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Cai A, Chen Y, Wang LS, Cusick JK, Shi Y. Depicting Biomarkers for HER2-Inhibitor Resistance: Implication for Therapy in HER2-Positive Breast Cancer. Cancers (Basel) 2024; 16:2635. [PMID: 39123362 PMCID: PMC11311605 DOI: 10.3390/cancers16152635] [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: 06/25/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
HER2 (human epidermal growth factor receptor 2) is highly expressed in a variety of cancers, including breast, lung, gastric, and pancreatic cancers. Its amplification is linked to poor clinical outcomes. At the genetic level, HER2 is encoded by the ERBB2 gene (v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2), which is frequently mutated or amplified in cancers, thus spurring extensive research into HER2 modulation and inhibition as viable anti-cancer strategies. An impressive body of FDA-approved drugs, including anti-HER2 monoclonal antibodies (mAbs), antibody-drug conjugates (ADCs), and HER2-tyrosine kinase inhibitors (TKIs), have demonstrated success in enhancing overall survival (OS) and disease progression-free survival (PFS). Yet, drug resistance remains a persistent challenge and raises the risks of metastatic potential and tumor relapse. Research into alternative therapeutic options for HER2+ breast cancer therefore proves critical for adapting to this ever-evolving landscape. This review highlights current HER2-targeted therapies, discusses predictive biomarkers for drug resistance, and introduces promising emergent therapies-especially combination therapies-that are aimed at overcoming drug resistance in the context of HER2+ breast cancer.
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Affiliation(s)
- Alvan Cai
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA; (A.C.); (J.K.C.)
| | - Yuan Chen
- Section Pathology of the Institute of Forensic Medicine, Jena University Hospital, Friedrich Schiller University Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Lily S. Wang
- University of California, Berkeley, CA 94720, USA;
| | - John K. Cusick
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA; (A.C.); (J.K.C.)
| | - Yihui Shi
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA; (A.C.); (J.K.C.)
- California Pacific Medical Center Research Institute, Sutter Bay Hospitals, San Francisco, CA 94107, USA
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2
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Alinger-Scharinger B, Kronberger C, Hutarew G, Hitzl W, Reitsamer R, Frederike KF, Hager M, Fischer T, Sotlar K, Jaksch-Bogensperger H. HER2 copy number determination in breast cancer using the highly sensitive droplet digital PCR method. Virchows Arch 2024; 485:53-62. [PMID: 37996704 PMCID: PMC11271376 DOI: 10.1007/s00428-023-03706-3] [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: 04/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Human epidermal growth factor receptor 2 (HER)-positive breast cancer (BC) is characterized by an aggressive clinical course. In the case of HER2 overexpression/amplification, patients benefit from HER2-targeting therapies. Standardized diagnostic HER2 assessment includes immunohistochemistry (IHC) and/or in situ hybridization (ISH). The aim of this study was to compare this "gold standard" with the Droplet Digital™ polymerase chain reaction (ddPCR), a method that allows sensitive and precise detection of copy number variations (CNV) in FFPE (formalin-fixed, paraffin-embedded) DNA samples. Partitioning of the PCR reaction into 20,000 droplets enables a precise quantitative "CN" discrimination also in heterogeneous samples. FFPE breast cancer samples (n = 170) with routinely assessed HER2 status by IHC/ISH were retrospectively analyzed using the ddPCR CNV ERBB2 assay. Comparison of HER2 status assessment by the two methods revealed concordant results in 92.9% (158/170) of the cases. Discrepant cases were verified and interpreted. For ddPCR, a cut off value of 3 HER2 copies was set to distinguish between HER2-negative and HER2-positive BC. Results obtained with the ddPCR CNV ERBB2 assay were consistent and reproducible, and serial dilutions demonstrated a high stability and sensitivity of the method. The ddPCR CNV ERBB2 assay may be a specific and convenient tool to quantify HER2 copy numbers in BC samples. In our study, this method showed high reproducibility in accuracy of HER2 assessment compared to IHC/ISH analysis.
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Affiliation(s)
- Beate Alinger-Scharinger
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria.
