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Wang Y, Zou H, Ji W, Huang M, You B, Sun N, Qiao Y, Liu P, Xu L, Zhang X, Cai M, Kuang Y, Fu S, Sun W, Jia X, Wu J. Repression of the SUMO-conjugating enzyme UBC9 is associated with lowered double minutes and reduced tumor progression. Cancer Biol Ther 2024; 25:2323768. [PMID: 38465861 PMCID: PMC10936631 DOI: 10.1080/15384047.2024.2323768] [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: 10/30/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Double minutes (DMs), extrachromosomal gene fragments found within certain tumors, have been noted to carry onco- and drug resistance genes contributing to tumor pathogenesis and progression. After screening for SUMO-related molecule expression within various tumor sample and cell line databases, we found that SUMO-conjugating enzyme UBC9 has been associated with genome instability and tumor cell DM counts, which was confirmed both in vitro and in vivo. Karyotyping determined DM counts post-UBC9 knockdown or SUMOylation inhibitor 2-D08, while RT-qPCR and Western blot were used to measure DM-carried gene expression in vitro. In vivo, fluorescence in situ hybridization (FISH) identified micronucleus (MN) expulsion. Western blot and immunofluorescence staining were then used to determine DNA damage extent, and a reporter plasmid system was constructed to detect changes in homologous recombination (HR) and non-homologous end joining (NHEJ) pathways. Our research has shown that UBC9 inhibition is able to attenuate DM formation and lower DM-carried gene expression, in turn reducing tumor growth and malignant phenotype, via MN efflux of DMs and lowering NHEJ activity to increase DNA damage. These findings thus reveal a relationship between heightened UBC9 activity, increased DM counts, and tumor progression, providing a potential approach for targeted therapies, via UBC9 inhibition.
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Affiliation(s)
- Yusi Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Hongyan Zou
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Wei Ji
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Min Huang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Benhui You
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Nan Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Yuandong Qiao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Peng Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Lidan Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Xuelong Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Mengdi Cai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Ye Kuang
- Department of Gynecology and Obstetrics, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Harbin, China
- Future Medical Laboratory, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
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2
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Abbosh C, Hodgson D, Doherty GJ, Gale D, Black JRM, Horn L, Reis-Filho JS, Swanton C. Implementing circulating tumor DNA as a prognostic biomarker in resectable non-small cell lung cancer. Trends Cancer 2024:S2405-8033(24)00089-X. [PMID: 38839544 DOI: 10.1016/j.trecan.2024.04.004] [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: 02/28/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Abstract
Systemic treatment of resectable non-small cell lung cancer (NSCLC) is evolving with emerging neoadjuvant, perioperative, and adjuvant immunotherapy approaches. Circulating tumor DNA (ctDNA) detection at clinical diagnosis, during neoadjuvant therapy, or after resection may discern high-risk patients who might benefit from therapy escalation or switch. This Review summarizes translational implications of data supporting ctDNA-based risk determination in NSCLC and outstanding questions regarding ctDNA validity/utility as a prognostic biomarker. We discuss emerging ctDNA capabilities to refine clinical tumor-node-metastasis (TNM) staging in lung adenocarcinoma, ctDNA dynamics during neoadjuvant therapy for identifying patients deriving suboptimal benefit, and postoperative molecular residual disease (MRD) detection to escalate systemic therapy. Considering differential relapse characteristics in landmark MRD-negative/MRD-positive patients, we propose how ctDNA might integrate with pathological response data for optimal postoperative risk stratification.
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Affiliation(s)
- Chris Abbosh
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | - Darren Hodgson
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | | | - Davina Gale
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Leora Horn
- Clinical Development, Late Oncology, AstraZeneca, Nashville, TN, USA
| | - Jorge S Reis-Filho
- Cancer Biomarker Development, Early Oncology, AstraZeneca, Gaithersburg, MD, USA
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
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3
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Carceles-Cordon M, Orme JJ, Domingo-Domenech J, Rodriguez-Bravo V. The yin and yang of chromosomal instability in prostate cancer. Nat Rev Urol 2024; 21:357-372. [PMID: 38307951 PMCID: PMC11156566 DOI: 10.1038/s41585-023-00845-9] [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] [Accepted: 12/13/2023] [Indexed: 02/04/2024]
Abstract
Metastatic prostate cancer remains an incurable lethal disease. Studies indicate that prostate cancer accumulates genomic changes during disease progression and displays the highest levels of chromosomal instability (CIN) across all types of metastatic tumours. CIN, which refers to ongoing chromosomal DNA gain or loss during mitosis, and derived aneuploidy, are known to be associated with increased tumour heterogeneity, metastasis and therapy resistance in many tumour types. Paradoxically, high CIN levels are also proposed to be detrimental to tumour cell survival, suggesting that cancer cells must develop adaptive mechanisms to ensure their survival. In the context of prostate cancer, studies indicate that CIN has a key role in disease progression and might also offer a therapeutic vulnerability that can be pharmacologically targeted. Thus, a comprehensive evaluation of the causes and consequences of CIN in prostate cancer, its contribution to aggressive advanced disease and a better understanding of the acquired CIN tolerance mechanisms can translate into new tumour classifications, biomarker development and therapeutic strategies.
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Affiliation(s)
| | - Jacob J Orme
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Josep Domingo-Domenech
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
| | - Veronica Rodriguez-Bravo
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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4
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Zhang D, Zhao F, Li J, Guo P, Liu H, Lu T, Li S, Li Z, Li Y. Comprehensive single-cell transcriptomic profiling reveals molecular subtypes and prognostic biomarkers with implications for targeted therapy in esophageal squamous cell carcinoma. Transl Oncol 2024; 44:101948. [PMID: 38582059 PMCID: PMC11004200 DOI: 10.1016/j.tranon.2024.101948] [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: 01/11/2024] [Revised: 02/05/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is a genetically heterogeneous disease with poor clinical outcomes. Identification of biomarkers linked to DNA replication stress may enable improved prognostic risk stratification and guide therapeutic decision making. We performed integrated single-cell RNA sequencing and computational analyses to define the molecular determinants and subtypes underlying ESCC heterogeneity. METHODS Single-cell RNA sequencing was performed on ESCC samples and analyzed using Seurat. Differential gene expression analysis was used to identify esophageal cell phenotypes. DNA replication stress-related genes were intersected with single-cell differential expression data to identify potential prognostic genes, which were used to generate a DNA replication stress (DRS) score. This score and associated genes were evaluated in survival analysis. Putative prognostic biomarkers were evaluated by Cox regression and consensus clustering. Mendelian randomization analyses assessed the causal role of PRKCB. RESULTS High DRS score associated with poor survival. Four genes (CDKN2A, NUP155, PPP2R2A, PRKCB) displayed prognostic utility. Three molecular subtypes were identified with discrete survival and immune properties. A 12-gene signature displayed robust prognostic performance. PRKCB was overexpressed in ESCC, while PRKCB knockdown reduced ESCC cell migration. CONCLUSIONS This integrated single-cell sequencing analysis provides new insights into the molecular heterogeneity and prognostic determinants underlying ESCC. The findings identify potential prognostic biomarkers and a gene expression signature that may enable improved patient risk stratification in ESCC. Experimental validation of the role of PRKCB substantiates the potential clinical utility of our results.
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Affiliation(s)
- Dengfeng Zhang
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Jing Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Pengfei Guo
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Haitao Liu
- College of Life Science, Inner Mongolia University, Hohhot 010000, China
| | - Tianxing Lu
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China.
| | - Zhirong Li
- Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, China.
| | - Yishuai Li
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang 050000, China; Hebei Provincial Key Laboratory of Pulmonary Diseases, Shijiazhuang 050000, China.
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5
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Ma J, Ren D, Wang Z, Li W, Li L, Liu T, Ye Q, Lei Y, Jian Y, Ma B, Fan Y, Liu J, Gao Y, Jin X, Huang H, Li L. CK2-dependent degradation of CBX3 dictates replication fork stalling and PARP inhibitor sensitivity. SCIENCE ADVANCES 2024; 10:eadk8908. [PMID: 38781342 PMCID: PMC11114232 DOI: 10.1126/sciadv.adk8908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
DNA replication is a vulnerable cellular process, and its deregulation leads to genomic instability. Here, we demonstrate that chromobox protein homolog 3 (CBX3) binds replication protein A 32-kDa subunit (RPA2) and regulates RPA2 retention at stalled replication forks. CBX3 is recruited to stalled replication forks by RPA2 and inhibits ring finger and WD repeat domain 3 (RFWD3)-facilitated replication restart. Phosphorylation of CBX3 at serine-95 by casein kinase 2 (CK2) kinase augments cadherin 1 (CDH1)-mediated CBX3 degradation and RPA2 dynamics at stalled replication forks, which permits replication fork restart. Increased expression of CBX3 due to gene amplification or CK2 inhibitor treatment sensitizes prostate cancer cells to poly(ADP-ribose) polymerase (PARP) inhibitors while inducing replication stress and DNA damage. Our work reveals CBX3 as a key regulator of RPA2 function and DNA replication, suggesting that CBX3 could serve as an indicator for targeted therapy of cancer using PARP inhibitors.
