin E. In a prospective melanoma cohort, presence of CTCs with high lipogenic and iron metabolic RNA signatures is correlated with adverse clinical outcome, irrespective of treatment regimen. Thus, SREBF2-driven iron homeostatic pathways contribute to cancer progression, drug resistance and metastasis.
77 citations
TL;DR: In this article, a high-confidence database of translated nuORFs across tissues (nuORFdb) was constructed and used to detect 3,555 translated unicast ORFs from MHC-I immunopeptidome mass spectrometry analysis.
Abstract: Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originating from novel or unannotated open reading frames (nuORFs) can contribute to antitumor immune responses remains unclear. Here we show that peptides originating from nuORFs detected by ribosome profiling of malignant and healthy samples can be displayed on MHC-I of cancer cells, acting as additional sources of cancer antigens. We constructed a high-confidence database of translated nuORFs across tissues (nuORFdb) and used it to detect 3,555 translated nuORFs from MHC-I immunopeptidome mass spectrometry analysis, including peptides that result from somatic mutations in nuORFs of cancer samples as well as tumor-specific nuORFs translated in melanoma, chronic lymphocytic leukemia and glioblastoma. NuORFs are an unexplored pool of MHC-I-presented, tumor-specific peptides with potential as immunotherapy targets. New tumor epitopes are discovered by ribosome profiling and immunopeptidome mass spectrometry.
73 citations
National Institutes of Health1, Broad Institute2, Academy of Medical Sciences, United Kingdom3, Nvidia4, Leidos5, University of North Carolina at Chapel Hill6, Imperial College London7, Nationwide Children's Hospital8, Ohio State University9, Radiation Effects Research Foundation10, Harvard University11
TL;DR: In this paper, the authors analyzed genomic, transcriptomic, and epigenomic characteristics of 440 Papillary thyroid carcinoma (PTC) from Ukraine (from 359 individuals with estimated childhood 131I exposure and 81 unexposed children born after 1986).
Abstract: The 1986 Chernobyl nuclear power plant accident increased papillary thyroid carcinoma (PTC) incidence in surrounding regions, particularly for radioactive iodine (131I)-exposed children. We analyzed genomic, transcriptomic, and epigenomic characteristics of 440 PTCs from Ukraine (from 359 individuals with estimated childhood 131I exposure and 81 unexposed children born after 1986). PTCs displayed radiation dose-dependent enrichment of fusion drivers, nearly all in the mitogen-activated protein kinase pathway, and increases in small deletions and simple/balanced structural variants that were clonal and bore hallmarks of nonhomologous end-joining repair. Radiation-related genomic alterations were more pronounced for individuals who were younger at exposure. Transcriptomic and epigenomic features were strongly associated with driver events but not radiation dose. Our results point to DNA double-strand breaks as early carcinogenic events that subsequently enable PTC growth after environmental radiation exposure.
61 citations
TL;DR: In this article, the authors identify mechanisms of SG resistance through RNA and whole-exome sequencing of pretreatment and post-progression specimens, highlighting the specificity of SG and illustrates how such mechanisms will inform therapeutic strategies to overcome ADC resistance.
Abstract: Sacituzumab govitecan (SG), the first antibody–drug conjugate (ADC) approved for triple-negative breast cancer, incorporates the anti-TROP2 antibody hRS7 conjugated to a topoisomerase-1 (TOP1) inhibitor payload. We sought to identify mechanisms of SG resistance through RNA and whole-exome sequencing of pretreatment and postprogression specimens. One patient exhibiting de novo progression lacked TROP2 expression, in contrast to robust TROP2 expression and focal genomic amplification of TACSTD2/TROP2 observed in a patient with a deep, prolonged response to SG. Analysis of acquired genomic resistance in this case revealed one phylogenetic branch harboring a canonical TOP1E418K resistance mutation and subsequent frameshift TOP1 mutation, whereas a distinct branch exhibited a novel TACSTD2/TROP2T256R missense mutation. Reconstitution experiments demonstrated that TROP2T256R confers SG resistance via defective plasma membrane localization and reduced cell-surface binding by hRS7. These findings highlight parallel genomic alterations in both antibody and payload targets associated with resistance to SG. Significance: These findings underscore TROP2 as a response determinant and reveal acquired SG resistance mechanisms involving the direct antibody and drug payload targets in distinct metastatic subclones of an individual patient. This study highlights the specificity of SG and illustrates how such mechanisms will inform therapeutic strategies to overcome ADC resistance. This article is highlighted in the In This Issue feature, p. 2355
47 citations
TL;DR: In this paper, the effects of radiation exposure from the Chernobyl nuclear accident were investigated in children born to parents employed as cleanup workers or exposed to occupational and environmental ionizing radiation after the accident.