| | - Cornelia Kronberger
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Georg Hutarew
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Wolfgang Hitzl
- Research Management and Technology Transfer, Paracelsus Medical University Salzburg, Strubergasse 16, 5020, Salzburg, Austria
- Department of Ophthalmology and Optometry, Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
- Research Program Experimental Ophthalmology and Glaucoma Research, Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Roland Reitsamer
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Klaassen-Federspiel Frederike
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Martina Hager
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Thorsten Fischer
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Karl Sotlar
- Department of Pathology, University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
| | - Heidi Jaksch-Bogensperger
- Department of Obstetrics and Gynaecology, Clinical Research Center Salzburg (CRCS), University Hospital and Paracelsus Medical University Salzburg, Muellner Hauptstraße 48, 5020, Salzburg, Austria
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3
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Henikoff S, Henikoff JG, Paranal RM, Greene JE, Zheng Y, Russell ZR, Szulzewsky F, Kugel S, Holland EC, Ahmad K. RNA Polymerase II hypertranscription in cancer FFPE samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582647. [PMID: 38559075 PMCID: PMC10979862 DOI: 10.1101/2024.02.28.582647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Hypertranscription is common in human cancers and predicts poor prognosis. However detection of hypertranscription is indirect, relying on accurately quantifying mRNA levels and estimating cell numbers. Previously, we introduced FFPE-CUTAC, a genome-wide method for mapping RNA Polymerase II (RNAPII) in formalin-fixed paraffin-embedded (FFPE) sections. Here we use FFPE-CUTAC to demonstrate genome-wide hypertranscription both in transgene-driven mouse gliomas and in assorted human tumors at active regulatory elements and replication-coupled histone genes with reduced mitochondrial DNA abundance. FFPE-CUTAC identified RNAPII-bound regulatory elements shared among diverse cancers and readily categorized human tumors despite using very small samples and low sequencing depths. Remarkably, RNAPII FFPE-CUTAC identified de novo and precisely mapped HER2 amplifications punctuated by likely selective sweeps including genes encoding direct positive regulators of RNAPII itself. Our results demonstrate that FFPE-CUTAC measurements of hypertranscription and classifications of tumors using small sections provides an affordable and sensitive genome-wide strategy for personalized medicine.
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Affiliation(s)
- Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jorja G. Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ronald M. Paranal
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jacob E. Greene
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease (M3D) PhD Program, University of Washington, Seattle, WA, USA
| | - Ye Zheng
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sita Kugel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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4
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Rodriguez I, Rossi NM, Keskus AG, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O'Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley KJ, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing. Am J Hum Genet 2024; 111:544-561. [PMID: 38307027 PMCID: PMC10940022 DOI: 10.1016/j.ajhg.2024.01.002] [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: 08/18/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/04/2024] Open
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and our study applies long-read sequencing to this important chromosomal rearrangement type. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes, and only one BFB breakpoint showed chromothripsis. Five cell lines have a chromosomal region 11q BFB event, with YAP1-BIRC3-BIRC2 amplification. Indeed, YAP1 amplification is associated with a 10-year-earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that individuals with cervical cancer and YAP1-BIRC3-BIRC2 amplification, especially those of African ancestry, might benefit from targeted therapy. In summary, we uncovered valuable insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse G Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tim O'Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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5
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Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. NATURE CANCER 2024; 5:228-239. [PMID: 38286829 PMCID: PMC7616040 DOI: 10.1038/s43018-023-00711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Mutational processes that alter large genomic regions occur frequently in developing tumors. They range from simple copy number gains and losses to the shattering and reassembly of entire chromosomes. These catastrophic events, such as chromothripsis, chromoplexy and the formation of extrachromosomal DNA, affect the expression of many genes and therefore have a substantial effect on the fitness of the cells in which they arise. In this review, we cover large genomic alterations, the mechanisms that cause them and their effect on tumor development and evolution.
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Affiliation(s)
- Toby M Baker
- The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Waise
- The Francis Crick Institute, London, UK
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Murata MM, Igari F, Urbanowicz R, Mouakkad L, Kim S, Chen Z, DiVizio D, Posadas EM, Giuliano AE, Tanaka H. A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.25.564058. [PMID: 37961589 PMCID: PMC10634834 DOI: 10.1101/2023.10.25.564058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Plasma cell-free DNA (cfDNA) is a promising source of gene mutations for cancer detection by liquid biopsy. However, no current tests interrogate chromosomal structural variants (SVs) genome-wide. Here, we report a simple molecular and sequencing workflow called Genome-wide Analysis of Palindrome Formation (GAPF-seq) to probe DNA palindromes, a type of SV that often demarcates gene amplification. With low-throughput next-generation sequencing and automated machine learning, tumor DNA showed skewed chromosomal distributions of high-coverage 1-kb bins (HCBs), which differentiated 39 breast tumors from matched normal DNA with an average Area Under the Curve (AUC) of 0.9819. A proof-of-concept liquid biopsy study using cfDNA from prostate cancer patients and healthy individuals yielded an average AUC of 0.965. HCBs on the X chromosome emerged as a determinant feature and were associated with androgen receptor gene amplification. As a novel agnostic liquid biopsy approach, GAPF-seq could fill the technological gap offering unique cancer-specific SV profiles.
