1
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Frank S, Persse T, Coleman I, Bankhead A, Li D, De-Sarkar N, Wilson D, Rudoy D, Vashisth M, Galipeau P, Yang M, Hanratty B, Dumpit R, Morrissey C, Corey E, Montgomery RB, Haffner MC, Pritchard C, Vasioukhin V, Ha G, Nelson PS. Molecular consequences of acute versus chronic CDK12 loss in prostate carcinoma nominates distinct therapeutic strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603734. [PMID: 39071291 PMCID: PMC11275783 DOI: 10.1101/2024.07.16.603734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Genomic loss of the transcriptional kinase CDK12 occurs in ~6% of metastatic castration-resistant prostate cancers (mCRPC) and correlates with poor patient outcomes. Prior studies demonstrate that acute CDK12 loss confers a homologous recombination (HR) deficiency (HRd) phenotype via premature intronic polyadenylation (IPA) of key HR pathway genes, including ATM. However, mCRPC patients have not demonstrated benefit from therapies that exploit HRd such as inhibitors of polyADP ribose polymerase (PARP). Based on this discordance, we sought to test the hypothesis that an HRd phenotype is primarily a consequence of acute CDK12 loss and the effect is greatly diminished in prostate cancers adapted to CDK12 loss. Analyses of whole genome sequences (WGS) and RNA sequences (RNAseq) of human mCRPCs determined that tumors with biallelic CDK12 alterations (CDK12 BAL ) lack genomic scar signatures indicative of HRd, despite carrying bi-allelic loss and the appearance of the hallmark tandem-duplicator phenotype (TDP). Experiments confirmed that acute CDK12 inhibition resulted in aberrant polyadenylation and downregulation of long genes (including BRCA1 and BRCA2) but such effects were modest or absent in tumors adapted to chronic CDK12 BAL . One key exception was ATM, which did retain transcript shortening and reduced protein expression in the adapted CDK12 BAL models. However, CDK12 BAL cells demonstrated intact HR as measured by RAD51 foci formation following irradiation. CDK12 BAL cells showed a vulnerability to targeting of CDK13 by sgRNA or CDK12/13 inhibitors and in vivo treatment of prostate cancer xenograft lines showed that tumors with CDK12 BAL responded to the CDK12/13 inhibitor SR4835, while CDK12-intact lines did not. Collectively, these studies show that aberrant polyadenylation and long HR gene downregulation is primarily a consequence of acute CDK12 deficiency, which is largely compensated for in cells that have adapted to CDK12 loss. These results provide an explanation for why PARPi monotherapy has thus far failed to consistently benefit patients with CDK12 alterations, though alternate therapies that target CDK13 or transcription are candidates for future research and testing.
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Affiliation(s)
- Sander Frank
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Thomas Persse
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Armand Bankhead
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Dapei Li
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Navonil De-Sarkar
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, 53226
- Research Member, Medical College of Wisconsin Cancer Center, WI-53226
| | - Divin Wilson
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, 53226
- Research Member, Medical College of Wisconsin Cancer Center, WI-53226
| | - Dmytro Rudoy
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Manasvita Vashisth
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Patty Galipeau
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Michael Yang
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA 98195
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA 98195
| | | | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195
| | - Colin Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195
| | - Valera Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Gavin Ha
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Divison of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA 98119
- Department of Urology, University of Washington, Seattle, WA 98195
- Department of Medicine, University of Washington, Seattle, WA 98195
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195
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2
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Skelly DA, Graham JP, Cheng M, Furuta M, Walter A, Stoklasek TA, Yang H, Stearns TM, Poirion O, Zhang JG, Grassmann JDS, Luo D, Flynn WF, Courtois ET, Chang CH, Serreze DV, Menghi F, Reinholdt LG, Liu ET. Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603136. [PMID: 39071392 PMCID: PMC11275897 DOI: 10.1101/2024.07.11.603136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Identifying host genetic factors modulating immune checkpoint inhibitor (ICI) efficacy has been experimentally challenging because of variations in both host and tumor genomes, differences in the microbiome, and patient life exposures. Utilizing the Collaborative Cross (CC) multi-parent mouse genetic resource population, we developed an approach that fixes the tumor genomic configuration while varying host genetics. With this approach, we discovered that response to anti-PD-1 (aPD1) immunotherapy was significantly heritable in four distinct murine tumor models (H2 between 0.18-0.40). For the MC38 colorectal carcinoma system (H2 = 0.40), we mapped four significant ICI response quantitative trait loci (QTL) localized to mouse chromosomes (mChr) 5, 9, 15 and 17, and identified significant epistatic interactions between specific QTL pairs. Differentially expressed genes within these QTL were highly enriched for immune genes and pathways mediating allograft rejection and graft vs host disease. Using a cross species analytical approach, we found a core network of 48 genes within the four QTLs that showed significant prognostic value for overall survival in aPD1 treated human cohorts that outperformed all other existing validated immunotherapy biomarkers, especially in human tumors of the previously defined immune subtype 4. Functional blockade of two top candidate immune targets within the 48 gene network, GM-CSF and high affinity IL-2/IL-15 signaling, completely abrogated the MC38 tumor transcriptional response to aPD1 therapy in vivo. Thus, we have established a powerful cross species in vivo platform capable of uncovering host genetic factors that establish the tumor immune microenvironment configuration propitious for ICI response.
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Affiliation(s)
- Daniel A. Skelly
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - John P. Graham
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Mayuko Furuta
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Andrew Walter
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | | | | | - Olivier Poirion
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ji-Gang Zhang
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Diane Luo
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - William F. Flynn
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Elise T. Courtois
- Single Cell Biology Lab, The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- OB/Gyn Department, UConn Health, Farmington, CT, USA
| | - Chih-Hao Chang
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - David V. Serreze
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Edison T. Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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3
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Yang X, Zheng G, Jia P, Wang S, Ye K. Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae008. [PMID: 38862430 DOI: 10.1093/gpbjnl/qzae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 06/13/2024]
Abstract
Tandem duplication (TD) is a major type of structural variations (SVs) that plays an important role in novel gene formation and human diseases. However, TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational signals. Herein, we developed a TD detection module for the Pindel tool, referred to as Pindel-TD, based on a TD-specific pattern growth approach. Pindel-TD is capable of detecting TDs with a wide size range at single nucleotide resolution. Using simulated and real read data from HG002, we demonstrated that Pindel-TD outperforms other leading methods in terms of precision, recall, F1-score, and robustness. Furthermore, by applying Pindel-TD to data generated from the K562 cancer cell line, we identified a TD located at the seventh exon of SAGE1, providing an explanation for its high expression. Pindel-TD is available for non-commercial use at https://github.com/xjtu-omics/pindel.
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Affiliation(s)
- Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- Center for Mathematical Medical, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Gaoyang Zheng
- Center for Mathematical Medical, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Peng Jia
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Songbo Wang
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Kai Ye
- Center for Mathematical Medical, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
- Faculty of Science, Leiden University, Leiden 2311 EZ, Netherland
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4
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Audano PA, Beck CR. Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement. Genome Res 2024; 34:7-19. [PMID: 38176712 PMCID: PMC10904011 DOI: 10.1101/gr.278203.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
High-quality genome assemblies and sophisticated algorithms have increased sensitivity for a wide range of variant types, and breakpoint accuracy for structural variants (SVs, ≥50 bp) has improved to near base pair precision. Despite these advances, many SV breakpoint locations are subject to systematic bias affecting variant representation. To understand why SV breakpoints are inconsistent across samples, we reanalyzed 64 phased haplotypes constructed from long-read assemblies released by the Human Genome Structural Variation Consortium (HGSVC). We identify 882 SV insertions and 180 SV deletions with variable breakpoints not anchored in tandem repeats (TRs) or segmental duplications (SDs). SVs called from aligned sequencing reads increase breakpoint disagreements by 2×-16×. Sequence accuracy had a minimal impact on breakpoints, but we observe a strong effect of ancestry. We confirm that SNP and indel polymorphisms are enriched at shifted breakpoints and are also absent from variant callsets. Breakpoint homology increases the likelihood of imprecise SV calls and the distance they are shifted, and tandem duplications are the most heavily affected SVs. Because graph genome methods normalize SV calls across samples, we investigated graphs generated by two different methods and find the resulting breakpoints are subject to other technical biases affecting breakpoint accuracy. The breakpoint inconsistencies we characterize affect ∼5% of the SVs called in a human genome and can impact variant interpretation and annotation. These limitations underscore a need for algorithm development to improve SV databases, mitigate the impact of ancestry on breakpoints, and increase the value of callsets for investigating breakpoint features.
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Affiliation(s)
- Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA;
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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5
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Audano PA, Beck CR. Small allelic variants are a source of ancestral bias in structural variant breakpoint placement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546295. [PMID: 37425850 PMCID: PMC10327140 DOI: 10.1101/2023.06.25.546295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
High-quality genome assemblies and sophisticated algorithms have increased sensitivity for a wide range of variant types, and breakpoint accuracy for structural variants (SVs, ≥ 50 bp) has improved to near basepair precision. Despite these advances, many SVs in unique regions of the genome are subject to systematic bias that affects breakpoint location. This ambiguity leads to less accurate variant comparisons across samples, and it obscures true breakpoint features needed for mechanistic inferences. To understand why SVs are not consistently placed, we reanalyzed 64 phased haplotypes constructed from long-read assemblies released by the Human Genome Structural Variation Consortium (HGSVC). We identified variable breakpoints for 882 SV insertions and 180 SV deletions not anchored in tandem repeats (TRs) or segmental duplications (SDs). While this is unexpectedly high for genome assemblies in unique loci, we find read-based callsets from the same sequencing data yielded 1,566 insertions and 986 deletions with inconsistent breakpoints also not anchored in TRs or SDs. When we investigated causes for breakpoint inaccuracy, we found sequence and assembly errors had minimal impact, but we observed a strong effect of ancestry. We confirmed that polymorphic mismatches and small indels are enriched at shifted breakpoints and that these polymorphisms are generally lost when breakpoints shift. Long tracts of homology, such as SVs mediated by transposable elements, increase the likelihood of imprecise SV calls and the distance they are shifted. Tandem Duplication (TD) breakpoints are the most heavily affected SV class with 14% of TDs placed at different locations across haplotypes. While graph genome methods normalize SV calls across many samples, the resulting breakpoints are sometimes incorrect, highlighting a need to tune graph methods for breakpoint accuracy. The breakpoint inconsistencies we characterize collectively affect ~5% of the SVs called in a human genome and underscore a need for algorithm development to improve SV databases, mitigate the impact of ancestry on breakpoint placement, and increase the value of callsets for investigating mutational processes.