Abstract: Effects of radiation exposure from the Chernobyl nuclear accident remain a topic of interest. We investigated germline de novo mutations (DNMs) in children born to parents employed as cleanup workers or exposed to occupational and environmental ionizing radiation after the accident. Whole-genome sequencing of 130 children (born 1987-2002) and their parents did not reveal an increase in the rates, distributions, or types of DNMs relative to the results of previous studies. We find no elevation in total DNMs, regardless of cumulative preconception gonadal paternal [mean = 365 milligrays (mGy), range = 0 to 4080 mGy] or maternal (mean = 19 mGy, range = 0 to 550 mGy) exposure to ionizing radiation. Thus, we conclude that, over this exposure range, evidence is lacking for a substantial effect on germline DNMs in humans, suggesting minimal impact from transgenerational genetic effects.
University of Toronto1, Harvard University2, Broad Institute3, McGill University4, Tulane University5, Alberta Children's Hospital6, University of Calgary7, University of Texas Southwestern Medical Center8, Laval University9, University of Hamburg10, Boston Children's Hospital11, Children's Hospital of Philadelphia12, University of Pennsylvania13, University of Padua14, Oregon Health & Science University15, Medical College of Wisconsin16, University of New South Wales17, Medical University of South Carolina18, University of Manitoba19, Sheba Medical Center20, University of Alabama at Birmingham21, West Virginia University22, Cliniques Universitaires Saint-Luc23, Hebrew University of Jerusalem24, Mount Sinai Hospital, Toronto25, National Institutes of Health26
TL;DR: In this article, a novel association between loss of polymerase proofreading and microsatellite instability (MSI), especially when both components are lost, was revealed by genome-wide analysis of tumors with germline and somatic deficiencies in replication repair, which can be used clinically for diagnosis of replication repair deficiency and immunotherapy response prediction.
Abstract: Although replication repair deficiency, either by mismatch repair deficiency (MMRD) and/or loss of DNA polymerase proofreading, can cause hypermutation in cancer, microsatellite instability (MSI) is considered a hallmark of MMRD alone. By genome-wide analysis of tumors with germline and somatic deficiencies in replication repair, we reveal a novel association between loss of polymerase proofreading and MSI, especially when both components are lost. Analysis of indels in microsatellites (MS-indels) identified five distinct signatures (MS-sigs). MMRD MS-sigs are dominated by multibase losses, whereas mutant-polymerase MS-sigs contain primarily single-base gains. MS deletions in MMRD tumors depend on the original size of the MS and converge to a preferred length, providing mechanistic insight. Finally, we demonstrate that MS-sigs can be a powerful clinical tool for managing individuals with germline MMRD and replication repair-deficient cancers, as they can detect the replication repair deficiency in normal cells and predict their response to immunotherapy. SIGNIFICANCE: Exome- and genome-wide MSI analysis reveals novel signatures that are uniquely attributed to mismatch repair and DNA polymerase. This provides new mechanistic insight into MS maintenance and can be applied clinically for diagnosis of replication repair deficiency and immunotherapy response prediction.This article is highlighted in the In This Issue feature, p. 995.