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7
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Tanaka H, Murata M, Igari F, Urbanowicz R, Mouakkad L, Kim S, Chen Z, Di Vizio D, Posadas E, Giuliano A. A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA. RESEARCH SQUARE 2024:rs.3.rs-3492157. [PMID: 38260372 PMCID: PMC10802711 DOI: 10.21203/rs.3.rs-3492157/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Interrogating plasma cell-free DNA (cfDNA) to detect cancer offers promise; however, no current tests scan structural variants (SVs) throughout the genome. Here, we report a simple molecular workflow to enrich a tumorigenic SV (DNA palindromes/fold-back inversions) that often demarcates genomic amplification and its feasibility for cancer detection by combining low-throughput next-generation sequencing with automated machine learning (Genome-wide Analysis of Palindrome Formation, GAPF-seq). Tumor DNA signal manifested as skewed chromosomal distributions of high-coverage 1-kb bins (HCBs), differentiating 39 matched breast tumor DNA from normal DNA with an average AUC of 0.9819. In a proof-of-concept liquid biopsy study, cfDNA from 0.5 mL plasma from prostate cancer patients was sufficient for binary classification against matched buffy coat DNA with an average AUC of 0.965. HCBs on the X chromosome emerged as a determinant feature and were associated with AR amplification. GAPF-seq could generate unique cancer-specific SV profiles in an agnostic liquid biopsy setting.
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8
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Brewer BJ, Dunham MJ, Raghuraman MK. A unifying model that explains the origins of human inverted copy number variants. PLoS Genet 2024; 20:e1011091. [PMID: 38175827 PMCID: PMC10766186 DOI: 10.1371/journal.pgen.1011091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
With the release of the telomere-to-telomere human genome sequence and the availability of both long-read sequencing and optical genome mapping techniques, the identification of copy number variants (CNVs) and other structural variants is providing new insights into human genetic disease. Different mechanisms have been proposed to account for the novel junctions in these complex architectures, including aberrant forms of DNA replication, non-allelic homologous recombination, and various pathways that repair DNA breaks. Here, we have focused on a set of structural variants that include an inverted segment and propose that they share a common initiating event: an inverted triplication with long, unstable palindromic junctions. The secondary rearrangement of these palindromes gives rise to the various forms of inverted structural variants. We postulate that this same mechanism (ODIRA: origin-dependent inverted-repeat amplification) that creates the inverted CNVs in inherited syndromes also generates the palindromes found in cancers.
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Affiliation(s)
- Bonita J. Brewer
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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9
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Duardo RC, Guerra F, Pepe S, Capranico G. Non-B DNA structures as a booster of genome instability. Biochimie 2023; 214:176-192. [PMID: 37429410 DOI: 10.1016/j.biochi.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Non-canonical secondary structures (NCSs) are alternative nucleic acid structures that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on the sequence. The majority of these structures form in the context of physiological processes, such as transcription-associated R-loops, G4s, as well as hairpins and slipped-strand DNA, whose formation can be dependent on DNA replication. It is therefore not surprising that NCSs play important roles in the regulation of key biological processes. In the last years, increasing published data have supported their biological role thanks to genome-wide studies and the development of bioinformatic prediction tools. Data have also highlighted the pathological role of these secondary structures. Indeed, the alteration or stabilization of NCSs can cause the impairment of transcription and DNA replication, modification in chromatin structure and DNA damage. These events lead to a wide range of recombination events, deletions, mutations and chromosomal aberrations, well-known hallmarks of genome instability which are strongly associated with human diseases. In this review, we summarize molecular processes through which NCSs trigger genome instability, with a focus on G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform and multi-stranded structures known as triplexes.
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Affiliation(s)
- Renée C Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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10
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Page-McCaw PS, Pokidysheva EN, Darris CE, Chetyrkin S, Fidler AL, Murawala P, Gallup J, Hudson JK, Hudson BG. Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling animal evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.563013. [PMID: 37905027 PMCID: PMC10614949 DOI: 10.1101/2023.10.18.563013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Collagen IV is a primordial component of basement membranes, a specialized form of extracellular matrix that enabled multi-cellular epithelial tissues. In mammals, collagen IV assembles from a family of six α-chains (α1 to α6), encoded by six genes (COL4A1 to COL4A6), into three distinct scaffolds: the α121, the α345 and a mixed scaffold containing both α121 and α565. The six mammalian COL4A genes occur in pairs that occur in a head-to-head arrangement on three distinct chromosomes. In Alport syndrome, variants in the COL4A3, 4 or 5 genes cause either loss or defective assembly of the collagen IV α345 scaffold which results in a dysfunctional glomerular basement membrane, proteinuria and progression to renal failure in millions of people worldwide. Here, we determine the evolutionary emergence and diversification of the COL4A genes using comparative genomics and biochemical analyses. Using syntenic relationships to genes closely linked to the COL4A genes, we determine that the COL4A3 and COL4A4 gene pair appeared in cyclostomes (hagfish and lampreys) while the COL4A5 and COL4A6 gene pair emerged in gnathostomes, jawed vertebrates. The more basal chordate species, lancelets and tunicates, do not have discrete kidneys and have a single COL4A gene pair, though often with single isolated COL4 genes similar to those found in C elegans . Remarkably, while the six COL4A genes are conserved in vertebrates, amphibians have lost the COL4A3 and COL4A4 genes. Our findings of the evolutionary emergence of these genes, together with the amphibian double-knockout, opens an experimental window to gain insights into functionality of the Col IV α345 scaffold.