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Affiliation(s)
- Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA
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6
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Vias M, Morrill Gavarró L, Sauer CM, Sanders DA, Piskorz AM, Couturier DL, Ballereau S, Hernando B, Schneider MP, Hall J, Correia-Martins F, Markowetz F, Macintyre G, Brenton JD. High-grade serous ovarian carcinoma organoids as models of chromosomal instability. eLife 2023; 12:e83867. [PMID: 37166279 PMCID: PMC10174694 DOI: 10.7554/elife.83867] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most genomically complex cancer, characterized by ubiquitous TP53 mutation, profound chromosomal instability, and heterogeneity. The mutational processes driving chromosomal instability in HGSOC can be distinguished by specific copy number signatures. To develop clinically relevant models of these mutational processes we derived 15 continuous HGSOC patient-derived organoids (PDOs) and characterized them using bulk transcriptomic, bulk genomic, single-cell genomic, and drug sensitivity assays. We show that HGSOC PDOs comprise communities of different clonal populations and represent models of different causes of chromosomal instability including homologous recombination deficiency, chromothripsis, tandem-duplicator phenotype, and whole genome duplication. We also show that these PDOs can be used as exploratory tools to study transcriptional effects of copy number alterations as well as compound-sensitivity tests. In summary, HGSOC PDO cultures provide validated genomic models for studies of specific mutational processes and precision therapeutics.
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Affiliation(s)
- Maria Vias
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Lena Morrill Gavarró
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
- The MRC Weatherall Institute of Molecular MedicineOxfordUnited Kingdom
| | - Carolin M Sauer
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Deborah A Sanders
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Anna M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | | | - Stéphane Ballereau
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Bárbara Hernando
- Centro Nacional de Investigaciones Oncológicas, C/Melchor Fernández AlmagroMadridSpain
| | - Michael P Schneider
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - James Hall
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Filipe Correia-Martins
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Geoff Macintyre
- Centro Nacional de Investigaciones Oncológicas, C/Melchor Fernández AlmagroMadridSpain
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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7
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Tao Z, Wang S, Wu C, Wu T, Zhao X, Ning W, Wang G, Wang J, Chen J, Diao K, Chen F, Liu XS. The repertoire of copy number alteration signatures in human cancer. Brief Bioinform 2023; 24:7048898. [PMID: 36806386 PMCID: PMC10025440 DOI: 10.1093/bib/bbad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/01/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
Copy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based on various fragment properties, which reflect the consequences of mutagenic processes and can be extracted from different types of data, including whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) array. The 14 signatures of CNA have been extracted from 2778 pan-cancer analysis of whole genomes WGS samples, and further validated with 10 851 the cancer genome atlas SNP array dataset. Novel patterns of CNA have been revealed through this study. The activities of some CNA signatures consistently predict cancer patients' prognosis. This study provides a repertoire for understanding the signatures of CNA in cancer, with potential implications for cancer prognosis, evolution and etiology.
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Affiliation(s)
- Ziyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shixiang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Bioinformatics Platform, Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Chenxu Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Wei Ning
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Guangshuai Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Jinyu Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Jing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Kaixuan Diao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Fuxiang Chen
- Department of Clinical Immunology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
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8
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Moore B, Herrera M, Gairin E, Li C, Miura S, Jolly J, Mercader M, Izumiyama M, Kawai E, Ravasi T, Laudet V, Ryu T. The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish. G3 (BETHESDA, MD.) 2023; 13:6982751. [PMID: 36626199 PMCID: PMC9997566 DOI: 10.1093/g3journal/jkad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.
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Affiliation(s)
- Billy Moore
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Marcela Herrera
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Emma Gairin
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Chengze Li
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Saori Miura
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Jeffrey Jolly
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Manon Mercader
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Michael Izumiyama
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Erina Kawai
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, I-Lan 262, Taiwan
| | - Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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9
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Schimmel J, van Wezel MD, van Schendel R, Tijsterman M. Chromosomal breaks at the origin of small tandem DNA duplications. Bioessays 2023; 45:e2200168. [PMID: 36385254 DOI: 10.1002/bies.202200168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/18/2022]
Abstract
Small tandem DNA duplications in the range of 15 to 300 base-pairs play an important role in the aetiology of human disease and contribute to genome diversity. Here, we discuss different proposed mechanisms for their occurrence and argue that this type of structural variation mainly results from mutagenic repair of chromosomal breaks. This hypothesis is supported by both bioinformatical analysis of insertions occurring in the genome of different species and disease alleles, as well as by CRISPR/Cas9-based experimental data from different model systems. Recent work points to fill-in synthesis at double-stranded DNA breaks with complementary sequences, regulated by end-joining mechanisms, to account for small tandem duplications. We will review the prevalence of small tandem duplications in the population, and we will speculate on the potential sources of DNA damage that could give rise to this mutational signature. With the development of novel algorithms to analyse sequencing data, small tandem duplications are now more frequently detected in the human genome and identified as oncogenic gain-of-function mutations. Understanding their origin could lead to optimized treatment regimens to prevent therapy-induced activation of oncogenes and might expose novel vulnerabilities in cancer.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marloes D van Wezel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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10
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Webster ALH, Sanders MA, Patel K, Dietrich R, Noonan RJ, Lach FP, White RR, Goldfarb A, Hadi K, Edwards MM, Donovan FX, Hoogenboezem RM, Jung M, Sridhar S, Wiley TF, Fedrigo O, Tian H, Rosiene J, Heineman T, Kennedy JA, Bean L, Rosti RO, Tryon R, Gonzalez AM, Rosenberg A, Luo JD, Carroll TS, Shroff S, Beaumont M, Velleuer E, Rastatter JC, Wells SI, Surrallés J, Bagby G, MacMillan ML, Wagner JE, Cancio M, Boulad F, Scognamiglio T, Vaughan R, Beaumont KG, Koren A, Imielinski M, Chandrasekharappa SC, Auerbach AD, Singh B, Kutler DI, Campbell PJ, Smogorzewska A. Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer. Nature 2022; 612:495-502. [PMID: 36450981 DOI: 10.1038/s41586-022-05253-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/18/2022] [Indexed: 12/03/2022]
Abstract
Fanconi anaemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink repair resulting in chromosome breakage1-3. The FA repair pathway protects against endogenous and exogenous carcinogenic aldehydes4-7. Individuals with FA are hundreds to thousands fold more likely to develop head and neck (HNSCC), oesophageal and anogenital squamous cell carcinomas8 (SCCs). Molecular studies of SCCs from individuals with FA (FA SCCs) are limited, and it is unclear how FA SCCs relate to sporadic HNSCCs primarily driven by tobacco and alcohol exposure or infection with human papillomavirus9 (HPV). Here, by sequencing genomes and exomes of FA SCCs, we demonstrate that the primary genomic signature of FA repair deficiency is the presence of high numbers of structural variants. Structural variants are enriched for small deletions, unbalanced translocations and fold-back inversions, and are often connected, thereby forming complex rearrangements. They arise in the context of TP53 loss, but not in the context of HPV infection, and lead to somatic copy-number alterations of HNSCC driver genes. We further show that FA pathway deficiency may lead to epithelial-to-mesenchymal transition and enhanced keratinocyte-intrinsic inflammatory signalling, which would contribute to the aggressive nature of FA SCCs. We propose that the genomic instability in sporadic HPV-negative HNSCC may arise as a result of the FA repair pathway being overwhelmed by DNA interstrand crosslink damage caused by alcohol and tobacco-derived aldehydes, making FA SCC a powerful model to study tumorigenesis resulting from DNA-crosslinking damage.
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Affiliation(s)
- Andrew L H Webster
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.,Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Krupa Patel
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Ralf Dietrich
- Deutsche Fanconi-Anämie-Hilfe e.V, Unna-Siddinghausen, Germany
| | - Raymond J Noonan
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Ryan R White
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Audrey Goldfarb
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Kevin Hadi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine and New York Genome Center, New York, NY, USA
| | - Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Remco M Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Moonjung Jung
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genomes Laboratory, Rockefeller University, New York, NY, USA
| | - Huasong Tian
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine and New York Genome Center, New York, NY, USA
| | - Joel Rosiene
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine and New York Genome Center, New York, NY, USA
| | - Thomas Heineman
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Jennifer A Kennedy
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Bean
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Rasim O Rosti
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Rebecca Tryon
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | | | - Allana Rosenberg
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, Rockefeller University, New York, NY, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, Rockefeller University, New York, NY, USA
| | - Sanjana Shroff
- Department of Genetics and Genomic Sciences. Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Michael Beaumont
- Department of Genetics and Genomic Sciences. Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Eunike Velleuer
- Institute for Pathology, Department for Cytopathology, University Hospital of Düsseldorf, Düsseldorf, Germany.,Pediatric Cancer Center, Helios Hospital Krefeld, Düsseldorf, Germany
| | - Jeff C Rastatter
- Division of Pediatric Otolaryngology-Head and Neck Surgery, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University, Chicago, IL, USA.,Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susanne I Wells
- Division of Oncology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jordi Surrallés
- Genomic Instability and DNA Repair Syndromes Group and Joint Research Unit on Genomic Medicine UAB-Sant Pau Biomedical Research Institute (IIB Sant Pau), Institut de Recerca Hospital de la Santa Creu i Sant Pau-IIB Sant Pau, Barcelona, Spain
| | - Grover Bagby
- Departments of Medicine and Molecular and Medical Genetics, Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - John E Wagner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Maria Cancio
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Farid Boulad
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Roger Vaughan
- Department of Biostatistics, The Rockefeller University, New York, NY, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences. Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine and New York Genome Center, New York, NY, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arleen D Auerbach
- Human Genetics and Hematology Program, The Rockefeller University, New York, NY, USA
| | - Bhuvanesh Singh
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David I Kutler
- Department of Otolaryngology-Head and Neck Surgery, Weill Cornell Medical College, New York, NY, USA
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, Rockefeller University, New York, NY, USA.