01 Jul 2021
TL;DR: This work developed a functionalized lineage-tracing system, ClonMapper, which integrates DNA barcoding with single-cell RNA sequencing and clonal isolation to comprehensively characterize thousands of clones within heterogeneous populations of a chronic lymphocytic leukemia cell line.
Abstract: Lineage-tracing methods have enabled characterization of clonal dynamics in complex populations, but generally lack the ability to integrate genomic, epigenomic and transcriptomic measurements with live-cell manipulation of specific clones of interest. We developed a functionalized lineage-tracing system, ClonMapper, which integrates DNA barcoding with single-cell RNA sequencing and clonal isolation to comprehensively characterize thousands of clones within heterogeneous populations. Using ClonMapper, we identified subpopulations of a chronic lymphocytic leukemia cell line with distinct clonal compositions, transcriptional signatures and chemotherapy survivorship trajectories; patterns that were also observed in primary human chronic lymphocytic leukemia. The ability to retrieve specific clones before, during and after treatment enabled direct measurements of clonal diversification and durable subpopulation transcriptional signatures. ClonMapper is a powerful multifunctional approach to dissect the complex clonal dynamics of tumor progression and therapeutic response. Wu and colleagues develop a barcoding tool, ClonMapper, which permits single-cell lineage tracing and clonal isolation and demonstrate its utility to study clonal dynamics in human CLL cells in the context of chemotherapy treatment and resistance.
TL;DR: In this article, the authors developed a CRISPR paralog targeting library to investigate the viability effects of disrupting 3,284 genes, 5,065 paralog pairs and 815 paralog families.
Abstract: Although single-gene perturbation screens have revealed a number of new targets, vulnerabilities specific to frequently altered drivers have not been uncovered. An important question is whether the compensatory relationship between functionally redundant genes masks potential therapeutic targets in single-gene perturbation studies. To identify digenic dependencies, we developed a CRISPR paralog targeting library to investigate the viability effects of disrupting 3,284 genes, 5,065 paralog pairs and 815 paralog families. We identified that dual inactivation of DUSP4 and DUSP6 selectively impairs growth in NRAS and BRAF mutant cells through the hyperactivation of MAPK signaling. Furthermore, cells resistant to MAPK pathway therapeutics become cross-sensitized to DUSP4 and DUSP6 perturbations such that the mechanisms of resistance to the inhibitors reinforce this mechanism of vulnerability. Together, multigene perturbation technologies unveil previously unrecognized digenic vulnerabilities that may be leveraged as new therapeutic targets in cancer. A CRISPR paralog targeting library profiling 815 paralog families across 11 cell lines identifies DUSP4 and DUSP6 as paralog pairs whose combined inactivation confers sensitivity to cells resistant to MAPK inhibitors or cells harboring NRAS or BRAF mutations.
TL;DR: RNA-SeQC 2 as discussed by the authors is an efficient re-implementation of RNASeqC that adds multiple metrics designed to characterize sample quality across a wide range of RNA-seq protocols.
Abstract: Summary Post-sequencing quality control is a crucial component of RNA sequencing (RNA-seq) data generation and analysis, as sample quality can be affected by sample storage, extraction, and sequencing protocols. RNA-seq is increasingly applied to cohorts ranging from hundreds to tens of thousands of samples in size, but existing tools do not readily scale to these sizes, and were not designed for a wide range of sample types and qualities. Here, we describe RNA-SeQC 2, an efficient reimplementation of RNA-SeQC (DeLuca et al., 2012) that adds multiple metrics designed to characterize sample quality across a wide range of RNA-seq protocols. Availability and implementation The command-line tool, documentation, and C ++ source code are available at the GitHub repository https://github.com/getzlab/rnaseqc. Supplementary information Supplementary data are available at Bioinformatics online.
TL;DR: In this article, the authors present findings from longitudinal whole-exome sequencing of cells from patients with multiply relapsed CLL (N = 28) enrolled in trials of PI3K inhibitors.