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Affiliation(s)
- Jian Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Dianyun Ren
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zixi Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wei Li
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Tianjie Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qi Ye
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yuzeshi Lei
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yanlin Jian
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Bohan Ma
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yizeng Fan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Jing Liu
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yang Gao
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Xin Jin
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
- Institute of Urologic Science and Technology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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6
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Bulanova D, Akimov Y, Senkowski W, Oikkonen J, Gall-Mas L, Timonen S, Elmadani M, Hynninen J, Hautaniemi S, Aittokallio T, Wennerberg K. A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells. SCIENCE ADVANCES 2024; 10:eadj1564. [PMID: 38781347 PMCID: PMC11114247 DOI: 10.1126/sciadv.adj1564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Resistance to therapy commonly develops in patients with high-grade serous ovarian carcinoma (HGSC) and triple-negative breast cancer (TNBC), urging the search for improved therapeutic combinations and their predictive biomarkers. Starting from a CRISPR knockout screen, we identified that loss of RB1 in TNBC or HGSC cells generates a synthetic lethal dependency on casein kinase 2 (CK2) for surviving the treatment with replication-perturbing therapeutics such as carboplatin, gemcitabine, or PARP inhibitors. CK2 inhibition in RB1-deficient cells resulted in the degradation of another RB family cell cycle regulator, p130, which led to S phase accumulation, micronuclei formation, and accelerated PARP inhibition-induced aneuploidy and mitotic cell death. CK2 inhibition was also effective in primary patient-derived cells. It selectively prevented the regrowth of RB1-deficient patient HGSC organoids after treatment with carboplatin or niraparib. As about 25% of HGSCs and 40% of TNBCs have lost RB1 expression, CK2 inhibition is a promising approach to overcome resistance to standard therapeutics in large strata of patients.
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Affiliation(s)
- Daria Bulanova
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
| | - Wojciech Senkowski
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Jaana Oikkonen
- Research Program in Systems Oncology (ONCOSYS), University of Helsinki, Helsinki, Finland
| | - Laura Gall-Mas
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Sanna Timonen
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
| | | | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital and University of Turku, Turku, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology (ONCOSYS), University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Helsinki Institute for Life Sciences, University of Helsinki, Helsinki, Finland
- Institute for Cancer Research, Department of Cancer Genetics, Oslo University Hospital, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology (OCBE), University of Oslo, Oslo, Norway
| | - Krister Wennerberg
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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7
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Li GX, Chen L, Hsiao Y, Mannan R, Zhang Y, Luo J, Petralia F, Cho H, Hosseini N, Leprevost FDV, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Kumar-Sinha C, Chugh S, Le A, Ponce S, Guo S, Zhang C, Schnaubelt M, Al Deen NN, Chen F, Caravan W, Houston A, Hopkins A, Newton CJ, Wang X, Polasky DA, Haynes S, Yu F, Jing X, Chen S, Robles AI, Mesri M, Thiagarajan M, An E, Getz GA, Linehan WM, Hostetter G, Jewell SD, Chan DW, Wang P, Omenn GS, Mehra R, Ricketts CJ, Ding L, Chinnaiyan AM, Cieslik MP, Dhanasekaran SM, Zhang H, Nesvizhskii AI. Comprehensive proteogenomic characterization of rare kidney tumors. Cell Rep Med 2024; 5:101547. [PMID: 38703764 PMCID: PMC11148773 DOI: 10.1016/j.xcrm.2024.101547] [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: 03/20/2023] [Revised: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
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Affiliation(s)
- Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanbyul Cho
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaoming Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Gad A Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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8
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Hu X, Zhu B, Vokes N, Fujimoto J, Rojas Alvarez FR, Heeke S, Moreira AL, Solis LM, Haymaker C, Velcheti V, Sterman DH, Pass HI, Cheng C, Lee JJ, Zhang J, Wei Z, Wu J, Le X, Ostrin E, Toumazis I, Gibbons D, Su D, Fukuoka J, Antonoff MB, Gerber DE, Li C, Kadara H, Wang L, Davis M, Heymach JV, Hannash S, Wistuba I, Dubinett S, Alexandrov L, Lippman S, Spira A, Futreal AP, Reuben A, Zhang J. The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. RESEARCH SQUARE 2024:rs.3.rs-4396272. [PMID: 38798564 PMCID: PMC11118701 DOI: 10.21203/rs.3.rs-4396272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Studying lung adenocarcinoma (LUAD) early carcinogenesis is challenging, primarily due to the lack of LUAD precursors specimens. We amassed multi-omics data from 213 LUAD and LUAD precursors to identify molecular features underlying LUAD precancer evolution. We observed progressively increasing mutations, chromosomal aberrations, whole genome doubling and genomic instability from precancer to invasive LUAD, indicating aggravating chromosomal instability (CIN). Telomere shortening, a crucial genomic alteration linked to CIN, emerged at precancer stage. Moreover, later-stage lesions demonstrated increasing cancer stemness and decreasing alveolar identity, suggesting epithelial de-differentiation during early LUAD carcinogenesis. The innate immune cells progressively diminished from precancer to invasive LUAD, concomitant with a gradual recruitment of adaptive immune cells (except CD8+ and gamma-delta T cells that decreased in later stages) and upregulation of numerous immune checkpoints, suggesting LUAD precancer evolution is associated with a shift from innate to adaptive immune response and immune evasion mediated by various mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bo Zhu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natalie Vokes
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Frank R. Rojas Alvarez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Simon Heeke
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andre L. Moreira
- Department of Pathology, New York University Langone Medical Center, New York, 10012, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vamsidhar Velcheti
- Department of Medical oncology, New York University, New York, 10012, USA
| | | | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, 10016, USA
| | - Chao Cheng
- Department of Medicine, Epidemiology and Population Science, Baylor College of Medicine. Houston, TX, 77030, USA
| | - Jack J. Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhubo Wei
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiuning Le
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Iakovos Toumazis
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Mara B. Antonoff
- Department of Thoracic & Cardiovasc Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David E. Gerber
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chenyang Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark Davis
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - John V. Heymach
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Steven Dubinett
- Departments of Medicine and Pathology, University of California Los Angeles and Greater Los Angeles Healthcare System, Los Angeles, CA, 90095, USA
| | - Ludmil Alexandrov
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Scott Lippman
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Avrum Spira
- Pathology & Laboratory Medicine, and Bioinformatics, Boston University, Boston, MA, 02215, USA
| | - Andrew P. Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Lead contact
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9
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Ya A, Deng C, Godek KM. Cell Competition Eliminates Aneuploid Human Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593217. [PMID: 38766106 PMCID: PMC11100710 DOI: 10.1101/2024.05.08.593217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Human pluripotent stem cells (hPSCs) maintain diploid populations for generations despite a persistently high rate of mitotic errors that cause aneuploidy, or chromosome imbalances. Consequently, to maintain genome stability, aneuploidy must inhibit hPSC proliferation, but the mechanisms are unknown. Here, we surprisingly find that homogeneous aneuploid populations of hPSCs proliferate unlike aneuploid non-transformed somatic cells. Instead, in mosaic populations, cell non-autonomous competition between neighboring diploid and aneuploid hPSCs eliminates less fit aneuploid cells. Aneuploid hPSCs with lower Myc or higher p53 levels relative to diploid neighbors are outcompeted but conversely gain a selective advantage when Myc and p53 relative abundance switches. Thus, although hPSCs frequently missegregate chromosomes and inherently tolerate aneuploidy, Myc- and p53-driven cell competition preserves their genome integrity. These findings have important implications for the use of hPSCs in regenerative medicine and for how diploid human embryos are established despite the prevalence of aneuploidy during early development.
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Affiliation(s)
- Amanda Ya
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Chenhui Deng
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Kristina M. Godek
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Lead contact
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10
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Hou Y, Zhang C, Liu L, Yu Y, Shi L, Qin Y. WDR61 ablation triggers R-loop accumulation and suppresses breast cancer progression. FEBS J 2024. [PMID: 38708718 DOI: 10.1111/febs.17145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/09/2024] [Accepted: 04/12/2024] [Indexed: 05/07/2024]
Abstract
Although, superkiller complex protein 8 (SKI8), previously known as WDR61 has been identified and mapped in breast tumor, little is currently known about its function. This study aims to elucidate the role of WDR61 in breast tumor development and its potential as a therapeutic target. Here, we show that tamoxifen-induced knockout of Wdr61 reduces the risk of breast tumors, resulting in smaller tumor size and weight, and improved overall survival. Furthermore, we show that knockdown of WDR61 compromises the proliferation of breast tumor cells with reduced colony-forming capacity. Further investigations demonstrate that the protective effect of WDR61 loss on breast tumor development is due to genomic instability. Mechanistic studies reveal that WDR61 interacts with the R-loop, and loss of WDR61 leads to R-loops accumulation in breast tumor cells, causing DNA damage and subsequent inhibition of cell proliferation. In summary, this study highlights the critical dependence of breast tumors on WDR61, which suppresses R-loop and counteracts endogenous DNA damage in tumor cells.
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Affiliation(s)
- Yayan Hou
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, China
| | - Chunyong Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, China
| | - Ling Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, China
| | - Ying Yu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, China
| | - Lei Shi
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, China
| | - Yan Qin
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, China
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11
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Watson EV, Lee JJK, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet 2024; 56:900-912. [PMID: 38388848 PMCID: PMC11096114 DOI: 10.1038/s41588-024-01665-2] [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: 03/16/2022] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Whole chromosome and arm-level copy number alterations occur at high frequencies in tumors, but their selective advantages, if any, are poorly understood. Here, utilizing unbiased whole chromosome genetic screens combined with in vitro evolution to generate arm- and subarm-level events, we iteratively selected the fittest karyotypes from aneuploidized human renal and mammary epithelial cells. Proliferation-based karyotype selection in these epithelial lines modeled tissue-specific tumor aneuploidy patterns in patient cohorts in the absence of driver mutations. Hi-C-based translocation mapping revealed that arm-level events usually emerged in multiples of two via centromeric translocations and occurred more frequently in tetraploids than diploids, contributing to the increased diversity in evolving tetraploid populations. Isogenic clonal lineages enabled elucidation of pro-tumorigenic mechanisms associated with common copy number alterations, revealing Notch signaling potentiation as a driver of 1q gain in breast cancer. We propose that intrinsic, tissue-specific proliferative effects underlie tumor copy number patterns in cancer.