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11
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Characterization of somatic structural variations in 528 Chinese individuals with Esophageal squamous cell carcinoma. Nat Commun 2022; 13:6296. [PMID: 36272974 PMCID: PMC9588063 DOI: 10.1038/s41467-022-33994-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) demonstrates high genome instability. Here, we analyze 528 whole genomes to investigate structural variations' mechanisms and biological functions. SVs show multi-mode distributions in size, indicating distinct mutational processes. We develop a tool and define five types of complex rearrangements with templated insertions. We highlight a type of fold-back inversion, which is associated with poor outcomes. Distinct rearrangement signatures demonstrate variable genomic metrics such as replicating time, spatial proximity, and chromatin accessibility. Specifically, fold-back inversion tends to occur near the centrosome; TD-c2 (Tandem duplication-cluster2) is significantly enriched in chromatin-accessibility and early-replication region compared to other signatures. Analyses of TD-c2 signature reveal 9 TD hotspots, of which we identify a hotspot consisting of a super-enhancer of PTHLH. We confirm the oncogenic effect of the PTHLH gene and its interaction with enhancers through functional experiments. Finally, extrachromosomal circular DNAs (ecDNAs) are present in 14% of ESCCs and have strong selective advantages to driver genes.
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12
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Heterogeneity of triple negative breast cancer: Current advances in subtyping and treatment implications. J Exp Clin Cancer Res 2022; 41:265. [PMID: 36050786 PMCID: PMC9434975 DOI: 10.1186/s13046-022-02476-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractAs the field of translational ‘omics has progressed, refined classifiers at both genomic and proteomic levels have emerged to decipher the heterogeneity of breast cancer in a clinically-applicable way. The integration of ‘omics knowledge at the DNA, RNA and protein levels is further expanding biologic understanding of breast cancer and opportunities for customized treatment, a particularly pressing need in clinically triple negative tumors. For this group of aggressive breast cancers, work from multiple groups has now validated at least four major biologically and clinically distinct omics-based subtypes. While to date most clinical trial designs have considered triple negative breast cancers as a single group, with an expanding arsenal of targeted therapies applicable to distinct biological pathways, survival benefits may be best realized by designing and analyzing clinical trials in the context of major molecular subtypes. While RNA-based classifiers are the most developed, proteomic classifiers proposed for triple negative breast cancer based on new technologies have the potential to more directly identify the most clinically-relevant biomarkers and therapeutic targets. Phospho-proteomic data further identify targetable signalling pathways in a unique subtype-specific manner. Single cell profiling of the tumor microenvironment represents a promising way to allow a better characterization of the heterogeneity of triple negative breast cancer which could be integrated in a spatially resolved context to build an ecosystem-based patient classification. Multi-omic data further allows in silico analysis of genetic and pharmacologic screens to map therapeutic vulnerabilities in a subtype-specific context. This review describes current knowledge about molecular subtyping of triple negative breast cancer, recent advances in omics-based genomics and proteomics diagnostics addressing the diversity of this disease, key advances made through single cell analysis approaches, and developments in treatments including targeted therapeutics being tested in major clinical trials.
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13
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Menghi F, Banda K, Kumar P, Straub R, Dobrolecki L, Rodriguez IV, Yost SE, Chandok H, Radke MR, Somlo G, Yuan Y, Lewis MT, Swisher EM, Liu ET. Genomic and epigenomic
BRCA
alterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas. Sci Transl Med 2022; 14:eabn1926. [PMID: 35857626 PMCID: PMC9585706 DOI: 10.1126/scitranslmed.abn1926] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Triple-negative breast cancer (TNBC) and ovarian carcinomas (OvCas) with
BRCA1
promoter methylation (
BRCA1
meth) respond more poorly to alkylating agents compared to those bearing mutations in
BRCA1
and
BRCA2
(
BRCA
mut). This is a conundrum given the biologically equivalent homologous recombination deficiency (HRD) induced by these genetic and epigenetic
BRCA
perturbations. We dissected this problem through detailed genomic analyses of TNBC and OvCa cohorts and experimentation with patient-derived xenografts and genetically engineered cell lines. We found that despite identical downstream genomic mutational signatures associated with
BRCA1
meth and
BRCA
mut states,
BRCA1
meth uniformly associates with poor outcomes. Exposure of
BRCA1
meth TNBCs to platinum chemotherapy, either as clinical treatment of a patient or as experimental in vivo exposure of preclinical patient derived xenografts, resulted in allelic loss of
BRCA1
methylation and increased
BRCA1
expression and platinum resistance. These data suggest that, unlike
BRCA
mut cancers, where
BRCA
loss is a genetically “fixed” deficiency state,
BRCA1
meth cancers are highly adaptive to genotoxin exposure and, through reversal of promoter methylation, recover
BRCA1
expression and become resistant to therapy. We further found a specific augmented immune transcriptional signal associated with enhanced response to platinum chemotherapy but only in patients with BRCA-proficient cancers. We showed how integrating both this cancer immune signature and the presence of
BRCA
mutations results in more accurate predictions of patient response when compared to either HRD status or
BRCA
status alone. This underscores the importance of defining
BRCA
heterogeneity in optimizing the predictive precision of assigning response probabilities in TNBC and OvCa.
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Affiliation(s)
- Francesca Menghi
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Kalyan Banda
- Division of Medical Oncology, UW Medical Center, Seattle, WA 98195, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pooja Kumar
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Robert Straub
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Isabel V. Rodriguez
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - Susan E. Yost
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Marc R. Radke
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - George Somlo
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Yuan Yuan
- Division of Medical Oncology and Therapeutic Research, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Michael T. Lewis
- Departments of Molecular and Cellular Biology and Radiology, Lester and Sue Smith Breast Center, Dan L Duncan Comprehensive Cancer Center, Houston, TX 77030, USA
| | - Elizabeth M. Swisher
- Department of Obstetrics and Gynecology, UW Medical Center, Seattle, WA 98195, USA
| | - Edison T. Liu
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
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14
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Hosur V, Low BE, Wiles MV. Programmable RNA-Guided Large DNA Transgenesis by CRISPR/Cas9 and Site-Specific Integrase Bxb1. Front Bioeng Biotechnol 2022; 10:910151. [PMID: 35866031 PMCID: PMC9294445 DOI: 10.3389/fbioe.2022.910151] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
The inability to insert large DNA constructs into the genome efficiently and precisely is a key challenge in genomic engineering. Random transgenesis, which is widely used, lacks precision, and comes with a slew of drawbacks. Lentiviral and adeno-associated viral methods are plagued by, respectively, DNA toxicity and a payload capacity of less than 5 kb. Homology-directed repair (HDR) techniques based on CRISPR-Cas9 can be effective, but only in the 1–5 kb range. In addition, long homology arms—DNA sequences that permit construct insertion—of lengths ranging from 0.5 to 5 kb are required by currently known HDR-based techniques. A potential new method that uses Cas9-guided transposases to insert DNA structures up to 10 kb in length works well in bacteria, but only in bacteria. Surmounting these roadblocks, a new toolkit has recently been developed that combines RNA-guided Cas9 and the site-specific integrase Bxb1 to integrate DNA constructs ranging in length from 5 to 43 kb into mouse zygotes with germline transmission and into human cells. This ground-breaking toolkit will give researchers a valuable resource for developing novel, urgently needed mouse and human induced pluripotent stem cell (hiPSC) models of cancer and other genetic diseases, as well as therapeutic gene integration and biopharmaceutical applications, such as the development of stable cell lines to produce therapeutic protein products.
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15
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Giles Doran C, Pennington SR. Copy number alteration signatures as biomarkers in cancer: a review. Biomark Med 2022; 16:371-386. [PMID: 35195030 DOI: 10.2217/bmm-2021-0476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Within certain cancers, extensive copy number alterations (CNAs) contribute to a complex and heterogenic genomic profile. This makes it difficult to understand and unravel the distinct molecular dynamics shaping the disease while preventing clinically effective patient stratification. CNA signature analysis represents a novel genomic stratification tool for probing this complexity, offering an intricate framework for deriving CNA patterns at the molecular level. This allows the underlying genomic mechanisms of specific cancers to be revealed, leading to the potential identification of therapeutic targets and prognostic associations. This review outlines the molecular and methodological basis of CNA signatures and focuses on recent advances highlighting their clinical utility, limitations and prospective future as novel diagnostic and prognostic cancer biomarkers.
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Affiliation(s)
- Conor Giles Doran
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stephen R Pennington
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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16
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Abstract
Gastric cancer (GC) is a leading contributor to global cancer incidence and mortality. Pioneering genomic studies, focusing largely on primary GCs, revealed driver alterations in genes such as ERBB2, FGFR2, TP53 and ARID1A as well as multiple molecular subtypes. However, clinical efforts targeting these alterations have produced variable results, hampered by complex co-alteration patterns in molecular profiles and intra-patient genomic heterogeneity. In this Review, we highlight foundational and translational advances in dissecting the genomic cartography of GC, including non-coding variants, epigenomic aberrations and transcriptomic alterations, and describe how these alterations interplay with environmental influences, germline factors and the tumour microenvironment. Mapping of these alterations over the GC life cycle in normal gastric tissues, metaplasia, primary carcinoma and distant metastasis will improve our understanding of biological mechanisms driving GC development and promoting cancer hallmarks. On the translational front, integrative genomic approaches are identifying diverse mechanisms of GC therapy resistance and emerging preclinical targets, enabled by technologies such as single-cell sequencing and liquid biopsies. Validating these insights will require specifically designed GC cohorts, converging multi-modal genomic data with longitudinal data on therapeutic challenges and patient outcomes. Genomic findings from these studies will facilitate 'next-generation' clinical initiatives in GC precision oncology and prevention.
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Affiliation(s)
- Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gastroenterology and Hepatology, National University Health System, Singapore, Singapore
- Singapore Gastric Cancer Consortium, Singapore, Singapore
| | - Patrick Tan
- Singapore Gastric Cancer Consortium, Singapore, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School Singapore, Singapore, Singapore.
- Genome Institute of Singapore, Singapore, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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17
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Abstract
Triple-negative breast cancer (TNBC) encompasses a heterogeneous group of fundamentally different diseases with different histologic, genomic, and immunologic profiles, which are aggregated under this term because of their lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 expression. Massively parallel sequencing and other omics technologies have demonstrated the level of heterogeneity in TNBCs and shed light into the pathogenesis of this therapeutically challenging entity in breast cancer. In this review, we discuss the histologic and molecular classifications of TNBC, the genomic alterations these different tumor types harbor, and the potential impact of these alterations on the pathogenesis of these tumors. We also explore the role of the tumor microenvironment in the biology of TNBCs and its potential impact on therapeutic response. Dissecting the biology and understanding the therapeutic dependencies of each TNBC subtype will be essential to delivering on the promise of precision medicine for patients with triple-negative disease.