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11
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Rodriguez I, Rossi NM, Keskus A, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O’Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley K, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer using Long-Read Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.21.23294276. [PMID: 37662332 PMCID: PMC10473792 DOI: 10.1101/2023.08.21.23294276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and this is one of the first analyses of these events using long-read sequencing. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes and only one BFB breakpoint showed chromothripsis. Five cell lines have a Chr11q BFB event, with YAP1/BIRC2/BIRC3 gene amplification. Indeed, YAP1 amplification is associated with a 10-year earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that cervical cancer patients with YAP1/BIRC2/BIRC3-amplification, especially those of African American ancestry, might benefit from targeted therapy. In summary, we uncovered new insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F. Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Tim O’Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Laksh Malik
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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12
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Murata MM, Giuliano AE, Tanaka H. Genome-Wide Analysis of Palindrome Formation with Next-Generation Sequencing (GAPF-Seq) and a Bioinformatics Pipeline for Assessing De Novo Palindromes in Cancer Genomes. Methods Mol Biol 2023; 2660:13-22. [PMID: 37191787 DOI: 10.1007/978-1-0716-3163-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA palindromes are a type of chromosomal aberration that appears frequently during tumorigenesis. They are characterized by sequences of nucleotides that are identical to their reverse complements and often arise due to illegitimate repair of DNA double-strand breaks, fusion of telomeres, or stalled replication forks, all of which are common adverse early events in cancer. Here, we describe the protocol for enriching palindromes from genomic DNA sources with low-input DNA amounts and detail a bioinformatics tool for assessing the enrichment and location of de novo palindrome formation from low-coverage whole-genome sequencing data.
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Affiliation(s)
- Michael M Murata
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
- Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
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13
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HER2 Overexpression and Cytogenetical Patterns in Canine Mammary Carcinomas. Vet Sci 2022; 9:vetsci9110583. [DOI: 10.3390/vetsci9110583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) is a tyrosine kinase receptor that promotes tumor cell growth and is implicated in the pathogenesis of human breast cancer. The role of HER2 in canine mammary carcinomas (CMCs) is not clear. Therefore, this study aimed to examine the protein expression and cytogenetic changes of HER2 and their correlation with other clinical–pathological parameters in CMC. We retrospectively selected 112 CMCs. HER2, ER, and Ki67 were assessed by immunohistochemistry. HER2 antibody validation was investigated by immunoblot on mammary tumor cell lines. Fluorescence in situ hybridization (FISH) was performed with probes for HER2 and CRYBA1 (control gene present on CFA9). HER2 protein overexpression was detected in 15 carcinomas (13.5%). A total of 90 carcinomas were considered technically adequate by FISH, and 8 out of 90 CMC (10%) were HER2 amplified, 3 of which showed a cluster-type pattern. HER2 overexpression was correlated with an increased number of HER2 gene copies (p = 0.01; R = 0.24) and overall survival (p = 0.03), but no correlation with ER, Ki67, grade, metastases, and tumor-specific survival was found. Surprisingly, co-amplification or polysomy was identified in three tumors, characterized by an increased copy number of both HER2 and CRYBA1. A morphological translocation-fusion pattern was recognized in 20 carcinomas (22%), with a co-localized signal of HER2 and CRYBA1. HER2 is not associated with clinical–pathological parameters of increased malignancy in canine mammary tumors, but it is suitable for studying different amplification patterns.
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14
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Abstract
In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.
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Affiliation(s)
- Vineet Bafna
- Department of Computer Science and Engineering and Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA;
| | - Paul S Mischel
- Department of Pathology and ChEM-H, Stanford University School of Medicine, Stanford, California, USA;
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15
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Katz-Summercorn AC, Jammula S, Frangou A, Peneva I, O'Donovan M, Tripathi M, Malhotra S, di Pietro M, Abbas S, Devonshire G, Januszewicz W, Blasko A, Nowicki-Osuch K, MacRae S, Northrop A, Redmond AM, Wedge DC, Fitzgerald RC. Multi-omic cross-sectional cohort study of pre-malignant Barrett's esophagus reveals early structural variation and retrotransposon activity. Nat Commun 2022; 13:1407. [PMID: 35301290 PMCID: PMC8931005 DOI: 10.1038/s41467-022-28237-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/14/2022] [Indexed: 12/11/2022] Open
Abstract
Barrett's esophagus is a pre-malignant lesion that can progress to esophageal adenocarcinoma. We perform a multi-omic analysis of pre-cancer samples from 146 patients with a range of outcomes, comprising 642 person years of follow-up. Whole genome sequencing reveals complex structural variants and LINE-1 retrotransposons, as well as known copy number changes, occurring even prior to dysplasia. The structural variant burden captures the most variance across the cohort and genomic profiles do not always match consensus clinical pathology dysplasia grades. Increasing structural variant burden is associated with: high levels of chromothripsis and breakage-fusion-bridge events; increased expression of genes related to cell cycle checkpoint, DNA repair and chromosomal instability; and epigenetic silencing of Wnt signalling and cell cycle genes. Timing analysis reveals molecular events triggering genomic instability with more clonal expansion in dysplastic samples. Overall genomic complexity occurs early in the Barrett's natural history and may inform the potential for cancer beyond the clinically discernible phenotype.