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Affiliation(s)
- Emma V Watson
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Giorgio E M Melloni
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rayna Y Magesh
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Abdulrazak Frederick
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kunitoshi Chiba
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Eric C Wooten
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Kamila Naxerova
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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12
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Guscott MA, McClelland SE. Experimental evolution of cancer chromosomal changes. Nat Genet 2024; 56:743-745. [PMID: 38684897 DOI: 10.1038/s41588-024-01742-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Affiliation(s)
- Molly A Guscott
- Barts Cancer Institute, Queen Mary University of London, London, UK
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13
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Lubachowski M, VanGenderen C, Valentine S, Belak Z, Davies GF, Arnason TG, Harkness TAA. Activation of the Anaphase Promoting Complex Restores Impaired Mitotic Progression and Chemosensitivity in Multiple Drug-Resistant Human Breast Cancer. Cancers (Basel) 2024; 16:1755. [PMID: 38730707 PMCID: PMC11083742 DOI: 10.3390/cancers16091755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
The development of multiple-drug-resistant (MDR) cancer all too often signals the need for toxic alternative therapy or palliative care. Our recent in vivo and in vitro studies using canine MDR lymphoma cancer cells demonstrate that the Anaphase Promoting Complex (APC) is impaired in MDR cells compared to normal canine control and drug-sensitive cancer cells. Here, we sought to establish whether this phenomena is a generalizable mechanism independent of species, malignancy type, or chemotherapy regime. To test the association of blunted APC activity with MDR cancer behavior, we used matched parental and MDR MCF7 human breast cancer cells, and a patient-derived xenograft (PDX) model of human triple-negative breast cancer. We show that APC activating mechanisms, such as APC subunit 1 (APC1) phosphorylation and CDC27/CDC20 protein associations, are reduced in MCF7 MDR cells when compared to chemo-sensitive matched cell lines. Consistent with impaired APC function in MDR cells, APC substrate proteins failed to be effectively degraded. Similar to our previous observations in canine MDR lymphoma cells, chemical activation of the APC using Mad2 Inhibitor-1 (M2I-1) in MCF7 MDR cells enhanced APC substrate degradation and resensitized MDR cells in vitro to the cytotoxic effects of the alkylating chemotherapeutic agent, doxorubicin (DOX). Using cell cycle arrest/release experiments, we show that mitosis is delayed in MDR cells with elevated substrate levels. When pretreated with M2I-1, MDR cells progress through mitosis at a faster rate that coincides with reduced levels of APC substrates. In our PDX model, mice growing a clinically MDR human triple-negative breast cancer tumor show significantly reduced tumor growth when treated with M2I-1, with evidence of increased DNA damage and apoptosis. Thus, our results strongly support the hypothesis that APC impairment is a driver of aggressive tumor development and that targeting the APC for activation has the potential for meaningful clinical benefits in treating recurrent cases of MDR malignancy.
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Affiliation(s)
- Mathew Lubachowski
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
- Division of Geriatrics, Department of Medicine, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Cordell VanGenderen
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (C.V.); (S.V.); (T.G.A.)
| | - Sarah Valentine
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (C.V.); (S.V.); (T.G.A.)
| | - Zach Belak
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
| | - Gerald Floyd Davies
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
| | - Terra Gayle Arnason
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (C.V.); (S.V.); (T.G.A.)
- Division of Endocrinology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2S2, Canada
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Troy Anthony Alan Harkness
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada; (M.L.); (Z.B.); (G.F.D.)
- Division of Geriatrics, Department of Medicine, University of Alberta, Edmonton, AB T6G 2S2, Canada
- 320 Heritage Medical Research Centre, University of Alberta, 11207-87 Ave NW, Edmonton, AB T6G 2S2, Canada
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14
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Bao K, Ma Y, Li Y, Shen X, Zhao J, Tian S, Zhang C, Liang C, Zhao Z, Yang Y, Zhang K, Yang N, Meng FL, Hao J, Yang J, Liu T, Yao Z, Ai D, Shi L. A di-acetyl-decorated chromatin signature couples liquid condensation to suppress DNA end synapsis. Mol Cell 2024; 84:1206-1223.e15. [PMID: 38423014 DOI: 10.1016/j.molcel.2024.02.002] [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: 07/26/2023] [Revised: 12/27/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Appropriate DNA end synapsis, regulated by core components of the synaptic complex including KU70-KU80, LIG4, XRCC4, and XLF, is central to non-homologous end joining (NHEJ) repair of chromatinized DNA double-strand breaks (DSBs). However, it remains enigmatic whether chromatin modifications can influence the formation of NHEJ synaptic complex at DNA ends, and if so, how this is achieved. Here, we report that the mitotic deacetylase complex (MiDAC) serves as a key regulator of DNA end synapsis during NHEJ repair in mammalian cells. Mechanistically, MiDAC removes combinatorial acetyl marks on histone H2A (H2AK5acK9ac) around DSB-proximal chromatin, suppressing hyperaccumulation of bromodomain-containing protein BRD4 that would otherwise undergo liquid-liquid phase separation with KU80 and prevent the proper installation of LIG4-XRCC4-XLF onto DSB ends. This study provides mechanistic insight into the control of NHEJ synaptic complex assembly by a specific chromatin signature and highlights the critical role of H2A hypoacetylation in restraining unscheduled compartmentalization of DNA repair machinery.
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Affiliation(s)
- Kaiwen Bao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanhui Ma
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yuan Li
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xilin Shen
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jiao Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shanshan Tian
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chunyong Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Can Liang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ziyan Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Yang
- Core Facilities Center, Capital Medical University, Beijing, China
| | - Kai Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jihui Hao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhi Yao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ding Ai
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Lei Shi
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
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15
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Marlin R, Loger JS, Joachim C, Ebring C, Robert-Siegwald G, Pennont S, Rose M, Raguette K, Suez-Panama V, Ulric-Gervaise S, Lusbec S, Bera O, Vallard A, Aline-Fardin A, Colomba E, Jean-Laurent M. Copy number signatures and CCNE1 amplification reveal the involvement of replication stress in high-grade endometrial tumors oncogenesis. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00942-w. [PMID: 38564163 DOI: 10.1007/s13402-024-00942-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Managing high-grade endometrial cancer in Martinique poses significant challenges. The diversity of copy number alterations in high-grade endometrial tumors, often associated with a TP53 mutation, is a key factor complicating treatment. Due to the high incidence of high-grade tumors with poor prognosis, our study aimed to characterize the molecular signature of these tumors within a cohort of 25 high-grade endometrial cases. METHODS We conducted a comprehensive pangenomic analysis to categorize the copy number alterations involved in these tumors. Whole-Exome Sequencing (WES) and Homologous Recombination (HR) analysis were performed. The alterations obtained from the WES were classified into various signatures using the Copy Number Signatures tool available in COSMIC. RESULTS We identified several signatures that correlated with tumor stage and disctinct prognoses. These signatures all seem to be linked to replication stress, with CCNE1 amplification identified as the primary driver of oncogenesis in over 70% of tumors analyzed. CONCLUSION The identification of CCNE1 amplification, which is currently being explored as a therapeutic target in clinical trials, suggests new treatment strategies for high-grade endometrial cancer. This finding holds particular significance for Martinique, where access to care is challenging.
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Affiliation(s)
- Regine Marlin
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique.
| | - Jean-Samuel Loger
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Clarisse Joachim
- General Cancer Registry of Martinique, University Hospital of Martinique, Fort-de-France, Martinique
| | - Coralie Ebring
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
| | - Guillaume Robert-Siegwald
- MitoVasc Unit, SFR ICAT, Mitolab Team, UMR CNRS 6015 INSERM U1083, University of Angers, Angers, France
| | - Sabrina Pennont
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Mickaelle Rose
- Martinique Regional Oncology Platform, University Hospital of Martinique, Fort-de-France, Martinique
| | - Kevin Raguette
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Valerie Suez-Panama
- Biological Resource Center, University Hospital of Martinique, Fort-de-France, Martinique
| | - Sylviane Ulric-Gervaise
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Sylvie Lusbec
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
| | - Odile Bera
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Alexis Vallard
- Department of Oncology Hematology Urology, University Hospital of Martinique, Fort-de-France, Martinique
| | | | - Emeline Colomba
- Department of Cancer Medicine, Institut Gustave Roussy, University of Paris Saclay, Gif-sur-Yvette, France
| | - Mehdi Jean-Laurent
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
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16
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Chen S, Pan C, Huang J, Liu T. ATR limits Rad18-mediated PCNA monoubiquitination to preserve replication fork and telomerase-independent telomere stability. EMBO J 2024; 43:1301-1324. [PMID: 38467834 PMCID: PMC10987609 DOI: 10.1038/s44318-024-00066-9] [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: 09/14/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Upon replication fork stalling, the RPA-coated single-stranded DNA (ssDNA) formed behind the fork activates the ataxia telangiectasia-mutated and Rad3-related (ATR) kinase, concomitantly initiating Rad18-dependent monoubiquitination of PCNA. However, whether crosstalk exists between these two events and the underlying physiological implications of this interplay remain elusive. In this study, we demonstrate that during replication stress, ATR phosphorylates human Rad18 at Ser403, an adjacent residue to a previously unidentified PIP motif (PCNA-interacting peptide) within Rad18. This phosphorylation event disrupts the interaction between Rad18 and PCNA, thereby restricting the extent of Rad18-mediated PCNA monoubiquitination. Consequently, excessive accumulation of the tumor suppressor protein SLX4, now characterized as a novel reader of ubiquitinated PCNA, at stalled forks is prevented, contributing to the prevention of stalled fork collapse. We further establish that ATR preserves telomere stability in alternative lengthening of telomere (ALT) cells by restricting Rad18-mediated PCNA monoubiquitination and excessive SLX4 accumulation at telomeres. These findings shed light on the complex interplay between ATR activation, Rad18-dependent PCNA monoubiquitination, and SLX4-associated stalled fork processing, emphasizing the critical role of ATR in preserving replication fork stability and facilitating telomerase-independent telomere maintenance.