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Affiliation(s)
- Fatemeh Derakhshan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA;
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA;
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18
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Koh G, Degasperi A, Zou X, Momen S, Nik-Zainal S. Mutational signatures: emerging concepts, caveats and clinical applications. Nat Rev Cancer 2021; 21:619-637. [PMID: 34316057 DOI: 10.1038/s41568-021-00377-7] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/08/2021] [Indexed: 02/05/2023]
Abstract
Whole-genome sequencing has brought the cancer genomics community into new territory. Thanks to the sheer power provided by the thousands of mutations present in each patient's cancer, we have been able to discern generic patterns of mutations, termed 'mutational signatures', that arise during tumorigenesis. These mutational signatures provide new insights into the causes of individual cancers, revealing both endogenous and exogenous factors that have influenced cancer development. This Review brings readers up to date in a field that is expanding in computational, experimental and clinical directions. We focus on recent conceptual advances, underscoring some of the caveats associated with using the mutational signature frameworks and highlighting the latest experimental insights. We conclude by bringing attention to areas that are likely to see advancements in clinical applications.
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Affiliation(s)
- Gene Koh
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Andrea Degasperi
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Xueqing Zou
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Sophie Momen
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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19
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Scully R, Elango R, Panday A, Willis NA. Recombination and restart at blocked replication forks. Curr Opin Genet Dev 2021; 71:154-162. [PMID: 34464818 DOI: 10.1016/j.gde.2021.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 01/07/2023]
Abstract
Replication fork stalling occurs when the replisome encounters a barrier to normal fork progression. Replisome stalling events are common during scheduled DNA synthesis, but vary in their severity. At one extreme, a lesion may induce only temporary pausing of a DNA polymerase; at the other, it may present a near-absolute barrier to the replicative helicase and effectively block fork progression. Many alternative pathways have evolved to respond to these different types of replication stress. Among these, the homologous recombination (HR) pathway plays an important role, protecting the stalled fork and processing it for repair. Here, we review recent advances in our understanding of how blocked replication forks in vertebrate cells can be processed for recombination and for replication restart.
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Affiliation(s)
- Ralph Scully
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.
| | - Rajula Elango
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Arvind Panday
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
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20
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A survey of cancer genome signatures identifies genes connected to distinct chromosomal instability phenotypes. THE PHARMACOGENOMICS JOURNAL 2021; 21:390-401. [PMID: 33731882 DOI: 10.1038/s41397-021-00217-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Certain breast and ovarian cancers are characterised by high levels of chromosomal instability. We established a suite of eleven SNP array-based signatures of various forms of chromosomal instability. To understand what biological mechanisms might underpin these signatures, we generated and assembled genetic-feature data including allele-specific expression, fusion genes, gene expression, methylation, somatic coding mutations and protein expression. For each signature, we extracted a compendium of significantly associated genetic features using machine learning. We established an association between subchromosomal allelic imbalance-based measures and DNA repair genes. Numerical chromosomal instability and chromothripsis were found to have distinct genetic associations but shared a relationship to mitotic processes, while whole-genome doubling was characterised by TP53 mutation, and high AURKA and GINS1 expression. Furthermore, we identified two genetically distinct forms of tandem duplicator phenotypes. These findings identify potentially novel genomic targets for validation and drug development for specific subsets of breast and ovarian cancer.
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21
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Wang S, Li H, Song M, Tao Z, Wu T, He Z, Zhao X, Wu K, Liu XS. Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PLoS Genet 2021; 17:e1009557. [PMID: 33945534 PMCID: PMC8121287 DOI: 10.1371/journal.pgen.1009557] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/14/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer. Copy number alterations are important drivers for the progression of multiple cancer. However, practical tools for studying the signatures of copy number alterations are still lacking. Here, a user-friendly open source bioinformatics tool "sigminer" has been constructed for copy number signature extraction, analysis and visualization. This tool has been applied in prostate cancer (PC), which is particularly driven by complex genome alterations. Five copy number signatures are identified from human PC genome with this tool. The underlying mutational processes for each copy number signature have been illustrated. Sample clustering based on copy number signature exposure reveals considerable heterogeneity of PC, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures. This copy number signature analysis in PC provides distinct insight into the etiology of PC, and potential biomarkers for PC stratification and prognosis.
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Affiliation(s)
- Shixiang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minfang Song
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zaoke He
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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22
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Panday A, Willis NA, Elango R, Menghi F, Duffey EE, Liu ET, Scully R. FANCM regulates repair pathway choice at stalled replication forks. Mol Cell 2021; 81:2428-2444.e6. [PMID: 33882298 DOI: 10.1016/j.molcel.2021.03.044] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 02/18/2021] [Accepted: 03/26/2021] [Indexed: 01/19/2023]
Abstract
Repair pathway "choice" at stalled mammalian replication forks is an important determinant of genome stability; however, the underlying mechanisms are poorly understood. FANCM encodes a multi-domain scaffolding and motor protein that interacts with several distinct repair protein complexes at stalled forks. Here, we use defined mutations engineered within endogenous Fancm in mouse embryonic stem cells to study how Fancm regulates stalled fork repair. We find that distinct FANCM repair functions are enacted by molecularly separable scaffolding domains. These findings define FANCM as a key mediator of repair pathway choice at stalled replication forks and reveal its molecular mechanism. Notably, mutations that inactivate FANCM ATPase function disable all its repair functions and "trap" FANCM at stalled forks. We find that Brca1 hypomorphic mutants are synthetic lethal with Fancm null or Fancm ATPase-defective mutants. The ATPase function of FANCM may therefore represent a promising "druggable" target for therapy of BRCA1-linked cancer.
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Affiliation(s)
- Arvind Panday
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA 02215, USA
| | - Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA 02215, USA
| | - Rajula Elango
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA 02215, USA
| | - Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Erin E Duffey
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA 02215, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Ralph Scully
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA 02215, USA.
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23
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How Chaotic Is Genome Chaos? Cancers (Basel) 2021; 13:cancers13061358. [PMID: 33802828 PMCID: PMC8002653 DOI: 10.3390/cancers13061358] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Cancer genomes can undergo major restructurings involving many chromosomal locations at key stages in tumor development. This restructuring process has been designated “genome chaos” by some authors. In order to examine how chaotic cancer genome restructuring may be, the cell and molecular processes for DNA restructuring are reviewed. Examination of the action of these processes in various cancers reveals a degree of specificity that indicates genome restructuring may be sufficiently reproducible to enable possible therapies that interrupt tumor progression to more lethal forms. Abstract Cancer genomes evolve in a punctuated manner during tumor evolution. Abrupt genome restructuring at key steps in this evolution has been called “genome chaos.” To answer whether widespread genome change is truly chaotic, this review (i) summarizes the limited number of cell and molecular systems that execute genome restructuring, (ii) describes the characteristic signatures of DNA changes that result from activity of those systems, and (iii) examines two cases where genome restructuring is determined to a significant degree by cell type or viral infection. The conclusion is that many restructured cancer genomes display sufficiently unchaotic signatures to identify the cellular systems responsible for major oncogenic transitions, thereby identifying possible targets for therapies to inhibit tumor progression to greater aggressiveness.
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24
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Kwon DH, Chou J, Yip SM, Reimers MA, Zhang L, Wright F, Dhawan MS, Borno HT, Desai A, Aggarwal RR, Wyatt AW, Small EJ, Alva AS, Chi KN, Feng FY, Koshkin VS. Differential treatment outcomes in BRCA1/2-, CDK12-, and ATM-mutated metastatic castration-resistant prostate cancer. Cancer 2021; 127:1965-1973. [PMID: 33690902 DOI: 10.1002/cncr.33487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/01/2020] [Accepted: 01/19/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND DNA damage repair mutations (DDRm) are common in patients with metastatic castration-resistant prostate cancer (mCRPC). The optimal standard therapy for this population is not well described. METHODS A multi-institutional, retrospective study of patients with mCRPC and DDRm was conducted. Patient data, including systemic therapies and responses, were collected. The decline in prostate-specific antigen ≥ 50% from baseline (PSA50) and overall survival (OS) from the treatment start were compared by mutation and treatment type. A multivariable Cox proportional hazards model for OS was created that controlled for DDRm, first-line treatment received for mCRPC, and clinical factors. RESULTS The most common DDRm observed among 149 men with mCRPC were BRCA1/2 (44%), CDK12 (32%), and ATM (15%). The majority received first-line abiraterone (40%) or enzalutamide (30%). The PSA50 rate with first-line abiraterone was lower for CDK12 (52%) than BRCA1/2 (89%; P = .02). After first-line abiraterone or enzalutamide, the median OS was longest with second-line carboplatin-chemotherapy (38 months) in comparison with abiraterone or enzalutamide (33 months), docetaxel (17 months), or cabazitaxel (11 months; P = .02). PSA50 responses to carboplatin-based chemotherapy were higher for BRCA1/2 (79%) than ATM (14%; P = .02) or CDK12 (38%; P = .08). In a multivariable analysis, neither the specific DDRm type nor the first-line treatment was associated with improved OS. CONCLUSIONS Responses to standard therapies were generally superior in patients with BRCA1/2 mutations and inferior in patients with ATM or CDK12 mutations. The DDRm type did not independently predict OS. After progression on first-line abiraterone or enzalutamide, carboplatin-based chemotherapy was associated with the longest OS. These findings may inform treatment discussions and clinical trial design and require prospective validation.
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Affiliation(s)
- Daniel H Kwon
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Steven M Yip
- Tom Baker Cancer Centre, University of Calgary, Calgary, Alberta, Canada
| | - Melissa A Reimers
- Division of Oncology, Department of Medicine, Washington University, St. Louis, Missouri
| | - Li Zhang
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California.,Department of Biostatistics and Epidemiology, University of California San Francisco, San Francisco, California
| | - Francis Wright
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Mallika S Dhawan
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Hala T Borno
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Arpita Desai
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Rahul R Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric J Small
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Ajjai S Alva
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kim N Chi
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Vadim S Koshkin
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
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25
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Quist J, Taylor L, Staaf J, Grigoriadis A. Random Forest Modelling of High-Dimensional Mixed-Type Data for Breast Cancer Classification. Cancers (Basel) 2021; 13:991. [PMID: 33673506 PMCID: PMC7956671 DOI: 10.3390/cancers13050991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 11/16/2022] Open
Abstract
Advances in high-throughput technologies encourage the generation of large amounts of multiomics data to investigate complex diseases, including breast cancer. Given that the aetiologies of such diseases extend beyond a single biological entity, and that essential biological information can be carried by all data regardless of data type, integrative analyses are needed to identify clinically relevant patterns. To facilitate such analyses, we present a permutation-based framework for random forest methods which simultaneously allows the unbiased integration of mixed-type data and assessment of relative feature importance. Through simulation studies and machine learning datasets, the performance of the approach was evaluated. The results showed minimal multicollinearity and limited overfitting. To further assess the performance, the permutation-based framework was applied to high-dimensional mixed-type data from two independent breast cancer cohorts. Reproducibility and robustness of our approach was demonstrated by the concordance in relative feature importance between the cohorts, along with consistencies in clustering profiles. One of the identified clusters was shown to be prognostic for clinical outcome after standard-of-care adjuvant chemotherapy and outperformed current intrinsic molecular breast cancer classifications.