TL;DR: In this paper, a framework for profiling multiple tissues across the human body at single-cell resolution using single nucleus RNA-Seq (snRNA-seq) was established, and applied to 8 diverse, archived, frozen tissue types (three donors per tissue).
Abstract: Understanding the function of genes and their regulation in tissue homeostasis and disease requires knowing the cellular context in which genes are expressed in tissues across the body. Single cell genomics allows the generation of detailed cellular atlases in human tissues, but most efforts are focused on single tissue types. Here, we establish a framework for profiling multiple tissues across the human body at single-cell resolution using single nucleus RNA-Seq (snRNA-seq), and apply it to 8 diverse, archived, frozen tissue types (three donors per tissue). We apply four snRNA-seq methods to each of 25 samples from 16 donors, generating a cross-tissue atlas of 209,126 nuclei profiles, and benchmark them vs. scRNA-seq of comparable fresh tissues. We use a conditional variational autoencoder (cVAE) to integrate an atlas across tissues, donors, and laboratory methods. We highlight shared and tissue-specific features of tissue-resident immune cells, identifying tissue-restricted and non-restricted resident myeloid populations. These include a cross-tissue conserved dichotomy between LYVE1- and HLA class II-expressing macrophages, and the broad presence of LAM-like macrophages across healthy tissues that is also observed in disease. For rare, monogenic muscle diseases, we identify cell types that likely underlie the neuromuscular, metabolic, and immune components of these diseases, and biological processes involved in their pathology. For common complex diseases and traits analyzed by GWAS, we identify the cell types and gene modules that potentially underlie disease mechanisms. The experimental and analytical frameworks we describe will enable the generation of large-scale studies of how cellular and molecular processes vary across individuals and populations.
TL;DR: In this paper, a single-cell mtDNA assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones.
Abstract: While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones in vivo. We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure indicating clonal persistence, but dramatic changes following tight bottlenecks including disease transformation and relapse post-therapy, paralleled by acquisition of copy number variants, changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into non-genetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally-occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics.
Broad Institute1, Brigham and Women's Hospital2, Boston Children's Hospital3, University of North Carolina at Chapel Hill4, Harvard University5, University of Amsterdam6, Erasmus University Rotterdam7, Medical University of Warsaw8, Medical University of Silesia9, New York University10, St. Jude Children's Research Hospital11
TL;DR: It is concluded that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2 loss is sufficient to drive tumor growth.
TL;DR: In this paper, single-cell RNA-sequencing can help in the prediction of drug resistance in patients with multiple myeloma (MML) and showed promising results in predicting drug resistance.
Abstract: Single-cell RNA-sequencing can help in the prediction of drug resistance in patients with multiple myeloma.
Massachusetts Institute of Technology1, Harvard University2, Memorial Sloan Kettering Cancer Center3, University of Washington4, Fred Hutchinson Cancer Research Center5, Karolinska University Hospital6, University of Pavia7, Lund University8, University of Michigan9, Kaiser Permanente10, Cornell University11, Brigham and Women's Hospital12, Icahn School of Medicine at Mount Sinai13, Yale University14, Stanford University15, Howard Hughes Medical Institute16
TL;DR: Common mutations in the 5-methylcytosine reader, ZBTB33, as well as in YLPM1, SRCAP, and ZNF318 are identified, potentially linking DNA methylation and RNA splicing, the two most commonly mutated pathways in clonal hematopoiesis and MDS.
Abstract: Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the 5-methylcytosine reader, ZBTB33, as well as in YLPM1, SRCAP, and ZNF318. We also identified these mutations at low frequency in myelodysplastic syndrome patients. Zbtb33 edited mouse hematopoietic stem and progenitor cells exhibited a competitive advantage in vivo and increased genome-wide intron retention. ZBTB33 mutations potentially link DNA methylation and RNA splicing, the two most commonly mutated pathways in clonal hematopoiesis and MDS.