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Affiliation(s)
- Siyuan Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chen Pan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China.
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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17
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Jin T, Ding L, Chen J, Zou X, Xu T, Xuan Z, Wang S, Chen J, Wang W, Zhu C, Zhang Y, Huang P, Pan Z, Ge M. BUB1/KIF14 complex promotes anaplastic thyroid carcinoma progression by inducing chromosome instability. J Cell Mol Med 2024; 28:e18182. [PMID: 38498903 PMCID: PMC10948175 DOI: 10.1111/jcmm.18182] [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: 03/16/2023] [Revised: 01/21/2024] [Accepted: 02/05/2024] [Indexed: 03/20/2024] Open
Abstract
Chromosome instability (CIN) is a common contributor driving the formation and progression of anaplastic thyroid cancer (ATC), but its mechanism remains unclear. The BUB1 mitotic checkpoint serine/threonine kinase (BUB1) is responsible for the alignment of mitotic chromosomes, which has not been thoroughly studied in ATC. Our research demonstrated that BUB1 was remarkably upregulated and closely related to worse progression-free survival. Knockdown of BUB1 attenuated cell viability, invasion, migration and induced cell cycle arrests, whereas overexpression of BUB1 promoted the cell cycle progression of papillary thyroid cancer cells. BUB1 knockdown remarkably repressed tumour growth and tumour formation of nude mice with ATC xenografts and suppressed tumour metastasis in a zebrafish xenograft model. Inhibition of BUB1 by its inhibitor BAY-1816032 also exhibited considerable anti-tumour activity. Further studies showed that enforced expression of BUB1 evoked CIN in ATC cells. BUB1 induced CIN through phosphorylation of KIF14 at serine1292 (Ser1292 ). Overexpression of the KIF14ΔSer1292 mutant was unable to facilitate the aggressiveness of ATC cells when compared with that of the wild type. Collectively, these findings demonstrate that the BUB1/KIF14 complex drives the aggressiveness of ATC by inducing CIN.
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Affiliation(s)
- Tiefeng Jin
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck SurgeryZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Lingling Ding
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck SurgeryZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Jinming Chen
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Xiaozhou Zou
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Tong Xu
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Zixue Xuan
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Shanshan Wang
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Jianqiang Chen
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Wei Wang
- Department of Pathology, Laboratory Medicine CenterZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Chaozhuang Zhu
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
| | - Yiwen Zhang
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouChina
| | - Ping Huang
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouChina
| | - Zongfu Pan
- Center for Clinical Pharmacy, Cancer Center, Department of PharmacyZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouChina
| | - Minghua Ge
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck SurgeryZhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical CollegeHangzhouChina
- Key Laboratory of Endocrine Gland Diseases of Zhejiang ProvinceHangzhouChina
- Clinical Research Center for Cancer of Zhejiang ProvinceHangzhouChina
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18
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Hosea R, Hillary S, Naqvi S, Wu S, Kasim V. The two sides of chromosomal instability: drivers and brakes in cancer. Signal Transduct Target Ther 2024; 9:75. [PMID: 38553459 PMCID: PMC10980778 DOI: 10.1038/s41392-024-01767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 04/02/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and is associated with tumor cell malignancy. CIN triggers a chain reaction in cells leading to chromosomal abnormalities, including deviations from the normal chromosome number or structural changes in chromosomes. CIN arises from errors in DNA replication and chromosome segregation during cell division, leading to the formation of cells with abnormal number and/or structure of chromosomes. Errors in DNA replication result from abnormal replication licensing as well as replication stress, such as double-strand breaks and stalled replication forks; meanwhile, errors in chromosome segregation stem from defects in chromosome segregation machinery, including centrosome amplification, erroneous microtubule-kinetochore attachments, spindle assembly checkpoint, or defective sister chromatids cohesion. In normal cells, CIN is deleterious and is associated with DNA damage, proteotoxic stress, metabolic alteration, cell cycle arrest, and senescence. Paradoxically, despite these negative consequences, CIN is one of the hallmarks of cancer found in over 90% of solid tumors and in blood cancers. Furthermore, CIN could endow tumors with enhanced adaptation capabilities due to increased intratumor heterogeneity, thereby facilitating adaptive resistance to therapies; however, excessive CIN could induce tumor cells death, leading to the "just-right" model for CIN in tumors. Elucidating the complex nature of CIN is crucial for understanding the dynamics of tumorigenesis and for developing effective anti-tumor treatments. This review provides an overview of causes and consequences of CIN, as well as the paradox of CIN, a phenomenon that continues to perplex researchers. Finally, this review explores the potential of CIN-based anti-tumor therapy.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Sumera Naqvi
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400045, China.
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing, 400030, China.
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19
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Wang B, Dong J, Yang F, Ju T, Wang J, Qu K, Wang Y, Tian Y, Wang Z. Determining the degree of chromosomal instability in breast cancer cells by atomic force microscopy. Analyst 2024; 149:1988-1997. [PMID: 38420857 DOI: 10.1039/d3an01815f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Chromosomal instability (CIN) is a source of genetic variation and is highly linked to the malignance of cancer. Determining the degree of CIN is necessary for understanding the role that it plays in tumor development. There is currently a lack of research on high-resolution characterization of CIN and the relationship between CIN and cell mechanics. Here, a method to determine CIN of breast cancer cells by high resolution imaging with atomic force microscopy (AFM) is explored. The numerical and structural changes of chromosomes in human breast cells (MCF-10A), moderately malignant breast cells (MCF-7) and highly malignant breast cells (MDA-MB-231) were observed and analyzed by AFM. Meanwhile, the nuclei, cytoskeleton and cell mechanics of the three kinds of cells were also investigated. The results showed the differences in CIN between the benign and cancer cells. Also, the degree of structural CIN increased with enhanced malignancy of cancer cells. This was also demonstrated by calculating the probability of micronucleus formation in these three kinds of cells. Meanwhile, we found that the area of the nucleus was related to the number of chromosomes in the nucleus. In addition, reduced or even aggregated actin fibers led to decreased elasticities in MCF-7 and MDA-MB-231 cells. It was found that the rearrangement of actin fibers would affect the nucleus, and then lead to wrong mitosis and CIN. Using AFM to detect chromosomal changes in cells with different malignancy degrees provides a new detection method for the study of cell carcinogenesis with a perspective for targeted therapy of cancer.