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Affiliation(s)
- Jelmar Quist
- Cancer Bioinformatics, Cancer Centre at Guy’s Hospital, King’s College London, London SE1 9RT, UK; (J.Q.); (L.T.)
- School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK
- Breast Cancer Now Research Unit, Cancer Centre at Guy’s Hospital, King’s College London, London SE1 9RT, UK
| | - Lawson Taylor
- Cancer Bioinformatics, Cancer Centre at Guy’s Hospital, King’s College London, London SE1 9RT, UK; (J.Q.); (L.T.)
- School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE-223 81 Lund, Sweden;
| | - Anita Grigoriadis
- Cancer Bioinformatics, Cancer Centre at Guy’s Hospital, King’s College London, London SE1 9RT, UK; (J.Q.); (L.T.)
- School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK
- Breast Cancer Now Research Unit, Cancer Centre at Guy’s Hospital, King’s College London, London SE1 9RT, UK
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26
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Willis NA, Scully R. Measurement of Homologous Recombination at Stalled Mammalian Replication Forks. Methods Mol Biol 2021; 2153:329-353. [PMID: 32840790 DOI: 10.1007/978-1-0716-0644-5_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Site-specific replication fork barriers (RFBs) have proven valuable tools for studying mechanisms of repair at sites of replication fork stalling in prokaryotes and yeasts. We adapted the Escherichia coli Tus-Ter RFB for use in mammalian cells and used it to trigger site-specific replication fork stalling and homologous recombination (HR) at a defined chromosomal locus in mammalian cells. By comparing HR responses induced at the Tus-Ter RFB with those induced by a site-specific double-strand break (DSB), we have begun to uncover how the mechanisms of mammalian stalled fork repair differ from those underlying the repair of a replication-independent DSB. Here, we outline how to transiently express the Tus protein in mES cells, how to use flow cytometry to score conservative and aberrant repair outcomes, and how to quantify distinct repair outcomes in response to replication fork stalling at the inducible Tus-Ter chromosomal RFB.
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Affiliation(s)
- Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology, Cancer Research Institute, Harvard Medical School, Boston, MA, USA.,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ralph Scully
- Department of Medicine, Division of Hematology-Oncology, Cancer Research Institute, Harvard Medical School, Boston, MA, USA. .,Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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27
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Heng J, Heng HH. Genome chaos: Creating new genomic information essential for cancer macroevolution. Semin Cancer Biol 2020; 81:160-175. [PMID: 33189848 DOI: 10.1016/j.semcancer.2020.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 12/15/2022]
Abstract
Cancer research has traditionally focused on the characterization of individual molecular mechanisms that can contribute to cancer. Due to the multiple levels of genomic and non-genomic heterogeneity, however, overwhelming molecular mechanisms have been identified, most with low clinical predictability. It is thus necessary to search for new concepts to unify these diverse mechanisms and develop better strategies to understand and treat cancer. In recent years, two-phased cancer evolution (comprised of the genome reorganization-mediated punctuated phase and gene mutation-mediated stepwise phase), initially described by tracing karyotype evolution, was confirmed by the Cancer Genome Project. In particular, genome chaos, the process of rapid and massive genome reorganization, has been commonly detected in various cancers-especially during key phase transitions, including cellular transformation, metastasis, and drug resistance-suggesting the importance of genome-level changes in cancer evolution. In this Perspective, genome chaos is used as a discussion point to illustrate new genome-mediated somatic evolutionary frameworks. By rephrasing cancer as a new system emergent from normal tissue, we present the multiple levels (or scales) of genomic and non-genomic information. Of these levels, evolutionary studies at the chromosomal level are determined to be of ultimate importance, since altered genomes change the karyotype coding and karyotype change is the key event for punctuated cellular macroevolution. Using this lens, we differentiate and analyze developmental processes and cancer evolution, as well as compare the informational relationship between genome chaos and its various subtypes in the context of macroevolution under crisis. Furthermore, the process of deterministic genome chaos is discussed to interpret apparently random events (including stressors, chromosomal variation subtypes, surviving cells with new karyotypes, and emergent stable cellular populations) as nonrandom patterns, which supports the new cancer evolutionary model that unifies genome and gene contributions during different phases of cancer evolution. Finally, the new perspective of using cancer as a model for organismal evolution is briefly addressed, emphasizing the Genome Theory as a new and necessary conceptual framework for future research and its practical implications, not only in cancer but evolutionary biology as a whole.
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Affiliation(s)
- Julie Heng
- Harvard College, 86 Brattle Street Cambridge, MA, 02138, USA
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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28
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CDK12: a potential therapeutic target in cancer. Drug Discov Today 2020; 25:2257-2267. [PMID: 33038524 DOI: 10.1016/j.drudis.2020.09.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/30/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Cyclin-dependent kinase (CDK) 12 engages in diversified biological functions, from transcription, post-transcriptional modification, cell cycle, and translation to cellular proliferation. Moreover, it regulates the expression of cancer-related genes involved in DNA damage response (DDR) and replication, which are responsible for maintaining genomic stability. CDK12 emerges as an oncogene or tumor suppressor in different cellular contexts, where its dysregulation results in tumorigenesis. Current CDK12 inhibitors are nonselective, which impedes the process of pharmacological target validation and drug development. Herein, we discuss the latest understanding of the biological roles of CDK12 in cancers and provide molecular analyses of CDK12 inhibitors to guide the rational design of selective inhibitors.
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29
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García-Cortés D, de Anda-Jáuregui G, Fresno C, Hernández-Lemus E, Espinal-Enríquez J. Gene Co-expression Is Distance-Dependent in Breast Cancer. Front Oncol 2020; 10:1232. [PMID: 32850369 PMCID: PMC7396632 DOI: 10.3389/fonc.2020.01232] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Breast carcinomas are characterized by anomalous gene regulatory programs. As is well-known, gene expression programs are able to shape phenotypes. Hence, the understanding of gene co-expression may shed light on the underlying mechanisms behind the transcriptional regulatory programs affecting tumor development and evolution. For instance, in breast cancer, there is a clear loss of inter-chromosomal (trans-) co-expression, compared with healthy tissue. At the same time cis- (intra-chromosomal) interactions are favored in breast tumors. In order to have a deeper understanding of regulatory phenomena in cancer, here, we constructed Gene Co-expression Networks by using TCGA-derived RNA-seq whole-genome samples corresponding to the four breast cancer molecular subtypes, as well as healthy tissue. We quantify the cis-/trans- co-expression imbalance in all phenotypes. Additionally, we measured the association between co-expression and physical distance between genes, and characterized the ratio of intra/inter-cytoband interactions per phenotype. We confirmed loss of trans- co-expression in all molecular subtypes. We also observed that gene cis- co-expression decays abruptly with distance in all tumors in contrast with healthy tissue. We observed co-expressed gene hotspots, that tend to be connected at cytoband regions, and coincide accurately with already known copy number altered regions, such as Chr17q12, or Chr8q24.3 for all subtypes. Our methodology recovered different alterations already reported for specific breast cancer subtypes, showing how co-expression network approaches might help to capture distinct events that modify the cell regulatory program.
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Affiliation(s)
- Diana García-Cortés
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Cristóbal Fresno
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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30
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Kamp JA, van Schendel R, Dilweg IW, Tijsterman M. BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining. Nat Commun 2020; 11:3615. [PMID: 32680986 PMCID: PMC7368036 DOI: 10.1038/s41467-020-17455-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/01/2020] [Indexed: 12/03/2022] Open
Abstract
Failure to preserve the integrity of the genome is a hallmark of cancer. Recent studies have revealed that loss of the capacity to repair DNA breaks via homologous recombination (HR) results in a mutational profile termed BRCAness. The enzymatic activity that repairs HR substrates in BRCA-deficient conditions to produce this profile is currently unknown. We here show that the mutational landscape of BRCA1 deficiency in C. elegans closely resembles that of BRCA1-deficient tumours. We identify polymerase theta-mediated end-joining (TMEJ) to be responsible: knocking out polq-1 suppresses the accumulation of deletions and tandem duplications in brc-1 and brd-1 animals. We find no additional back-up repair in HR and TMEJ compromised animals; non-homologous end-joining does not affect BRCAness. The notion that TMEJ acts as an alternative to HR, promoting the genome alteration of HR-deficient cells, supports the idea that polymerase theta is a promising therapeutic target for HR-deficient tumours.
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Affiliation(s)
- J A Kamp
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - R van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - I W Dilweg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - M Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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31
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Pilarova K, Herudek J, Blazek D. CDK12: cellular functions and therapeutic potential of versatile player in cancer. NAR Cancer 2020; 2:zcaa003. [PMID: 34316683 PMCID: PMC8210036 DOI: 10.1093/narcan/zcaa003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) phosphorylates the C-terminal domain of RNA polymerase II and is needed for the optimal transcription elongation and translation of a subset of human protein-coding genes. The kinase has a pleiotropic effect on the maintenance of genome stability, and its inactivation in prostate and ovarian tumours results in focal tandem duplications, a CDK12-unique genome instability phenotype. CDK12 aberrations were found in many other malignancies and have the potential to be used as biomarkers for therapeutic intervention. Moreover, the inhibition of CDK12 emerges as a promising strategy for treatment in several types of cancers. In this review, we summarize mechanisms that CDK12 utilizes for the regulation of gene expression and discuss how the perturbation of CDK12-sensitive genes contributes to the disruption of cell cycle progression and the onset of genome instability. Furthermore, we describe tumour-suppressive and oncogenic functions of CDK12 and its potential as a biomarker and inhibition target in anti-tumour treatments.