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Affiliation(s)
- A C Katz-Summercorn
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S Jammula
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - A Frangou
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - I Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | - M O'Donovan
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - M Tripathi
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - S Malhotra
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Histopathology, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - M di Pietro
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S Abbas
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - G Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - W Januszewicz
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - A Blasko
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - K Nowicki-Osuch
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - S MacRae
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - A Northrop
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - A M Redmond
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - D C Wedge
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK
| | - R C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, CB2 0XZ, UK.
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16
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The Mammalian Ecdysoneless Protein Interacts with RNA Helicase DDX39A To Regulate Nuclear mRNA Export. Mol Cell Biol 2021; 41:e0010321. [PMID: 33941617 PMCID: PMC8224239 DOI: 10.1128/mcb.00103-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The mammalian orthologue of ecdysoneless (ECD) protein is required for embryogenesis, cell cycle progression, and mitigation of endoplasmic reticulum stress. Here, we identified key components of the mRNA export complexes as binding partners of ECD and characterized the functional interaction of ECD with key mRNA export-related DEAD BOX protein helicase DDX39A. We find that ECD is involved in RNA export through its interaction with DDX39A. ECD knockdown (KD) blocks mRNA export from the nucleus to the cytoplasm, which is rescued by expression of full-length ECD but not an ECD mutant that is defective in interaction with DDX39A. We have previously shown that ECD protein is overexpressed in ErbB2+ breast cancers (BC). In this study, we extended the analyses to two publicly available BC mRNA The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) data sets. In both data sets, ECD mRNA overexpression correlated with short patient survival, specifically ErbB2+ BC. In the METABRIC data set, ECD overexpression also correlated with poor patient survival in triple-negative breast cancer (TNBC). Furthermore, ECD KD in ErbB2+ BC cells led to a decrease in ErbB2 mRNA level due to a block in its nuclear export and was associated with impairment of oncogenic traits. These findings provide novel mechanistic insight into the physiological and pathological functions of ECD.
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17
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Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions. Microbiol Mol Biol Rev 2020; 85:85/1/e00110-20. [PMID: 33361270 DOI: 10.1128/mmbr.00110-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.
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18
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Toledo F. Mechanisms Generating Cancer Genome Complexity: Back to the Future. Cancers (Basel) 2020; 12:E3783. [PMID: 33334014 PMCID: PMC7765419 DOI: 10.3390/cancers12123783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding the mechanisms underlying cancer genome evolution has been a major goal for decades. A recent study combining live cell imaging and single-cell genome sequencing suggested that interwoven chromosome breakage-fusion-bridge cycles, micronucleation events and chromothripsis episodes drive cancer genome evolution. Here, I discuss the "interphase breakage model," suggested from prior fluorescent in situ hybridization data that led to a similar conclusion. In this model, the rapid genome evolution observed at early stages of gene amplification was proposed to result from the interweaving of an amplification mechanism (breakage-fusion-bridge cycles) and of a deletion mechanism (micronucleation and stitching of DNA fragments retained in the nucleus).
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Affiliation(s)
- Franck Toledo
- Genetics of Tumor Suppression, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR3244 Dynamics of Genetic Information, 26 rue d'Ulm, CEDEX 05, 75248 Paris, France
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19
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A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. Hum Genome Var 2020; 7:40. [PMID: 33298903 PMCID: PMC7680136 DOI: 10.1038/s41439-020-00127-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/24/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA is like a palindrome in language, but when read backwards, it is a complement of the forward sequence; effectively, the two halves of a sequence complement each other from its midpoint like in a double strand of DNA. Palindromes are distributed throughout the human genome and play significant roles in gene expression and regulation. Palindromic mutations are linked to many human diseases, such as neuronal disorders, mental retardation, and various cancers. In this work, we computed and analyzed the palindromic sequences in the human genome and studied their conservation in personal genomes using 1000 Genomes data. We found that ~30% of the palindromes exhibit variation, some of which are caused by rare variants. The analysis of disease/trait-associated single-nucleotide polymorphisms in palindromic regions showed that disease-associated risk variants are 14 times more likely to be present in palindromic regions than in other regions. The catalog of palindromes in the reference genome and 1000 Genomes is being made available here with details on their variations in each individual genome to serve as a resource for future and retrospective whole-genome studies identifying statistically significant palindrome variations associated with diseases or traits and their roles in disease mechanisms.