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Affiliation(s)
- Bowei Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Jianjun Dong
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Fan Yang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Tuoyu Ju
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Junxi Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Kaige Qu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Ying Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Yanling Tian
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- JR3CN & IRAC, University of Bedfordshire, Luton LU1 3JU, UK
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20
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Benedetti F, Silvestri G, Denaro F, Finesso G, Contreras-Galindo R, Munawwar A, Williams S, Davis H, Bryant J, Wang Y, Radaelli E, Rathinam CV, Gallo RC, Zella D. Mycoplasma DnaK expression increases cancer development in vivo upon DNA damage. Proc Natl Acad Sci U S A 2024; 121:e2320859121. [PMID: 38412130 DOI: 10.1073/pnas.2320859121] [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: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
Well-controlled repair mechanisms are involved in the maintenance of genomic stability, and their failure can precipitate DNA abnormalities and elevate tumor risk. In addition, the tumor microenvironment, enriched with factors inducing oxidative stress and affecting cell cycle checkpoints, intensifies DNA damage when repair pathways falter. Recent research has unveiled associations between certain bacteria, including Mycoplasmas, and various cancers, and the causative mechanism(s) are under active investigation. We previously showed that Mycoplasma fermentans DnaK, an HSP70 family chaperone protein, hampers the activity of proteins like PARP1 and p53, crucial for genomic integrity. Moreover, our analysis of its interactome in human cancer cell lines revealed DnaK's engagement with several components of DNA-repair machinery. Finally, in vivo experiments performed in our laboratory using a DnaK knock-in mouse model generated by our group demonstrated that DnaK exposure led to increased DNA copy number variants, indicative of genomic instability. We present here evidence that expression of DnaK is linked to increased i) incidence of tumors in vivo upon exposure to urethane, a DNA damaging agent; ii) spontaneous DNA damage ex vivo; and iii) expression of proinflammatory cytokines ex vivo, variations in reactive oxygen species levels, and increased β-galactosidase activity across tissues. Moreover, DnaK was associated with increased centromeric instability. Overall, these findings highlight the significance of Mycoplasma DnaK in the etiology of cancer and other genetic disorders providing a promising target for prevention, diagnostics, and therapeutics.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Giovannino Silvestri
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Frank Denaro
- Department of Biology, Morgan State University, Baltimore, MD 21251
| | - Giovanni Finesso
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Arshi Munawwar
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Sumiko Williams
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biology, Morgan State University, Baltimore, MD 21251
| | - Harry Davis
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Joseph Bryant
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Yin Wang
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Surgery, School of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Enrico Radaelli
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Chozha V Rathinam
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Robert C Gallo
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201
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21
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Shih YL, Hsu SY, Lai KC, Chueh FS, Huang YL, Kuo CL, Chen YL, Chen CJ, Peng SF, Huang WW, Lu HF. Allyl isothiocyanate induces DNA damage and inhibits DNA repair-associated proteins in a human gastric cancer cells in vitro. ENVIRONMENTAL TOXICOLOGY 2024; 39:1303-1314. [PMID: 37966020 DOI: 10.1002/tox.24020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/07/2023] [Accepted: 10/07/2023] [Indexed: 11/16/2023]
Abstract
Allyl isothiocyanate (AITC) is abundant in cruciferous vegetables and it present pharmacological activity including anticancer activity in many types of human cancer cells in vitro and in vivo. Currently, no available information to show AITC affecting DNA damage and repair-associated protein expression in human gastric cancer cells. Therefore, in the present studies, we investigated AITC-induced cytotoxic effects on human gastric cancer in AGS and SNU-1 cells whether or not via the induction of DNA damage and affected DNA damage and repair associated poteins expressions in vitro. Cell viability and morphological changes were assayed by flow cytometer and phase contrast microscopy, respectively, the results indicated AITC induced cell morphological changes and decreased total viable cells in AGS and SNU-1 cells in a dose-dependently. AITC induced DNA condensation and damage in a dose-dependently which based on the cell nuclei was stained by 4', 6-diamidino-2-phenylindole present in AGS and SNU-1 cells. DNA damage and repair associated proteins expression in AGS and SNU-1 cells were measured by Western blotting. The results indicated AITC decreased nuclear factor erythroid 2-related factor 2 (NRF2), heme oxygenase-1 (HO-1), glutathione, and catalase, but increased superoxide dismutase (SOD (Cu/Zn)), and nitric oxide synthase (iNOS) in AGS cells, however, in SNU-1 cells are increased HO-1. AITC increased DNA-dependent protein kinase (DNA-PK), phosphorylation of gamma H2A histone family member X on Ser139 (γH2AXpSer139 ), and heat shock protein 90 (HSP90) in AGS cells. AITC increased DNA-PK, mediator of DNA damage checkpoint protein 1 (MDC1), γH2AXpSer139 , topoisomerase II alpha (TOPIIα), topoisomerase II beta (TOPIIβ), HSP90, and heat shock protein 70 (HSP70) in SNU-1 cells. AITC increased p53, p53pSer15 , and p21 but decreased murine double minute 2 (MDM2)pSer166 and O6 -methylguanine-DNA methyltransferase (MGMT) in AGS cells; however, it has a similar effect of AITC except increased ataxia telangiectasia and Rad3 -related protein (ATR)pSer428 , checkpoint kinase 1 (CHK1), and checkpoint kinase 2 (CHK2) in SNU-1 cells. Apparently, both cell responses to AITC are different, nonetheless, all of these observations suggest that AITC inhibits the growth of gastric cancer cells may through induction off DNA damage in vitro.
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Affiliation(s)
- Yung-Luen Shih
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei, Taiwan
- Department of Pathology and Laboratory Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Sheng-Yao Hsu
- Department of Ophthalmology, An Nan Hospital, China Medical University, Tainan, Taiwan
- Department of Optometry, Chung Hwa University of Medical Technology, Tainan, Taiwan
| | - Kuang-Chi Lai
- Department of Surgery, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung Hwa University of Medical Technology, Tainan, Taiwan
| | - Fu-Shin Chueh
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung, Taiwan
| | - Yuan-Li Huang
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Chao-Lin Kuo
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan
| | - Yung-Liang Chen
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University, Hsinchu, Taiwan
| | - Chiung-Ju Chen
- Department of Pathology and Laboratory Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
- Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli, Taiwan
| | - Shu-Fen Peng
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
| | - Wen-Wen Huang
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
| | - Hsu-Fen Lu
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
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22
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Day M, Tetik B, Parlak M, Almeida-Hernández Y, Räschle M, Kaschani F, Siegert H, Marko A, Sanchez-Garcia E, Kaiser M, Barker IA, Pearl LH, Oliver AW, Boos D. TopBP1 utilises a bipartite GINS binding mode to support genome replication. Nat Commun 2024; 15:1797. [PMID: 38413589 PMCID: PMC10899662 DOI: 10.1038/s41467-024-45946-0] [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: 06/21/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Activation of the replicative Mcm2-7 helicase by loading GINS and Cdc45 is crucial for replication origin firing, and as such for faithful genetic inheritance. Our biochemical and structural studies demonstrate that the helicase activator GINS interacts with TopBP1 through two separate binding surfaces, the first involving a stretch of highly conserved amino acids in the TopBP1-GINI region, the second a surface on TopBP1-BRCT4. The two surfaces bind to opposite ends of the A domain of the GINS subunit Psf1. Mutation analysis reveals that either surface is individually able to support TopBP1-GINS interaction, albeit with reduced affinity. Consistently, either surface is sufficient for replication origin firing in Xenopus egg extracts and becomes essential in the absence of the other. The TopBP1-GINS interaction appears sterically incompatible with simultaneous binding of DNA polymerase epsilon (Polε) to GINS when bound to Mcm2-7-Cdc45, although TopBP1-BRCT4 and the Polε subunit PolE2 show only partial competitivity in binding to Psf1. Our TopBP1-GINS model improves the understanding of the recently characterised metazoan pre-loading complex. It further predicts the coordination of three molecular origin firing processes, DNA polymerase epsilon arrival, TopBP1 ejection and GINS integration into Mcm2-7-Cdc45.
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Affiliation(s)
- Matthew Day
- School of Biological and Behavioural Sciences, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Bilal Tetik
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Milena Parlak
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Räschle
- Molecular Genetics, Technical University Kaiserslautern, Paul-Ehrlich Straße 24, 67663, Kaiserslautern, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Heike Siegert
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Anika Marko
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Kaiser
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Isabel A Barker
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK.
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Dominik Boos
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany.
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23
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Ma W, Zhou T, Song M, Liu J, Chen G, Zhan J, Ji L, Luo F, Gao X, Li P, Xia X, Huang Y, Zhang L. Genomic and transcriptomic profiling of combined small-cell lung cancer through microdissection: unveiling the transformational pathway of mixed subtype. J Transl Med 2024; 22:189. [PMID: 38383412 PMCID: PMC10880258 DOI: 10.1186/s12967-024-04968-4] [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: 12/20/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Combined small-cell lung carcinoma (cSCLC) represents a rare subtype of SCLC, the mechanisms governing the evolution of cancer genomes and their impact on the tumor immune microenvironment (TIME) within distinct components of cSCLC remain elusive. METHODS Here, we conducted whole-exome and RNA sequencing on 32 samples from 16 cSCLC cases. RESULTS We found striking similarities between two components of cSCLC-LCC/LCNEC (SCLC combined with large-cell carcinoma/neuroendocrine) in terms of tumor mutation burden (TMB), tumor neoantigen burden (TNB), clonality structure, chromosomal instability (CIN), and low levels of immune cell infiltration. In contrast, the two components of cSCLC-ADC/SCC (SCLC combined with adenocarcinoma/squamous-cell carcinoma) exhibited a high level of tumor heterogeneity. Our investigation revealed that cSCLC originated from a monoclonal source, with two potential transformation modes: from SCLC to SCC (mode 1) and from ADC to SCLC (mode 2). Therefore, cSCLC might represent an intermediate state, potentially evolving into another histological tumor morphology through interactions between tumor and TIME surrounding it. Intriguingly, RB1 inactivation emerged as a factor influencing TIME heterogeneity in cSCLC, possibly through neoantigen depletion. CONCLUSIONS Together, these findings delved into the clonal origin and TIME heterogeneity of different components in cSCLC, shedding new light on the evolutionary processes underlying this enigmatic subtype.
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Affiliation(s)
- Wenjuan Ma
- Department of Intensive Care Unit, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Ting Zhou
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Mengmeng Song
- Geneplus-Beijing Institute, Beijing, 102206, People's Republic of China
| | - Jiaqing Liu
- Department of Intensive Care Unit, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Gang Chen
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Jianhua Zhan
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Liyan Ji
- Geneplus-Beijing Institute, Beijing, 102206, People's Republic of China
| | - Fan Luo
- Department of Intensive Care Unit, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, Guangdong, People's Republic of China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing, 102206, People's Republic of China
| | - Pansong Li
- Geneplus-Beijing Institute, Beijing, 102206, People's Republic of China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing, 102206, People's Republic of China
| | - Yan Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China.
| | - Li Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, People's Republic of China.