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Affiliation(s)
- Kveta Pilarova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jan Herudek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
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32
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Chou J, Quigley DA, Robinson TM, Feng FY, Ashworth A. Transcription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy. Cancer Discov 2020; 10:351-370. [DOI: 10.1158/2159-8290.cd-19-0528] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022]
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33
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Current concepts in breast cancer genomics: An evidence based review by the CGC breast cancer working group. Cancer Genet 2020; 244:11-20. [PMID: 32087595 DOI: 10.1016/j.cancergen.2020.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genomic abnormalities in breast cancer have been described according to diverse conceptual frameworks, including histologic subtypes, clinical molecular subtypes, intrinsic DNA, RNA, and epigenetic profiles, and activated molecular pathways. METHODS The Cancer Genomics Consortium (CGC) Breast Cancer Workgroup performed an evidence based literature review to summarize current knowledge of clinically significant genomic alterations in breast cancer using CGC levels of evidence. Targetable or disease-defining alterations were prioritized. RESULTS We summarized genomic alterations in breast cancer within a framework of existing clinical tools for diagnosis, risk stratification, and therapeutic management. Using CGC levels of evidence, we catalog copy number profiles, gene expression profiles, and mutations in clinically significant genes. We also describe emerging molecular markers such as methylation profiling and immunotherapy biomarkers. CONCLUSION A summary of currently available information on breast cancer genomics will enhance precision medicine by serving as an interpretive resource for clinical laboratory geneticists, providing a foundation for future practice guidelines, and identifying knowledge gaps to address in future research.
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34
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Cuevas D, Velasco A, Vaquero M, Santacana M, Gatius S, Eritja N, Estaran E, Matias‐Guiu X. Intratumour heterogeneity in endometrial serous carcinoma assessed by targeted sequencing and multiplex ligation‐dependent probe amplification: a descriptive study. Histopathology 2020; 76:447-460. [DOI: 10.1111/his.14001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Dolors Cuevas
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Ana Velasco
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Marta Vaquero
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Maria Santacana
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Sònia Gatius
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Núria Eritja
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Elena Estaran
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
| | - Xavier Matias‐Guiu
- Hospital Universitari Arnau de Vilanova Universitat de Lleida IRBLleida Ciberonc Lleida Spain
- Hospital Universitari de Bellvitge Idibell Barcelona Spain
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Linked-read Sequencing Analysis Reveals Tumor-specific Genome Variation Landscapes in Neurofibromatosis Type 2 (NF2) Patients. Otol Neurotol 2020; 40:e150-e159. [PMID: 30624408 DOI: 10.1097/mao.0000000000002096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
HYPOTHESIS We hypothesize that genomic variants including deletions, insertions, inversions, and tandem duplications beyond the changes in tumor suppressor NF2 gene affect gene expression of tumor-specific pathways in vestibular schwannomas (VS) patients with Neurofibromatosis type 2 (NF2), thus contributing to their clinical behavior. BACKGROUND Genomic variation could reconfigure transcription in NF2 transformation process. Therefore, genome-wide high-resolution characterization of structural variants (SV) landscapes in NF2 tumors can expand our understanding of the genes regulating the clinical phenotypes in NF2-associated VS. METHODS We performed whole-genome haplotype-specific structural variation analysis using synthetic linked reads generated through microfluidics-based barcoding of high molecular weight DNA followed by high-coverage Illumina paired-end whole-genome sequencing from 10 patients' tumors of different growth rates and their matching blood samples. RESULTS NF2 tumor-specific deletions and large SVs were detected and can be classified based on their association with tumor growth rates. Through detailed annotation of these mutations, we uncover common alleles affected by these deletions and large SVs that can be associated with signaling pathways implicated in cell proliferation and tumorigenesis. CONCLUSION The genomic variation landscape of NF2-related VS was investigated through whole-genome linked-read sequencing. Large SVs, in addition to deletions, were identified and may serve as modulators of clinical behavior.
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Foulkes WD, Polak P. Journey's end: the quest for BRCA-like hereditary breast cancer genes is nearly over. Ann Oncol 2019; 30:1023-1025. [PMID: 31090898 PMCID: PMC6637371 DOI: 10.1093/annonc/mdz152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- W D Foulkes
- Department of Human Genetics, McGill University, Montreal, Canada.
| | - P Polak
- Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai Hospital, New York, USA
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Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance. BMC Cancer 2019; 19:1039. [PMID: 31684899 PMCID: PMC6829976 DOI: 10.1186/s12885-019-6278-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/21/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Understanding mechanisms underlying specific chemotherapeutic responses in subtypes of cancer may improve identification of treatment strategies most likely to benefit particular patients. For example, triple-negative breast cancer (TNBC) patients have variable response to the chemotherapeutic agent cisplatin. Understanding the basis of treatment response in cancer subtypes will lead to more informed decisions about selection of treatment strategies. METHODS In this study we used an integrative functional genomics approach to investigate the molecular mechanisms underlying known cisplatin-response differences among subtypes of TNBC. To identify changes in gene expression that could explain mechanisms of resistance, we examined 102 evolutionarily conserved cisplatin-associated genes, evaluating their differential expression in the cisplatin-sensitive, basal-like 1 (BL1) and basal-like 2 (BL2) subtypes, and the two cisplatin-resistant, luminal androgen receptor (LAR) and mesenchymal (M) subtypes of TNBC. RESULTS We found 20 genes that were differentially expressed in at least one subtype. Fifteen of the 20 genes are associated with cell death and are distributed among all TNBC subtypes. The less cisplatin-responsive LAR and M TNBC subtypes show different regulation of 13 genes compared to the more sensitive BL1 and BL2 subtypes. These 13 genes identify a variety of cisplatin-resistance mechanisms including increased transport and detoxification of cisplatin, and mis-regulation of the epithelial to mesenchymal transition. CONCLUSIONS We identified gene signatures in resistant TNBC subtypes indicative of mechanisms of cisplatin. Our results indicate that response to cisplatin in TNBC has a complex foundation based on impact of treatment on distinct cellular pathways. We find that examination of expression data in the context of heterogeneous data such as drug-gene interactions leads to a better understanding of mechanisms at work in cancer therapy response.
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Hernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez J, Ochoa S. The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. Genes (Basel) 2019; 10:E865. [PMID: 31671657 PMCID: PMC6896122 DOI: 10.3390/genes10110865] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease at many different levels. The molecular phenomenology of cancer is also quite rich. The mutational and genomic origins of cancer and their downstream effects on processes such as the reprogramming of the gene regulatory control and the molecular pathways depending on such control have been recognized as central to the characterization of the disease. More important though is the understanding of their causes, prognosis, and therapeutics. There is a multitude of factors associated with anomalous control of gene expression in cancer. Many of these factors are now amenable to be studied comprehensively by means of experiments based on diverse omic technologies. However, characterizing each dimension of the phenomenon individually has proven to fall short in presenting a clear picture of expression regulation as a whole. In this review article, we discuss some of the more relevant factors affecting gene expression control both, under normal conditions and in tumor settings. We describe the different omic approaches that we can use as well as the computational genomic analysis needed to track down these factors. Then we present theoretical and computational frameworks developed to integrate the amount of diverse information provided by such single-omic analyses. We contextualize this within a systems biology-based multi-omic regulation setting, aimed at better understanding the complex interplay of gene expression deregulation in cancer.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Helena Reyes-Gopar
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico.
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Reimers MA, Yip SM, Zhang L, Cieslik M, Dhawan M, Montgomery B, Wyatt AW, Chi KN, Small EJ, Chinnaiyan AM, Alva AS, Feng FY, Chou J. Clinical Outcomes in Cyclin-dependent Kinase 12 Mutant Advanced Prostate Cancer. Eur Urol 2019; 77:333-341. [PMID: 31640893 DOI: 10.1016/j.eururo.2019.09.036] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cyclin-dependent kinase 12 (CDK12) loss occurs in 3-7% of metastatic prostate cancer patients and is characterized by a genomic instability signature, but the clinical implications of CDK12 loss are not well established. OBJECTIVE To determine the clinical course of patients with CDK12 mutant advanced prostate cancer compared with other genomic subtypes. DESIGN, SETTING, AND PARTICIPANTS A retrospective analysis of data from three academic medical centers, including 317 patients with advanced prostate cancer and prior next-generation sequencing from tumor tissue (n = 172) or circulating tumor DNA (n = 145), was performed. Forty-six patients had CDK12 mutations; 34 had biallelic CDK12 loss (79%). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Patients were stratified by mutation status (CDK12, homologous recombination deficiency [HRD; BRCA1/2 and ATM], TP53, and other cohort). The Kaplan-Meier method was used to evaluate time to event outcomes: time to development of metastatic disease, time to development of castration resistance, and time to prostate-specific antigen (PSA) progression after first-line androgen receptor pathway inhibitor (ARPI) therapy in a patient subset. RESULTS AND LIMITATIONS The median follow-up was 66.6 mo. Patients with CDK12 mutant prostate cancer exhibited shorter time to metastasis (median = 34.9 mo, p = 0.004) and development of castration-resistant disease (median = 32.7 mo, p < 0.001), compared with other genomic subtypes, with shorter time to PSA progression on first-line ARPI treatment of metastatic castration-resistant disease (median = 3.6 mo, p = 0.0219). CDK12 mutant patients did not have overall shorter time on treatment compared with other mutation subgroups, and CDK12 status did not demonstrate statistical significance in multivariate analysis. Limitations include variable center-dependent practice patterns and heterogeneity due to combining tumor and liquid biopsy data. CONCLUSIONS Our data suggest that advanced prostate cancers harboring CDK12 mutations display aggressive clinical behavior, underscoring the need to fully delineate the molecular and clinical characteristics, and appropriate therapeutic approaches for distinct subtypes of advanced prostate cancers. PATIENT SUMMARY In this report, we evaluate the clinical characteristics and outcomes of patients with prostate cancer and CDK12 mutation in their tumors. These patients seem to have more aggressive disease, with more high-grade Gleason ≥8 cancers and shorter time to developing metastatic cancer. Cases of advanced CDK12-mutated prostate cancer may warrant consideration of therapy intensification or combination approaches.