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20
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Zhou W, Wu J, Zhang J, Liu X, Guo S, Jia S, Zhang X, Zhu Y, Wang M. Integrated bioinformatics analysis to decipher molecular mechanism of compound Kushen injection for esophageal cancer by combining WGCNA with network pharmacology. Sci Rep 2020; 10:12745. [PMID: 32728182 PMCID: PMC7391752 DOI: 10.1038/s41598-020-69708-2] [Citation(s) in RCA: 12] [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: 02/07/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
Compound Kushen injection (CKI), a medicine in widespread clinical use in China, has proven therapeutic effects on cancer. However, few molecular mechanism analyses have been carried out. To address this problem, bioinformatics approaches combining weighted gene co-expression network analysis with network pharmacology methods were undertaken to elucidate the underlying molecular mechanisms of CKI in the treatment of esophageal cancer (ESCA). First, the key gene modules related to the clinical traits of ESCA were analysed by WCGNA. Based on the results, the hub genes related to CKI treatment for ESCA were explored through network pharmacology. Molecular docking simulation was performed to recognize the binding activity of hub genes with CKI compounds. The results showed that the potential hub targets, including EGFR, ErbB2, CCND1 and IGF1R, are therapeutic targets of CKI for the treatment of ESCA. Moreover, these targets were significantly enriched in many pathways related to cancer and signalling pathways, such as the PI3K-Akt signalling pathway and ErbB signalling pathway. In conclusion, this research partially highlighted the molecular mechanism of CKI in the treatment of ESCA, offering great potential in the identification of the effective compounds in CKI and biomarkers for ESCA treatment.
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MESH Headings
- Algorithms
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Computational Biology/methods
- Cyclin D1/chemistry
- Cyclin D1/metabolism
- Databases, Genetic
- Drugs, Chinese Herbal/chemistry
- Drugs, Chinese Herbal/pharmacology
- ErbB Receptors/chemistry
- ErbB Receptors/metabolism
- Esophageal Neoplasms/drug therapy
- Esophageal Neoplasms/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Regulatory Networks/drug effects
- Humans
- Kaplan-Meier Estimate
- Models, Molecular
- Molecular Docking Simulation
- Receptor, ErbB-2/chemistry
- Receptor, ErbB-2/metabolism
- Receptor, IGF Type 1/chemistry
- Receptor, IGF Type 1/metabolism
- Sequence Analysis, RNA
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Affiliation(s)
- Wei Zhou
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Jiarui Wu
- Beijing University of Chinese Medicine, Beijing, 100102, China.
| | - Jingyuan Zhang
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Xinkui Liu
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Siyu Guo
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - ShanShan Jia
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Xiaomeng Zhang
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Yingli Zhu
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Miaomiao Wang
- Beijing University of Chinese Medicine, Beijing, 100102, China
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21
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Todd RT, Selmecki A. Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs. eLife 2020; 9:e58349. [PMID: 32687060 PMCID: PMC7371428 DOI: 10.7554/elife.58349] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Previously, we identified long repeat sequences that are frequently associated with genome rearrangements, including copy number variation (CNV), in many diverse isolates of the human fungal pathogen Candida albicans (Todd et al., 2019). Here, we describe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal drugs. Single-cell karyotype analysis indicates that these CNVs appear to arise via a dicentric chromosome intermediate and breakage-fusion-bridge cycles that are repaired using multiple distinct long inverted repeat sequences. Subsequent removal of the antifungal drug can lead to a dramatic loss of the CNV and reversion to the progenitor genotype and drug susceptibility phenotype. These findings support a novel mechanism for the rapid acquisition of antifungal drug resistance and provide genomic evidence for the heterogeneity frequently observed in clinical settings.
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Affiliation(s)
- Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
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22
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Tanaka H, Watanabe T. Mechanisms Underlying Recurrent Genomic Amplification in Human Cancers. Trends Cancer 2020; 6:462-477. [PMID: 32383436 PMCID: PMC7285850 DOI: 10.1016/j.trecan.2020.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Focal copy-number increases (genomic amplification) pinpoint oncogenic driver genes and therapeutic targets in cancer genomes. With the advent of genomic technologies, recurrent genomic amplification has been mapped throughout the genome. Recurrent amplification could be solely due to positive selection for the tumor-promoting effects of amplified gene products. Alternatively, recurrence could result from the susceptibility of the loci to amplification. Distinguishing between these possibilities requires a full understanding of the amplification mechanisms. Two mechanisms, the formation of double minute (DM) chromosomes and breakage-fusion-bridge (BFB) cycles, have been repeatedly linked to genomic amplification, and the impact of both mechanisms has been confirmed in cancer genomics data. We review the details of these mechanisms and discuss the mechanisms underlying recurrence.
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Affiliation(s)
- Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA.