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24
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Peripolli S, Meneguello L, Perrod C, Singh T, Patel H, Rahman ST, Kiso K, Thorpe P, Calvanese V, Bertoli C, de Bruin RAM. Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy in a CTCF-dependent manner. Nat Commun 2024; 15:1579. [PMID: 38383676 PMCID: PMC10881979 DOI: 10.1038/s41467-024-45955-z] [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: 11/04/2020] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Oncogene-induced replication stress is a crucial driver of genomic instability and one of the key events contributing to the onset and evolution of cancer. Despite its critical role in cancer, the mechanisms that generate oncogene-induced replication stress remain not fully understood. Here, we report that an oncogenic c-Myc-dependent increase in cohesins on DNA contributes to the induction of replication stress. Accumulation of cohesins on chromatin is not sufficient to cause replication stress, but also requires cohesins to accumulate at specific sites in a CTCF-dependent manner. We propose that the increased accumulation of cohesins at CTCF site interferes with the progression of replication forks, contributing to oncogene-induced replication stress. This is different from, and independent of, previously suggested mechanisms of oncogene-induced replication stress. This, together with the reported protective role of cohesins in preventing replication stress-induced DNA damage, supports a double-edge involvement of cohesins in causing and tolerating oncogene-induced replication stress.
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Affiliation(s)
- Silvia Peripolli
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Leticia Meneguello
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
- UCL Cancer Institute, University College London, Gower Street, London, UK
| | - Chiara Perrod
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Tanya Singh
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | | | - Sazia T Rahman
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Koshiro Kiso
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Peter Thorpe
- Queen Mary University, Mile End Road, London, UK
| | - Vincenzo Calvanese
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK
| | - Cosetta Bertoli
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK.
| | - Robertus A M de Bruin
- Laboratory Molecular Cell Biology, University College London, Gower Street, London, UK.
- UCL Cancer Institute, University College London, Gower Street, London, UK.
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25
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Keuper K, Bartek J, Maya-Mendoza A. The nexus of nuclear envelope dynamics, circular economy and cancer cell pathophysiology. Eur J Cell Biol 2024; 103:151394. [PMID: 38340500 DOI: 10.1016/j.ejcb.2024.151394] [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: 10/29/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
The nuclear envelope (NE) is a critical component in maintaining the function and structure of the eukaryotic nucleus. The NE and lamina are disassembled during each cell cycle to enable an open mitosis. Nuclear architecture construction and deconstruction is a prime example of a circular economy, as it fulfills a highly efficient recycling program bound to continuous assessment of the quality and functionality of the building blocks. Alterations in the nuclear dynamics and lamina structure have emerged as important contributors to both oncogenic transformation and cancer progression. However, the knowledge of the NE breakdown and reassembly is still limited to a fraction of participating proteins and complexes. As cancer cells contain highly diverse nuclei in terms of DNA content, but also in terms of nuclear number, size, and shape, it is of great interest to understand the intricate relationship between these nuclear features in cancer cell pathophysiology. In this review, we provide insights into how those NE dynamics are regulated, and how lamina destabilization processes may alter the NE circular economy. Moreover, we expand the knowledge of the lamina-associated domain region by using strategic algorithms, including Artificial Intelligence, to infer protein associations, assess their function and location, and predict cancer-type specificity with implications for the future of cancer diagnosis, prognosis and treatment. Using this approach we identified NUP98 and MECP2 as potential proteins that exhibit upregulation in Acute Myeloid Leukemia (LAML) patients with implications for early diagnosis.
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Affiliation(s)
- Kristina Keuper
- DNA Replication and Cancer Group, Danish Cancer Institute, Copenhagen, Denmark; Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SciLifeLab, Stockholm, Sweden
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26
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Joy J, Fusari E, Milán M. Aneuploidy-induced cellular behaviors: Insights from Drosophila. Dev Cell 2024; 59:295-307. [PMID: 38320484 DOI: 10.1016/j.devcel.2023.12.009] [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: 02/02/2023] [Revised: 08/09/2023] [Accepted: 12/15/2023] [Indexed: 02/08/2024]
Abstract
A balanced gene complement is crucial for proper cell function. Aneuploidy, the condition of having an imbalanced chromosome set, alters the stoichiometry of gene copy numbers and protein complexes and has dramatic consequences at the cellular and organismal levels. In humans, aneuploidy is associated with different pathological conditions including cancer, microcephaly, mental retardation, miscarriages, and aging. Over the last century, Drosophila has provided a valuable system for studying the consequences of systemic aneuploidies. More recently, it has contributed to the identification and molecular dissection of aneuploidy-induced cellular behaviors and their impact at the tissue and organismal levels. In this perspective, we review this active field of research, first by comparing knowledge from yeast, mouse, and human cells, then by highlighting the contributions of Drosophila. The aim of these discussions was to further our understanding of the functional interplay between aneuploidy, cell physiology, and tissue homeostasis in human development and disease.
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Affiliation(s)
- Jery Joy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Elena Fusari
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Marco Milán
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10-12, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys, 23, 08010 Barcelona, Spain.
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27
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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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28
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Spoor JKH, den Braber M, Dirven CMF, Pennycuick A, Bartkova J, Bartek J, van Dis V, van den Bosch TPP, Leenstra S, Venkatesan S. Investigating chromosomal instability in long-term survivors with glioblastoma and grade 4 astrocytoma. Front Oncol 2024; 13:1218297. [PMID: 38260852 PMCID: PMC10800987 DOI: 10.3389/fonc.2023.1218297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Background Only a small group of patients with glioblastoma multiforme (GBM) survives more than 36 months, so-called long-term survivors. Recent studies have shown that chromosomal instability (CIN) plays a prognostic and predictive role among different cancer types. Here, we compared histological (chromosome missegregation) and bioinformatic metrics (CIN signatures) of CIN in tumors of GBM typical survivors (≤36 months overall survival), GBM long-term survivors and isocitrate dehydrogenase (IDH)-mutant grade 4 astrocytomas. Methods Tumor sections of all gliomas were examined for anaphases and chromosome missegregation. Further CIN signature activity analysis in the The Cancer Genome Atlas (TCGA)-GBM cohort was performed. Results Our data show that chromosome missegregation is pervasive in high grade gliomas and is not different between the 3 groups. We find only limited evidence of altered CIN levels in tumors of GBM long-term survivors relative to the other groups, since a significant depletion in CIN signature 11 relative to GBM typical survivors was the only alteration detected. In contrast, within IDH-mutant grade 4 astrocytomas we detected a significant enrichment of CIN signature 5 and 10 activities and a depletion of CIN signature 1 activity relative to tumors of GBM typical survivors. Conclusions Our data suggest that CIN is pervasive in high grade gliomas, however this is unlikely to be a major contributor to the phenomenon of long-term survivorship in GBM. Nevertheless, further evaluation of specific types of CIN (signatures) could have prognostic value in patients suffering from grade 4 gliomas.
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Affiliation(s)
- Jochem K. H. Spoor
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Paediatric Neurosurgery, Erasmus Medical Center Sophia Children’s Hospital, Rotterdam, Netherlands
| | - May den Braber
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Clemens M. F. Dirven
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Adam Pennycuick
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Jirina Bartkova
- Genome Integrity Group, Danish Cancer Institute, Danish Cancer Society, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Danish Cancer Society, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Vera van Dis
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Sieger Leenstra
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Subramanian Venkatesan
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Oncology, University College London, London, United Kingdom
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29
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Mazzagatti A, Engel JL, Ly P. Boveri and beyond: Chromothripsis and genomic instability from mitotic errors. Mol Cell 2024; 84:55-69. [PMID: 38029753 PMCID: PMC10842135 DOI: 10.1016/j.molcel.2023.11.002] [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: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023]
Abstract
Mitotic cell division is tightly monitored by checkpoints that safeguard the genome from instability. Failures in accurate chromosome segregation during mitosis can cause numerical aneuploidy, which was hypothesized by Theodor Boveri over a century ago to promote tumorigenesis. Recent interrogation of pan-cancer genomes has identified unexpected classes of chromosomal abnormalities, including complex rearrangements arising through chromothripsis. This process is driven by mitotic errors that generate abnormal nuclear structures that provoke extensive yet localized shattering of mis-segregated chromosomes. Here, we discuss emerging mechanisms underlying chromothripsis from micronuclei and chromatin bridges, as well as highlight how this mutational cascade converges on the DNA damage response. A fundamental understanding of these catastrophic processes will provide insight into how initial errors in mitosis can precipitate rapid cancer genome evolution.
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Affiliation(s)
- Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Justin L Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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30
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Chavli EA, Klaasen SJ, Van Opstal D, Laven JS, Kops GJ, Baart EB. Single-cell DNA sequencing reveals a high incidence of chromosomal abnormalities in human blastocysts. J Clin Invest 2024; 134:e174483. [PMID: 38175717 PMCID: PMC10940095 DOI: 10.1172/jci174483] [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: 08/04/2023] [Accepted: 01/02/2024] [Indexed: 01/05/2024] Open
Abstract
Aneuploidy, a deviation from the normal chromosome copy number, is common in human embryos and is considered a primary cause of implantation failure and early pregnancy loss. Meiotic errors lead to uniformly abnormal karyotypes, while mitotic errors lead to chromosomal mosaicism: the presence of cells with at least 2 different karyotypes within an embryo. Knowledge about mosaicism in blastocysts mainly derives from bulk DNA sequencing (DNA-Seq) of multicellular trophectoderm (TE) and/or inner cell mass (ICM) samples. However, this can only detect an average net gain or loss of DNA above a detection threshold of 20%-30%. To accurately assess mosaicism, we separated the TE and ICM of 55 good-quality surplus blastocysts and successfully applied single-cell whole-genome sequencing (scKaryo-Seq) on 1,057 cells. Mosaicism involving numerical and structural chromosome abnormalities was detected in 82% of the embryos, in which most abnormalities affected less than 20% of the cells. Structural abnormalities, potentially caused by replication stress and DNA damage, were observed in 69% of the embryos. In conclusion, our findings indicated that mosaicism was prevalent in good-quality blastocysts, whereas these blastocysts would likely be identified as normal with current bulk DNA-Seq techniques used for preimplantation genetic testing for aneuploidy.