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Affiliation(s)
- Melissa A Reimers
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Steven M Yip
- BC Cancer, Vancouver Cancer Centre, Vancouver, British Columbia, Canada
| | - Li Zhang
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mallika Dhawan
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA; Veterans Affairs Puget Sound Health Care System, University of Washington, Seattle, WA, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kim N Chi
- BC Cancer, Vancouver Cancer Centre, Vancouver, British Columbia, Canada; Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric J Small
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Ajjai S Alva
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Felix Y Feng
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA; Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA; Department of Urology, University of California San Francisco, San Francisco, CA, USA.
| | - Jonathan Chou
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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Chirackal Manavalan AP, Pilarova K, Kluge M, Bartholomeeusen K, Rajecky M, Oppelt J, Khirsariya P, Paruch K, Krejci L, Friedel CC, Blazek D. CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes. EMBO Rep 2019; 20:e47592. [PMID: 31347271 PMCID: PMC6727028 DOI: 10.15252/embr.201847592] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/09/2019] [Accepted: 06/24/2019] [Indexed: 12/31/2022] Open
Abstract
CDK12 is a kinase associated with elongating RNA polymerase II (RNAPII) and is frequently mutated in cancer. CDK12 depletion reduces the expression of homologous recombination (HR) DNA repair genes, but comprehensive insight into its target genes and cellular processes is lacking. We use a chemical genetic approach to inhibit analog-sensitive CDK12, and find that CDK12 kinase activity is required for transcription of core DNA replication genes and thus for G1/S progression. RNA-seq and ChIP-seq reveal that CDK12 inhibition triggers an RNAPII processivity defect characterized by a loss of mapped reads from 3'ends of predominantly long, poly(A)-signal-rich genes. CDK12 inhibition does not globally reduce levels of RNAPII-Ser2 phosphorylation. However, individual CDK12-dependent genes show a shift of P-Ser2 peaks into the gene body approximately to the positions where RNAPII occupancy and transcription were lost. Thus, CDK12 catalytic activity represents a novel link between regulation of transcription and cell cycle progression. We propose that DNA replication and HR DNA repair defects as a consequence of CDK12 inactivation underlie the genome instability phenotype observed in many cancers.
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Affiliation(s)
| | - Kveta Pilarova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Michael Kluge
- Institut für InformatikLudwig‐Maximilians‐Universität MünchenMünchenGermany
| | - Koen Bartholomeeusen
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
- Present address:
Department of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| | - Michal Rajecky
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jan Oppelt
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Prashant Khirsariya
- Department of ChemistryCZ OpenscreenFaculty of ScienceMasaryk UniversityBrnoCzech Republic
- Center of Biomolecular and Cellular EngineeringInternational Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Kamil Paruch
- Department of ChemistryCZ OpenscreenFaculty of ScienceMasaryk UniversityBrnoCzech Republic
- Center of Biomolecular and Cellular EngineeringInternational Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
| | - Lumir Krejci
- Center of Biomolecular and Cellular EngineeringInternational Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- National Centre for Biomolecular ResearchMasaryk UniversityBrnoCzech Republic
| | - Caroline C Friedel
- Institut für InformatikLudwig‐Maximilians‐Universität MünchenMünchenGermany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
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42
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Dutta UR, Rao SN, Pidugu VK, V.S. V, Bhattacherjee A, Bhowmik AD, Ramaswamy SK, Singh KG, Dalal A. Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing. Genomics 2019; 111:1108-1114. [DOI: 10.1016/j.ygeno.2018.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/21/2018] [Accepted: 07/06/2018] [Indexed: 01/20/2023]
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43
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Gómez-Miragaya J, Díaz-Navarro A, Tonda R, Beltran S, Palomero L, Palafox M, Dobrolecki LE, Huang C, Vasaikar S, Zhang B, Wulf GM, Collado-Sole A, Trinidad EM, Muñoz P, Paré L, Prat A, Bruna A, Caldas C, Arribas J, Soler-Monso MT, Petit A, Balmaña J, Cruz C, Serra V, Pujana MA, Lewis MT, Puente XS, González-Suárez E. Chromosome 12p Amplification in Triple-Negative/ BRCA1-Mutated Breast Cancer Associates with Emergence of Docetaxel Resistance and Carboplatin Sensitivity. Cancer Res 2019; 79:4258-4270. [PMID: 31213465 DOI: 10.1158/0008-5472.can-18-3835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/05/2019] [Accepted: 06/07/2019] [Indexed: 11/16/2022]
Abstract
Taxanes are the mainstay of treatment in triple-negative breast cancer (TNBC), with de novo and acquired resistance limiting patient's survival. To investigate the genetic basis of docetaxel resistance in TNBC, exome sequencing was performed on matched TNBC patient-derived xenografts (PDX) sensitive to docetaxel and their counterparts that developed resistance in vivo upon continuous drug exposure. Most mutations, small insertions/deletions, and copy number alterations detected in the initial TNBC human metastatic samples were maintained after serial passages in mice and emergence of resistance. We identified a chromosomal amplification of chr12p in a human BRCA1-mutated metastatic sample and the derived chemoresistant PDX, but not in the matched docetaxel-sensitive PDX tumor. Chr12p amplification was validated in a second pair of docetaxel-sensitive/resistant BRCA1-mutated PDXs and after short-term docetaxel treatment in several TNBC/BRCA1-mutated PDXs and cell lines, as well as during metastatic recurrence in a patient with BRCA1-mutated breast cancer who had progressed on docetaxel treatment. Analysis of clinical data indicates an association between chr12p amplification and patients with TNBC/basal-like breast cancer, a BRCA1 mutational signature, and poor survival after chemotherapy. Detection of chr12p amplification in a cohort of TNBC PDX models was associated with an improved response to carboplatin. Our findings reveal tumor clonal dynamics during chemotherapy treatments and suggest that a preexisting population harboring chr12p amplification is associated with the emergence of docetaxel resistance and carboplatin responsiveness in TNBC/BRCA1-mutated tumors. SIGNIFICANCE: Chr12p copy number gains indicate rapid emergence of resistance to docetaxel and increased sensitivity to carboplatin, therefore sequential docetaxel/carboplatin treatment could improve survival in TNBC/BRCA1 patients. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/16/4258/F1.large.jpg.
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Affiliation(s)
- Jorge Gómez-Miragaya
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ander Díaz-Navarro
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), CIBERONC, Universidad de Oviedo, Oviedo, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Centre for Genomic Analysis (CNAG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Centre for Genomic Analysis (CNAG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luis Palomero
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Marta Palafox
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lacey E Dobrolecki
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Chen Huang
- Departments of Molecular and Human Genetics, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Suhas Vasaikar
- Departments of Molecular and Human Genetics, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Bing Zhang
- Departments of Molecular and Human Genetics, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Gerburg M Wulf
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Alejandro Collado-Sole
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eva M Trinidad
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Purificación Muñoz
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Paré
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Aleix Prat
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
| | - Alejandra Bruna
- Cancer Research UK Cancer Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Carlos Caldas
- Cancer Research UK Cancer Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Joaquín Arribas
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Anna Petit
- Pathology Department, University Hospital of Bellvitge, IDIBELL, Barcelona, Spain
| | - Judith Balmaña
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Cristina Cruz
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Violeta Serra
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Miguel Angel Pujana
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - Michael T Lewis
- Departments of Molecular and Cellular Biology and Radiology, The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Xose S Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), CIBERONC, Universidad de Oviedo, Oviedo, Spain
| | - Eva González-Suárez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran Via, 199-203, L'Hospitalet de Llobregat, Barcelona, Spain.
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Byrum AK, Vindigni A, Mosammaparast N. Defining and Modulating 'BRCAness'. Trends Cell Biol 2019; 29:740-751. [PMID: 31362850 DOI: 10.1016/j.tcb.2019.06.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 02/08/2023]
Abstract
The concept of 'BRCAness' defines the pathogenesis and vulnerability of multiple cancers. The canonical definition of BRCAness is a defect in homologous recombination repair, mimicking BRCA1 or BRCA2 loss. In turn, BRCA-deficient cells utilize error-prone DNA-repair pathways, causing increased genomic instability, which may be responsible for their sensitivity to DNA damaging agents and poly-(ADP)-ribose polymerase inhibitors (PARPis). However, recent work has expanded the mechanistic basis of BRCAness, to include defects in replication fork protection (RFP). Here, we broaden the definition of BRCAness to include RFP and regulatory mechanisms that cause synthetic lethality with PARPis. We highlight these recent discoveries, which include mechanisms of RFP regulation, DNA damage checkpoint proteins, as well as kinases that regulate BRCA1/2 function. Importantly, many of these emerging mechanisms may be targeted for inhibition with small molecule inhibitors, thus inducing BRCAness in a much larger subset of BRCA-proficient tumors, with significant translational potential.
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Affiliation(s)
- Andrea K Byrum
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA.
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Bogdanova NV, Schürmann P, Valova Y, Dubrowinskaja N, Turmanov N, Yugay T, Essimsiitova Z, Mingazheva E, Prokofyeva D, Bermisheva M, Khusnutdinova E, Dörk T. A Splice Site Variant of CDK12 and Breast Cancer in Three Eurasian Populations. Front Oncol 2019; 9:493. [PMID: 31259151 PMCID: PMC6587039 DOI: 10.3389/fonc.2019.00493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/24/2019] [Indexed: 12/23/2022] Open
Abstract
CDK12 is a member of the cyclin-dependent kinase family that acts as regulator of DNA damage response gene expression. A c.1047-2A>G splice site variant of the CDK12 gene was recently reported to strongly associate with hereditary breast and ovarian cancer in patients of Tatar ethnic origin. To gain more insight into the potential risk and the population spread of the c.1047-2A>G variant, we have genotyped three breast cancer case-control series of Tatar, Bashkir and Kazakh ethnicity. We identified c.1047-2A>G in 6/155 cases and 12/362 controls of Tatar ancestry, 0/96 cases and 9/189 controls of Bashkir ancestry, and 1/131 cases and 0/154 controls of Kazakh ancestry (Mantel-Haenszel odds ratio 0.72, 95% CI 0.30-1.70, p = 0.45). Consistent with the absence of a large effect, bioinformatic analyses predicted that c.1047-2A>G modulates alternative splicing of a NAGNAG sequence rather than constituting a loss-of-function allele, and RT-PCR analyses of c.1047-2A>G heterozygous lymphocytes verified the usage of the predicted alternative acceptor site. Our study confirms a high prevalence of CDK12*c.1047-2A>G in the Tatar and Bashkir population but excludes a role as a clinically actionable high-risk breast cancer mutation.
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Affiliation(s)
- Natalia V Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hanover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hanover, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Hannover Medical School, Hanover, Germany
| | - Yana Valova
- Gynaecology Research Unit, Hannover Medical School, Hanover, Germany.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Natalia Dubrowinskaja
- Gynaecology Research Unit, Hannover Medical School, Hanover, Germany.,Department of Clinical Immunology, Hannover Medical School, Hanover, Germany
| | - Nurzhan Turmanov
- Gynaecology Research Unit, Hannover Medical School, Hanover, Germany.,Oncology Clinic of Almaty, Almaty, Kazakhstan
| | | | - Zura Essimsiitova
- Department of Biology and Biotechnology, Kazakh State National University of Al-Farabi, Almaty, Kazakhstan
| | - Elvira Mingazheva
- Gynaecology Research Unit, Hannover Medical School, Hanover, Germany.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Darya Prokofyeva
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Elza Khusnutdinova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.,Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hanover, Germany
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Scully R, Panday A, Elango R, Willis NA. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat Rev Mol Cell Biol 2019; 20:698-714. [PMID: 31263220 DOI: 10.1038/s41580-019-0152-0] [Citation(s) in RCA: 792] [Impact Index Per Article: 158.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 11/09/2022]
Abstract
The major pathways of DNA double-strand break (DSB) repair are crucial for maintaining genomic stability. However, if deployed in an inappropriate cellular context, these same repair functions can mediate chromosome rearrangements that underlie various human diseases, ranging from developmental disorders to cancer. The two major mechanisms of DSB repair in mammalian cells are non-homologous end joining (NHEJ) and homologous recombination. In this Review, we consider DSB repair-pathway choice in somatic mammalian cells as a series of 'decision trees', and explore how defective pathway choice can lead to genomic instability. Stalled, collapsed or broken DNA replication forks present a distinctive challenge to the DSB repair system. Emerging evidence suggests that the 'rules' governing repair-pathway choice at stalled replication forks differ from those at replication-independent DSBs.