Harvard University1, Cornell University2, Washington University in St. Louis3, University of North Carolina at Chapel Hill4, Cedars-Sinai Medical Center5, University of California, Santa Cruz6, University of Tennessee Health Science Center7, National Institutes of Health8, Federal University of Paraná9, University of Chicago10, Buck Institute for Research on Aging11, Van Andel Institute12, University of Texas MD Anderson Cancer Center13, Broad Institute14, Fred Hutchinson Cancer Research Center15, University of California, San Francisco16, Brigham and Women's Hospital17, Memorial Sloan Kettering Cancer Center18, Boston University19, Princess Margaret Cancer Centre20
TL;DR: In this article, the authors used whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of lung adenocarcinoma (LUAD) lacking apparent alterations in this pathway.
TL;DR: In this article, the authors performed whole-exome and transcriptome sequencing on pre-treatment multi-regional tumor biopsies from exceptional responders (ERs) and non-responders (NRs, pathologic T3 or lymph node-positive disease) to intensive neoadjuvant anti-androgen therapies.
TL;DR: In this article, the authors report that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy.
Abstract: Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem Although many drivers of acquired drug resistance have been identified1‒6, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood The extent to which therapy actively drives tumor evolution by promoting mutagenic processes7 or simply provides the selective pressure necessary for the outgrowth of drug-resistant clones8 remains an open question Here, we report that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug-tolerant cancer cells persisting during therapy Induction of A3A facilitated the formation of double-strand DNA breaks (DSBs) in cycling drug-treated cells, and fully resistant clones that evolved from drug-tolerant intermediates exhibited an elevated burden of chromosomal aberrations such as copy number alterations and structural variations Preventing therapy-induced A3A mutagenesis either by gene deletion or RNAi-mediated suppression delayed the emergence of drug resistance Finally, we observed accumulation of A3A mutations in lung cancer patients who developed drug resistance after treatment with sequential targeted therapies These data suggest that induction of A3A mutagenesis in response to targeted therapy treatment may facilitate the development of acquired resistance in non-small-cell lung cancer Thus, suppressing expression or enzymatic activity of A3A may represent a potential therapeutic strategy to prevent or delay acquired resistance to lung cancer targeted therapy
TL;DR: PANOPLY as mentioned in this paper is a cloud-based platform for automated and reproducible proteogenomic data analysis, which can be used for the analysis of cancer proteogenomics data.
Abstract: Proteogenomics involves the integrative analysis of genomic, transcriptomic, proteomic and post-translational modification data produced by next-generation sequencing and mass spectrometry-based proteomics. Several publications by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and others have highlighted the impact of proteogenomics in enabling deeper insight into the biology of cancer and identification of potential drug targets. In order to encapsulate the complex data processing required for proteogenomics, and provide a simple interface to deploy a range of algorithms developed for data analysis, we have developed PANOPLY—a cloud-based platform for automated and reproducible proteogenomic data analysis. A wide array of algorithms have been implemented, and we highlight the application of PANOPLY to the analysis of cancer proteogenomic data.
Broad Institute1, Harvard University2, Washington University in St. Louis3, University of North Carolina at Chapel Hill4, Cedars-Sinai Medical Center5, University of California, Santa Cruz6, University of Tennessee Health Science Center7, National Institutes of Health8, Federal University of Paraná9, University of Chicago10, Cornell University11, University of California, San Francisco12, Buck Institute for Research on Aging13, Van Andel Institute14, University of Texas MD Anderson Cancer Center15, Fred Hutchinson Cancer Research Center16, Brigham and Women's Hospital17, Memorial Sloan Kettering Cancer Center18, Boston University19, Princess Margaret Cancer Centre20, Hebrew University of Jerusalem21
TL;DR: In this paper, the authors used whole-genome sequencing (WGS) of 85 cases found to be RPA(−) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of lung adenocarcinoma (LUAD) lacking apparent alterations in this pathway.
TL;DR: In this paper, the authors studied the evolution dynamics of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) by multi-regional whole-genome sequencing analysis.