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Affiliation(s)
- Effrosyni A. Chavli
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sjoerd J. Klaasen
- Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Joop S.E. Laven
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Geert J.P.L. Kops
- Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Esther B. Baart
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Developmental Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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31
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Liang Y, Wei X, Yue PJ, Zhang HC, Li ZN, Wang XX, Sun YY, Fu WN. MYCT1 inhibits hematopoiesis in diffuse large B-cell lymphoma by suppressing RUNX1 transcription. Cell Mol Biol Lett 2024; 29:5. [PMID: 38172714 PMCID: PMC10763471 DOI: 10.1186/s11658-023-00522-0] [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: 08/15/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The abnormality of chromosomal karyotype is one factor causing poor prognosis of lymphoma. In the analysis of abnormal karyotype of lymphoma patients, three smallest overlap regions were found, in which MYCT1 was located. MYCT1 is the first tumor suppressor gene cloned by our research team, but its studies relating to the occurrence and development of lymphoma have not been reported. METHODS R banding analyses were employed to screen the abnormality of chromosomal karyotype in clinical specimen and MYCT1 over-expression cell lines. FISH was to monitor MYCT1 copy number aberration. RT-PCR and Western blot were to detect the mRNA and protein levels of the MYCT1 and RUNX1 genes, respectively. The MYCT1 and RUNX1 protein levels in clinical specimen were evaluated by immunohistochemical DAB staining. The interaction between MYCT1 and MAX proteins was identified via Co-IP and IF. The binding of MAX on the promoter of the RUNX1 gene was detected by ChIP and Dual-luciferase reporter assay, respectively. Flow cytometry and CCK-8 assay were to explore the effects of MYCT1 and RUNX1 on the cell cycle and proliferation, respectively. RESULTS MYCT1 was located in one of three smallest overlap regions of diffuse large B-cell lymphoma, it altered chromosomal instability of diffuse large B-cell lymphoma cells. MYCT1 negatively correlated with RUNX1 in lymphoma tissues of the patients. MAX directly promoted the RUNX1 gene transcription by binding to its promoter region. MYCT1 may represses RUNX1 transcription by binding MAX in diffuse large B-cell lymphoma cells. MYCT1 binding to MAX probably suppressed RUNX1 transcription, leading to the inhibition of proliferation and cell cycle of the diffuse large B-cell lymphoma cells. CONCLUSION This study finds that there is a MYCT1-MAX-RUNX1 signaling pathway in diffuse large B-cell lymphoma. And the study provides clues and basis for the in-depth studies of MYCT1 in the diagnosis, treatment and prognosis of lymphoma.
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Affiliation(s)
- Ying Liang
- Department of Medical Genetics, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, People's Republic of China
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Xin Wei
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Peng-Jie Yue
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - He-Cheng Zhang
- Department of Medical Genetics, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, People's Republic of China
| | - Zhen-Ning Li
- Department of Oromaxillofacial-Head and Neck Surgery, Liaoning Province Key Laboratory of Oral Disease, School and Hospital of Stomatology, China Medical University, Shenyang, People's Republic of China
| | - Xiao-Xue Wang
- Department of Hematology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Yuan-Yuan Sun
- Department of Medical Genetics, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, People's Republic of China.
| | - Wei-Neng Fu
- Department of Medical Genetics, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, 110122, People's Republic of China.
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Tijhuis AE, Foijer F. Characterizing chromosomal instability-driven cancer evolution and cell fitness at a glance. J Cell Sci 2024; 137:jcs260199. [PMID: 38224461 DOI: 10.1242/jcs.260199] [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] [Indexed: 01/16/2024] Open
Abstract
Chromosomal instability (CIN), an increased rate of chromosome segregation errors during mitosis, is a hallmark of cancer cells. CIN leads to karyotype differences between cells and thus large-scale heterogeneity among individual cancer cells; therefore, it plays an important role in cancer evolution. Studying CIN and its consequences is technically challenging, but various technologies have been developed to track karyotype dynamics during tumorigenesis, trace clonal lineages and link genomic changes to cancer phenotypes at single-cell resolution. These methods provide valuable insight not only into the role of CIN in cancer progression, but also into cancer cell fitness. In this Cell Science at a Glance article and the accompanying poster, we discuss the relationship between CIN, cancer cell fitness and evolution, and highlight techniques that can be used to study the relationship between these factors. To that end, we explore methods of assessing cancer cell fitness, particularly for chromosomally unstable cancer.
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Affiliation(s)
- Andréa E Tijhuis
- European Research Institute for the Biology of Ageing , University Medical Center Groningen, University of Groningen,9713 AV Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing , University Medical Center Groningen, University of Groningen,9713 AV Groningen, The Netherlands
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Sun X, Dong M, Li J, Sun Y, Gao Y, Wang Y, Du L, Liu Y, Ji K, He N, Wang J, Zhang M, Song H, Xu C, Liu Q. NRF2 promotes radiation resistance by cooperating with TOPBP1 to activate the ATR-CHK1 signaling pathway. Theranostics 2024; 14:681-698. [PMID: 38169561 PMCID: PMC10758056 DOI: 10.7150/thno.88899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
Background: Radiation resistance is the main limitation of the application of radiotherapy. Ionizing radiation (IR) kills cancer cells mainly by causing DNA damage, particularly double-strand breaks (DSBs). Radioresistant cancer cells have developed the robust capability of DNA damage repair to survive IR. Nuclear factor erythroid 2-related factor 2 (NRF2) has been correlated with radiation resistance. We previously reported a novel function of NRF2 as an ATR activator in response to DSBs. However, little is known about the mechanism that how NRF2 regulates DNA damage repair and radiation resistance. Methods: The TCGA database and tissue microarray were used to analyze the correlation between NRF2 and the prognosis of lung cancer patients. The radioresistant lung cancer cells were constructed, and the role of NRF2 in radiation resistance was explored by in vivo and in vitro experiments. Immunoprecipitation, immunofluorescence and extraction of chromatin fractions were used to explore the underlying mechanisms. Results: In this study, the TCGA database and clinical lung cancer samples showed that high expression of NRF2 was associated with poor prognosis in lung cancer patients. We established radioresistant lung cancer cells expressing NRF2 at high levels, which showed increased antioxidant and DNA repair abilities. In addition, we found that NRF2 can be involved in the DNA damage response independently of its antioxidant function. Mechanistically, we demonstrated that NRF2 promoted the phosphorylation of replication protein A 32 (RPA32), and DNA topoisomerase 2-binding protein 1 (TOPBP1) was recruited to DSB sites in an NRF2-dependent manner. Conclusion: This study explored the novel role of NRF2 in promoting radiation resistance by cooperating with RPA32 and TOPBP1 to activate the ATR-CHK1 signaling pathway. In addition, the findings of this study not only provide novel insights into the molecular mechanisms underlying the radiation resistance of lung cancer cells but also validate NRF2 as a potential target for radiotherapy.
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Affiliation(s)
| | | | | | | | | | | | - Liqing Du
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | | | | | | | | | | | | | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
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Gregorczyk M, Parkes EE. Targeting mitotic regulators in cancer as a strategy to enhance immune recognition. DNA Repair (Amst) 2023; 132:103583. [PMID: 37871511 DOI: 10.1016/j.dnarep.2023.103583] [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: 07/26/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023]
Abstract
Eukaryotic DNA has evolved to be enclosed within the nucleus to protect the cellular genome from autoinflammatory responses driven by the immunogenic nature of cytoplasmic DNA. Cyclic GMP-AMP Synthase (cGAS) is the cytoplasmic dsDNA sensor, which upon activation of Stimulator of Interferon Genes (STING), mediates production of pro-inflammatory interferons (IFNs) and interferon stimulated genes (ISGs). However, although this pathway is crucial in detection of viral and microbial genetic material, cytoplasmic DNA is not always of foreign origin. It is now recognised that specifically in genomic instability, a hallmark of cancer, extranuclear material in the form of micronuclei (MN) can be generated as a result of unresolved DNA lesions during mitosis. Activation of cGAS-STING in cancer has been shown to regulate numerous tumour-immune interactions such as acquisition of 'immunologically hot' phenotype which stimulates immune-mediated elimination of transformed cells. Nonetheless, a significant percentage of poorly prognostic cancers is 'immunologically cold'. As this state has been linked with low proportion of tumour-infiltrating lymphocytes (TILs), improving immunogenicity of cold tumours could be clinically relevant by exhibiting synergy with immunotherapy. This review aims to present how inhibition of vital mitotic regulators could provoke cGAS-STING response in cancer and improve the efficacy of current immunotherapy regimens.
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Affiliation(s)
- Mateusz Gregorczyk
- Oxford Centre for Immuno-Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Eileen E Parkes
- Oxford Centre for Immuno-Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom.