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Affiliation(s)
- Ralph Scully
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - Arvind Panday
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Rajula Elango
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Nicholas A Willis
- Department of Medicine, Division of Hematology-Oncology and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
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47
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Woo XY, Srivastava A, Graber JH, Yadav V, Sarsani VK, Simons A, Beane G, Grubb S, Ananda G, Liu R, Stafford G, Chuang JH, Airhart SD, Karuturi RKM, George J, Bult CJ. Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines. BMC Med Genomics 2019; 12:92. [PMID: 31262303 PMCID: PMC6604205 DOI: 10.1186/s12920-019-0551-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Patient-derived xenograft (PDX) models are in vivo models of human cancer that have been used for translational cancer research and therapy selection for individual patients. The Jackson Laboratory (JAX) PDX resource comprises 455 models originating from 34 different primary sites (as of 05/08/2019). The models undergo rigorous quality control and are genomically characterized to identify somatic mutations, copy number alterations, and transcriptional profiles. Bioinformatics workflows for analyzing genomic data obtained from human tumors engrafted in a mouse host (i.e., Patient-Derived Xenografts; PDXs) must address challenges such as discriminating between mouse and human sequence reads and accurately identifying somatic mutations and copy number alterations when paired non-tumor DNA from the patient is not available for comparison. RESULTS We report here data analysis workflows and guidelines that address these challenges and achieve reliable identification of somatic mutations, copy number alterations, and transcriptomic profiles of tumors from PDX models that lack genomic data from paired non-tumor tissue for comparison. Our workflows incorporate commonly used software and public databases but are tailored to address the specific challenges of PDX genomics data analysis through parameter tuning and customized data filters and result in improved accuracy for the detection of somatic alterations in PDX models. We also report a gene expression-based classifier that can identify EBV-transformed tumors. We validated our analytical approaches using data simulations and demonstrated the overall concordance of the genomic properties of xenograft tumors with data from primary human tumors in The Cancer Genome Atlas (TCGA). CONCLUSIONS The analysis workflows that we have developed to accurately predict somatic profiles of tumors from PDX models that lack normal tissue for comparison enable the identification of the key oncogenic genomic and expression signatures to support model selection and/or biomarker development in therapeutic studies. A reference implementation of our analysis recommendations is available at https://github.com/TheJacksonLaboratory/PDX-Analysis-Workflows .
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Affiliation(s)
- Xing Yi Woo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Joel H Graber
- MDI Biological Laboratory, Bar Harbor, ME, 04609, USA
| | - Vinod Yadav
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Present Address: Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vishal Kumar Sarsani
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
- Present Address: University of Massachusetts, Amherst, MA, 01003, USA
| | - Al Simons
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Glen Beane
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Stephen Grubb
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Guruprasad Ananda
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Rangjiao Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Present Address: Novogene Corporation, Rockville, MD, 20850, USA
| | - Grace Stafford
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA
| | - Susan D Airhart
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA
| | | | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06030, USA.
| | - Carol J Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, 04609, USA.
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Lal A, Ramazzotti D, Weng Z, Liu K, Ford JM, Sidow A. Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations. BMC Med Genomics 2019; 12:84. [PMID: 31182087 PMCID: PMC6558765 DOI: 10.1186/s12920-019-0545-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/31/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to breast and ovarian cancer, and there remains a need to identify the specific genomic mechanisms by which cancer evolves in these patients. Here we present a systematic genomic analysis of breast tumors with BRCA1 and BRCA2 mutations. METHODS We analyzed genomic data from breast tumors, with a focus on comparing tumors with BRCA1/BRCA2 gene mutations with common classes of sporadic breast tumors. RESULTS We identify differences between BRCA-mutated and sporadic breast tumors in patterns of point mutation, DNA methylation and structural variation. We show that structural variation disproportionately affects tumor suppressor genes and identify specific driver gene candidates that are enriched for structural variation. CONCLUSIONS Compared to sporadic tumors, BRCA-mutated breast tumors show signals of reduced DNA methylation, more ancestral cell divisions, and elevated rates of structural variation that tend to disrupt highly expressed protein-coding genes and known tumor suppressors. Our analysis suggests that BRCA-mutated tumors are more aggressive than sporadic breast cancers because loss of the BRCA pathway causes multiple processes of mutagenesis and gene dysregulation.
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Affiliation(s)
- Avantika Lal
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Present address: NVIDIA Corporation, 2788 San Tomas Expy, Santa Clara, CA 95051 USA
| | - Daniele Ramazzotti
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Department of Computer Science, Stanford University, Stanford, CA 94305 USA
| | - Ziming Weng
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
| | - Keli Liu
- Department of Statistics, Stanford University, Stanford, CA 94305 USA
| | - James M. Ford
- Department of Medicine, Stanford University, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
| | - Arend Sidow
- Department of Pathology, Stanford University, Stanford, CA 94305 USA
- Department of Genetics, Stanford University, Stanford, CA 94305 USA
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49
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Xing R, Zhou Y, Yu J, Yu Y, Nie Y, Luo W, Yang C, Xiong T, Wu WKK, Li Z, Bing Y, Lin S, Zhang Y, Hu Y, Li L, Han L, Yang C, Huang S, Huang S, Zhou R, Li J, Wu K, Fan D, Tang G, Dou J, Zhu Z, Ji J, Fang X, Lu Y. Whole-genome sequencing reveals novel tandem-duplication hotspots and a prognostic mutational signature in gastric cancer. Nat Commun 2019; 10:2037. [PMID: 31048690 PMCID: PMC6497673 DOI: 10.1038/s41467-019-09644-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/22/2019] [Indexed: 01/22/2023] Open
Abstract
Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer (GC) tumorigenesis. Here, we analysis structural variations (SVs) and mutational signatures via whole-genome sequencing of 168 GCs. Our data demonstrates diverse models of complex SVs operative in GC, which lead to high-level amplification of oncogenes. We find varying proportion of tandem-duplications (TDs) among individuals and identify 24 TD hotspots involving well-established cancer genes such as CCND1, ERBB2 and MYC. Specifically, we nominate a novel hotspot involving the super-enhancer of ZFP36L2 presents in approximately 10% GCs from different cohorts, the oncogenic role of which is further confirmed by experimental data. In addition, our data reveal a mutational signature, specifically occurring in noncoding region, significantly enriched in tumors with cadherin 1 mutations, and associated with poor prognoses. Collectively, our data suggest that TDs might serve as an important mechanism for cancer gene activation and provide a novel signature for stratification. Structural variations in gastric cancer impact progression. Here, the authors perform whole-genome sequencing on 168 gastric cancer patients and identified tandem-duplications of super-enhancer ZFP36L2 in 10% of gastric cancer, and mutational signatures in tumors with cadherin 1 mutations that associated with poor prognoses.
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Affiliation(s)
- Rui Xing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China.
| | - Yong Zhou
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Shenzhen, 518000, China
| | - Yingyan Yu
- Department of Surgery, Rui-jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Wen Luo
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Chao Yang
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Teng Xiong
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - William K K Wu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Shenzhen, 518000, China
| | - Zhongwu Li
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yang Bing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Shuye Lin
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yaping Zhang
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Yingqi Hu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Lin Li
- Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumours, Rui-Jin Hospital, Shanghai Jiao-Tong University School of Medicine, 200025, Shanghai, China
| | - Lijuan Han
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Chen Yang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Shaogang Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Suiping Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China
| | - Rui Zhou
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jing Li
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Guangbo Tang
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Jianhua Dou
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Shanxi, 710032, China
| | - Zhenggang Zhu
- Department of Surgery, Rui-jin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jiafu Ji
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China.
| | - Xiaodong Fang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 510120, Guangzhou, China.
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, 100142, Beijing, China. .,Department of Medical Oncology, Beijing Hospital, 100730, Beijing, China.
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50
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DNA Rereplication Is Susceptible to Nucleotide-Level Mutagenesis. Genetics 2019; 212:445-460. [PMID: 31028114 PMCID: PMC6553831 DOI: 10.1534/genetics.119.302194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
The initiation of eukaryotic DNA replication at replication origins is tightly regulated to prevent re-initiation and re-replication within each cell cycle. This regulation is critical for genome stability as re-replication is an extremely potent inducer... The sources of genome instability, a hallmark of cancer, remain incompletely understood. One potential source is DNA rereplication, which arises when the mechanisms that prevent the reinitiation of replication origins within a single cell cycle are compromised. Using the budding yeast Saccharomyces cerevisiae, we previously showed that DNA rereplication is extremely potent at inducing gross chromosomal alterations and that this arises in part because of the susceptibility of rereplication forks to break. Here, we examine the ability of DNA rereplication to induce nucleotide-level mutations. During normal replication these mutations are restricted by three overlapping error-avoidance mechanisms: the nucleotide selectivity of replicative polymerases, their proofreading activity, and mismatch repair. Using lys2InsEA14, a frameshift reporter that is poorly proofread, we show that rereplication induces up to a 30× higher rate of frameshift mutations and that this mutagenesis is due to passage of the rereplication fork, not secondary to rereplication fork breakage. Rereplication can also induce comparable rates of frameshift and base-substitution mutations in a more general mutagenesis reporter CAN1, when the proofreading activity of DNA polymerase ε is inactivated. Finally, we show that the rereplication-induced mutagenesis of both lys2InsEA14 and CAN1 disappears in the absence of mismatch repair. These results suggest that mismatch repair is attenuated during rereplication, although at most sequences DNA polymerase proofreading provides enough error correction to mitigate the mutagenic consequences. Thus, rereplication can facilitate nucleotide-level mutagenesis in addition to inducing gross chromosomal alterations, broadening its potential role in genome instability.
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