| | - Takaaki Watanabe
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
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23
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Pavlenko IA, Zavalishina LE, Povilaitite PE. [HER2/neu gene amplification as a mechanism of clonal heterogeneity in breast cancer]. Arkh Patol 2019; 81:49-55. [PMID: 31851192 DOI: 10.17116/patol20198106149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To estimate the heterogeneity of HER2/neu gene amplification in HER2/neu-positive breast cancer (BC). MATERIAL AND METHODS Fluorescence in situ hybridization (FISH) assay was used to estimate HER2/neu gene amplification and HER2/CEP17 ratios in BC samples with an immunohistochemical evaluation of HER2/neu2+ expression. The results were interpreted according to the 2018 ASCO/CAP guidelines. BC samples with HER2/neu gene amplification (n = 25) was evaluated for variability in HER2/neu amplification and HER2/CEP17 ratios in 20 tumor cells counted using the FISH assay. RESULTS Significant intratumoral variability was found in the HER2/neu gene copy number and HER2/CEP17 ratios. HER2/neu-negative cells (5-15%) were present in 28% of the examined samples found to be HER2/neu positive. The HER2/neu gene copy number and HER2/CEP17 ratios for these tumors were statistically significantly lower than those in the group in which all the counted cells were characterized by HER2/neu amplification: 6.25 (95% CI 4.3-12.45; p=0.0166) and 2.37 (95% CI 2.06-3.43; p=0.0076), respectively. The threshold value of HER2/CEP17, at which cells without amplification were detected in HER2/neu-positive tumors, was 2.5. CONCLUSION HER2/neu gene amplification in BC is extremely variable both within a single tumor and between the tumors of the same biological subtype. Amplification heterogeneity is statistically significantly more common in HER2/neu-positive BC with a HER2/CEP17 ratio <2.5 and may affect the outcome of the disease and also be important in the choice of treatment policy.
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Affiliation(s)
- I A Pavlenko
- GBU 'Rostov Regional Bureau of Pathology', Rostov-on-Don, Russia
| | - L E Zavalishina
- FSBEI FPE Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russia, Moscow, Russia
| | - P E Povilaitite
- GBU 'Rostov Regional Bureau of Pathology', Rostov-on-Don, Russia
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24
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Maoz M, Devir M, Inbar M, Inbar-Daniel Z, Sherill-Rofe D, Bloch I, Meir K, Edelman D, Azzam S, Nechushtan H, Maimon O, Uziely B, Kadouri L, Sonnenblick A, Eden A, Peretz T, Zick A. Clinical Implications of Sub-grouping HER2 Positive Tumors by Amplicon Structure and Co-amplified Genes. Sci Rep 2019; 9:18795. [PMID: 31827209 PMCID: PMC6906288 DOI: 10.1038/s41598-019-55455-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
ERBB2 amplification is a prognostic marker for aggressive tumors and a predictive marker for prolonged survival following treatment with HER2 inhibitors. We attempt to sub-group HER2+ tumors based on amplicon structures and co-amplified genes. We examined five HER2+ cell lines, three HER2+ xenographs and 57 HER2+ tumor tissues. ERBB2 amplification was analyzed using digital droplet PCR and low coverage whole genome sequencing. In some HER2+ tumors PPM1D, that encodes WIP1, is co-amplified. Cell lines were treated with HER2 and WIP1 inhibitors. We find that inverted duplication is the amplicon structure in the majority of HER2+ tumors. In patients suffering from an early stage disease the ERBB2 amplicon is composed of a single segment while in patients suffering from advanced cancer the amplicon is composed of several different segments. We find robust WIP1 inhibition in some HER2+ PPM1D amplified cell lines. Sub-grouping HER2+ tumors using low coverage whole genome sequencing identifies inverted duplications as the main amplicon structure and based on the number of segments, differentiates between local and advanced tumors. In addition, we found that we could determine if a tumor is a recurrent tumor or second primary tumor and identify co-amplified oncogenes that may serve as targets for therapy.
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Affiliation(s)
- Myriam Maoz
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Michal Devir
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Michal Inbar
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Ziva Inbar-Daniel
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Dana Sherill-Rofe
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Idit Bloch
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Karen Meir
- Department of Pathology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - David Edelman
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Salah Azzam
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Hovav Nechushtan
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Ofra Maimon
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Beatrice Uziely
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Luna Kadouri
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Amir Sonnenblick
- The Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Amir Eden
- Department of Cell & Developmental Biology, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Tamar Peretz
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Aviad Zick
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
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25
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Waisertreiger I, Popovich K, Block M, Anderson KR, Barlow JH. Visualizing locus-specific sister chromatid exchange reveals differential patterns of replication stress-induced fragile site breakage. Oncogene 2019; 39:1260-1272. [PMID: 31636383 PMCID: PMC7002298 DOI: 10.1038/s41388-019-1054-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 11/09/2022]
Abstract
Chromosomal fragile sites are genomic loci sensitive to replication stress which accumulate high levels of DNA damage, and are frequently mutated in cancers. Fragile site damage is thought to arise from the aberrant repair of spontaneous replication stress, however successful fragile site repair cannot be calculated using existing techniques. Here, we report a new assay measuring recombination-mediated repair at endogenous genomic loci by combining a sister chromatid exchange (SCE) assay with fluorescent in situ hybridization (SCE-FISH). Using SCE-FISH, we find that endogenous and exogenous replication stress generated unrepaired breaks and SCEs at fragile sites. We also find that distinct sources of replication stress induce distinct patterns of breakage: ATR inhibition induces more breaks at early replicating fragile sites (ERFS), while ERFS and late-replicating common fragile sites (CFS) are equally fragile in response to aphidicolin. Furthermore, SCEs were suppressed at fragile sites near centromeres in response to replication stress, suggesting that genomic location influences DNA repair pathway choice. SCE-FISH also measured successful recombination in human primary lymphocytes, and identificed the proto-oncogene BCL2 as a replication stress-induced fragile site. These findings demonstrate that SCE-FISH frequency at fragile sites is a sensitive indicator of replication stress, and that large-scale genome organization influences DNA repair pathway choice.