Abstract: Complex chromosomal alterations are a hallmark of advanced cancers but rarely seen in normal tissue. The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations that can drive their transformation through focal oncogenic amplifications. However, the etiology and evolution dynamics of these alterations are poorly understood. Here we study chromosomal copy-number evolution in the progression of Barrett’s esophagus (BE) to esophageal adenocarcinoma (EAC) by multi-regional whole-genome sequencing analysis of BE samples with dysplasia and microscopic EAC foci. Through haplotype-specific copy-number analysis of BE genome evolution, we identified distinct patterns of episodic copy-number evolution consistent with the outcomes of abnormal mitosis and dicentric chromosome breakage. While abnormal mitosis, including whole-genome duplication, accounts for most chromosome or arm-level copy-number changes, segmental copy-number alterations display signatures of multi-generational evolution of unstable dicentric chromosomes. Continuous evolution of dicentric chromosomes through breakage-fusion-bridge cycles and chromothripsis rapidly increases genomic complexity and diversity among BE cells, culminating in the generation of distinct focal amplifications. These mutational processes enable multiple subclones within small dysplastic areas to undergo parallel transformation to cancer following acquisition of distinct oncogenic amplifications. Our results demonstrate how chromosomal instability drives clonal diversification in precancer evolution and promotes tumorigenesis in primary human samples.
TL;DR: In this paper, the authors performed whole exome (WES) and whole transcriptome sequencing (RNA-seq) on pre-treatment multi-regional tumor biopsies from exceptional responders (ER: pCR and MRD patients) and non-responders (NR: pathologic T3 or lymph node positive disease) treated with intensive anti-androgen therapies prior to prostatectomy.
Abstract: High-risk localized prostate cancer (HRLPC) is associated with a substantial risk of recurrence and prostate cancer-specific mortality1. Recent clinical trials have shown that intensifying anti-androgen therapies administered prior to prostatectomy can induce pathologic complete responses (pCR) or minimal residual disease (MRD) (<5 mm), together termed exceptional response, although the molecular determinants of these clinical outcomes are largely unknown. Here, we performed whole exome (WES) and whole transcriptome sequencing (RNA-seq) on pre-treatment multi-regional tumor biopsies from exceptional responders (ER: pCR and MRD patients) and non-responders (NR: pathologic T3 or lymph node positive disease) treated with intensive anti-androgen therapies prior to prostatectomy. SPOP mutation and SPOPL copy number loss were exclusively observed in ER, while TP53 mutation and PTEN copy number loss were exclusively observed in NR. These alterations were clonal in all tumor phylogenies per patient. Additionally, transcriptional programs involving androgen signaling and TGF{beta} signaling were enriched in ER and NR, respectively. The presence of these alterations in routine biopsies from patients with HRLPC may inform the prospective identification of responders to neoadjuvant anti-androgen therapies to improve clinical outcomes and stratify other patients to alternative biologically informed treatment strategies.
TL;DR: Single-cell RNA sequencing identifies an inflammatory subpopulation of mesenchymal stromal cells in patients with multiple myeloma.
Abstract: Single-cell RNA sequencing identifies an inflammatory subpopulation of mesenchymal stromal cells in patients with multiple myeloma.
TL;DR: The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.
Abstract: A lymphocyte suffers many threats to its genome, including programmed mutation during differentiation, antigen-driven proliferation and residency in diverse microenvironments. After developing protocols for single-cell lymphocyte expansions, we sequenced whole genomes from 717 normal naive and memory B and T lymphocytes and hematopoietic stem cells. Lymphocytes carried more point mutations and structural variation than stem cells, accruing at higher rates in T than B cells, attributable to both exogenous and endogenous mutational processes. Ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every one on-target IGV mutation during the germinal center reaction. Structural variation was 16-fold higher in lymphocytes than stem cells, with ~15% of deletions being attributable to off-target RAG activity. One Sentence Summary: The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.