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Affiliation(s)
- Irina Waisertreiger
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Katherine Popovich
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Maya Block
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Krista R Anderson
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Jacqueline H Barlow
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA. .,Genome Center, University of California, Davis, CA, 95616, USA.
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26
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Watanabe T, Tanaka H, Horiuchi T. Complex repeat structure promotes hyper-amplification and amplicon evolution through rolling-circle replication. Nucleic Acids Res 2018; 46:5097-5108. [PMID: 29718479 PMCID: PMC6007334 DOI: 10.1093/nar/gky275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/04/2018] [Indexed: 11/30/2022] Open
Abstract
Inverted repeats (IRs) are abundant in genomes and frequently serve as substrates for chromosomal aberrations, including gene amplification. In the early stage of amplification, repeated cycles of chromosome breakage and rearrangement, called breakage-fusion-bridge (BFB), generate a large inverted structure, which evolves into highly-amplified, complex end products. However, it remains to be determined how IRs mediate chromosome rearrangements and promote subsequent hyper-amplification and amplicon evolutions. To dissect the complex processes, we constructed repetitive structures in a yeast chromosome and selected amplified cells using genetic markers with limited expression. The genomic architecture was associated with replication stress and produced extra-/intra-chromosomal amplification. Genetic analysis revealed structure-specific endonucleases, Mus81 and Rad27, and post-replication DNA repair protein, Rad18, suppress the amplification processes. Following BFB cycles, the intra-chromosomal products undergo intensive rearrangements, such as frequent inversions and deletions, indicative of rolling-circle replication. This study presents an integrated view linking BFB cycles to hyper-amplification driven by rolling-circle replication.
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Affiliation(s)
- Takaaki Watanabe
- Department of Molecular Life Science, Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan.,Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.,National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Takashi Horiuchi
- Department of Molecular Life Science, Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan.,National Institute for Basic Biology, Okazaki, Aichi, Japan
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27
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June CH, O'Connor RS, Kawalekar OU, Ghassemi S, Milone MC. CAR T cell immunotherapy for human cancer. Science 2018; 359:1361-1365. [PMID: 29567707 DOI: 10.1126/science.aar6711] [Citation(s) in RCA: 1764] [Impact Index Per Article: 294.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adoptive T cell transfer (ACT) is a new area of transfusion medicine involving the infusion of lymphocytes to mediate antitumor, antiviral, or anti-inflammatory effects. The field has rapidly advanced from a promising form of immuno-oncology in preclinical models to the recent commercial approvals of chimeric antigen receptor (CAR) T cells to treat leukemia and lymphoma. This Review describes opportunities and challenges for entering mainstream oncology that presently face the CAR T field, with a focus on the challenges that have emerged over the past several years.
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Affiliation(s)
- Carl H June
- Center for Cellular Immunotherapies, Perlman School of Medicine, Philadelphia, PA, USA. .,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perlman School of Medicine, Philadelphia, PA, USA
| | - Roddy S O'Connor
- Center for Cellular Immunotherapies, Perlman School of Medicine, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA
| | - Omkar U Kawalekar
- Center for Cellular Immunotherapies, Perlman School of Medicine, Philadelphia, PA, USA
| | - Saba Ghassemi
- Center for Cellular Immunotherapies, Perlman School of Medicine, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C Milone
- Center for Cellular Immunotherapies, Perlman School of Medicine, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perlman School of Medicine, Philadelphia, PA, USA
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28
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SbcC-SbcD and ExoI process convergent forks to complete chromosome replication. Proc Natl Acad Sci U S A 2017; 115:349-354. [PMID: 29208713 DOI: 10.1073/pnas.1715960114] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SbcC-SbcD are the bacterial orthologs of Mre11-Rad50, a nuclease complex essential for genome stability, normal development, and viability in mammals. In vitro, these enzymes degrade long DNA palindromic structures. When inactivated along with ExoI in Escherichia coli, or Sae2 in eukaryotes, palindromic amplifications arise and propagate in cells. However, long DNA palindromes are not normally found in bacterial or human genomes, leaving the cellular substrates and function of these enzymes unknown. Here, we show that during the completion of DNA replication, convergent replication forks form a palindrome-like structural intermediate that requires nucleolytic processing by SbcC-SbcD and ExoI before chromosome replication can be completed. Inactivation of these nucleases prevents completion from occurring, and under these conditions, cells maintain viability by shunting the reaction through an aberrant recombinational pathway that leads to amplifications and instability in this region. The results identify replication completion as an event critical to maintain genome integrity and cell viability, demonstrate SbcC-SbcD-ExoI acts before RecBCD and is required to initiate the completion reaction, and reveal how defects in completion result in genomic instability.
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