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35
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Vittoria MA, Quinton RJ, Ganem NJ. Whole-genome doubling in tissues and tumors. Trends Genet 2023; 39:954-967. [PMID: 37714734 PMCID: PMC10840902 DOI: 10.1016/j.tig.2023.08.004] [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: 06/20/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
The overwhelming majority of proliferating somatic human cells are diploid, and this genomic state is typically maintained across successive cell divisions. However, failures in cell division can induce a whole-genome doubling (WGD) event, in which diploid cells transition to a tetraploid state. While some WGDs are developmentally programmed to produce nonproliferative tetraploid cells with specific cellular functions, unscheduled WGDs can be catastrophic: erroneously arising tetraploid cells are ill-equipped to cope with their doubled cellular and chromosomal content and quickly become genomically unstable and tumorigenic. Deciphering the genetics that underlie the genesis, physiology, and evolution of whole-genome doubled (WGD+) cells may therefore reveal therapeutic avenues to selectively eliminate pathological WGD+ cells.
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Affiliation(s)
- Marc A Vittoria
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Ryan J Quinton
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neil J Ganem
- Department of Medicine, Division of Hematology and Oncology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; Department of Pharmacology, Physiology, and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA.
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36
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Crozier L, Foy R, Adib R, Kar A, Holt JA, Pareri AU, Valverde JM, Rivera R, Weston WA, Wilson R, Regnault C, Whitfield P, Badonyi M, Bennett LG, Vernon EG, Gamble A, Marsh JA, Staples CJ, Saurin AT, Barr AR, Ly T. CDK4/6 inhibitor-mediated cell overgrowth triggers osmotic and replication stress to promote senescence. Mol Cell 2023; 83:4062-4077.e5. [PMID: 37977118 DOI: 10.1016/j.molcel.2023.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 07/10/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Abnormal increases in cell size are associated with senescence and cell cycle exit. The mechanisms by which overgrowth primes cells to withdraw from the cell cycle remain unknown. We address this question using CDK4/6 inhibitors, which arrest cells in G0/G1 and are licensed to treat advanced HR+/HER2- breast cancer. We demonstrate that CDK4/6-inhibited cells overgrow during G0/G1, causing p38/p53/p21-dependent cell cycle withdrawal. Cell cycle withdrawal is triggered by biphasic p21 induction. The first p21 wave is caused by osmotic stress, leading to p38- and size-dependent accumulation of p21. CDK4/6 inhibitor washout results in some cells entering S-phase. Overgrown cells experience replication stress, resulting in a second p21 wave that promotes cell cycle withdrawal from G2 or the subsequent G1. We propose that the levels of p21 integrate signals from overgrowth-triggered stresses to determine cell fate. This model explains how hypertrophy can drive senescence and why CDK4/6 inhibitors have long-lasting effects in patients.
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Affiliation(s)
- Lisa Crozier
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Reece Foy
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Rozita Adib
- MRC Laboratory of Medical Sciences, London, UK
| | - Ananya Kar
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK
| | | | - Aanchal U Pareri
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Juan M Valverde
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Rene Rivera
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK
| | | | - Rona Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Clement Regnault
- Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK
| | - Phil Whitfield
- Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK
| | - Mihaly Badonyi
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Laura G Bennett
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Ellen G Vernon
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Amelia Gamble
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Christopher J Staples
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Adrian T Saurin
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK.
| | - Alexis R Barr
- MRC Laboratory of Medical Sciences, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Tony Ly
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK.
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37
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Oshima M, Takayama KI, Yamada Y, Kimura N, Kume H, Fujimura T, Inoue S. Identification of DNA damage response-related genes as biomarkers for castration-resistant prostate cancer. Sci Rep 2023; 13:19602. [PMID: 37950047 PMCID: PMC10638319 DOI: 10.1038/s41598-023-46651-6] [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: 02/18/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
Although hormone therapy is effective for the treatment of prostate cancer (Pca), many patients develop a lethal type of Pca called castration-resistant prostate cancer (CRPC). Dysregulation of DNA damage response (DDR)-related genes leads to Pca progression. Here, we explored DDR-related signals upregulated in CRPC tissues. We analyzed the gene expression profiles in our RNA-sequence (RNA-seq) dataset containing benign prostate, primary Pca, and CRPC samples. We identified six DDR-related genes (Ribonuclease H2 Subunit A (RNASEH2A), replication factor C subunit 2 (RFC2), RFC4, DNA Ligase 1 (LIG1), DNA polymerase D1 (POLD1), and DNA polymerase E4 (POLE4)) that were upregulated in CRPC compared with Pca tissues. By analyzing public databases and validation studies, we focused on RFC2 as a new biomarker. Functional analysis demonstrated that silencing of RFC2 expression inhibited cell proliferation and induced the expression of DNA damage and apoptosis markers in CRPC model cells. Furthermore, immunohistochemical (IHC) analysis revealed that high expression of RFC2 protein correlated with poor prognosis in patients with Pca and increased expression in CRPC tissues compared with localized Pca. Thus, our study suggests that six DDR-related genes would be important for Pca progression. RFC2 could be a useful biomarker associated with poor outcomes of patients with Pca.
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Affiliation(s)
- Masashi Oshima
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakaecho Itabashi-ku, Tokyo, 173-0015, Japan
- Department of Urology, Jichi Medical University, Tochigi, Japan
- Department of Urology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakaecho Itabashi-ku, Tokyo, 173-0015, Japan
| | - Yuta Yamada
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Naoki Kimura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, 35-2 Sakaecho Itabashi-ku, Tokyo, 173-0015, Japan.
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, Saitama, Japan.
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Fragkos M, Choleza M, Papadopoulou P. The Role of γH2AX in Replication Stress-induced Carcinogenesis: Possible Links and Recent Developments. CANCER DIAGNOSIS & PROGNOSIS 2023; 3:639-648. [PMID: 37927801 PMCID: PMC10619570 DOI: 10.21873/cdp.10266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
Cancer is a condition characterized by genomic instability and gross chromosomal aberrations. The inability of the cell to timely and efficiently complete its replication cycle before entering mitosis is one of the most common causes of DNA damage and carcinogenesis. Phosphorylation of histone 2AX (H2AX) on S139 (γH2AX) is an indispensable step in the response to DNA damage, as it is required for the assembly of repair factors at the sites of damage. γH2AX is also a marker of DNA replication stress, mainly due to fork collapse that often follows prolonged replication stalling or repair of arrested forks, which involves the generation of DNA breaks. Although the role of γH2AX in the repair of DNA breaks has been well defined, the function of γH2AX in replicative stress remains unclear. In this review, we present the recent advances in the field of replication stress, and highlight a novel function for γH2AX that is independent of its role in the response to DNA damage. We discuss studies that support a role for γΗ2ΑΧ early in the response to replicative stress, which does not involve the repair of DNA breaks. We also highlight recent data proposing that γH2AX acts as a chromatin remodeling component, implicated in the efficient resolution of stalled replication forks. Understanding the mechanism by which γH2AX enables cellular recovery after replication stress will allow identification of novel cancer biomarkers, as well as new targets for cancer therapies.
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Affiliation(s)
- Michalis Fragkos
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
| | - Maria Choleza
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
| | - Paraskevi Papadopoulou
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
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39
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Zhu Y, Li S, Wang H, Chi K, Ren W, Huang X, Zhuo M, Lin D. Molecular subtype expression and genomic profiling differ between surgically resected pure and combined small cell lung carcinoma. Hum Pathol 2023; 141:118-129. [PMID: 37586462 DOI: 10.1016/j.humpath.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023]
Abstract
A new molecular subtype classification method has been proposed for small cell lung carcinoma (SCLC). However, little is known about the differences between the pure (P-SCLC) and combined subtypes (C-SCLC). We aimed to compare the molecular subtype expression and genomic profiling in terms of clinical relevance between the two groups. 154 surgically resected SCLCs were analyzed for protein expression of four subtypes (ASCL1, NEUROD1, POU2F3, and YAP1) and two predictive markers (DLL3 and MYC) by immunohistochemistry (IHC). We also performed whole exome sequencing of 60 samples to examine genomic profiles. A total of 113 patients with P-SCLC and 41 with C-SCLC were included. In P-SCLC and C-SCLC, the expression of these markers was 78.8% and 41.5%, 98.2% and 97.6%, 42.5% and 51.2%, 38.9% and 85.4%, 85.0% and 68.3%, and 24.8% and 34.1%, respectively. ASCL1 and DLL3 were highly expressed in P-SCLC (p = 0.000 and p = 0.021, respectively), and YAP1 expression was significantly enriched in C-SCLC (p = 0.000). NGS results, including 45 P-SCLCs and 15 C-SCLCs, indicated that EGFR gene mutations were mostly observed in C-SCLCs (p = 0.000). C-SCLC showed higher CNA burden and wGII than P-SCLC (p < 0.01 and p < 0.05); conversely, P-SCLC had higher TMB burden and SDI (p < 0.05 and p < 0.05). YAP1 expression was associated with poor prognosis in P-SCLC but with favorable prognosis in C-SCLC. P-SCLC and C-SCLC are heterogeneous diseases characterized by different molecular subtype expressions and genomic profiles. Our data provide a basis for adopting histological subtype-based treatments, and further prospective studies are required to confirm our conclusions.
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Affiliation(s)
- Yanli Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Sheng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department I of Thoracic Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Haiyue Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Kaiwen Chi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Wenhao Ren
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Xiaozheng Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Minglei Zhuo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department I of Thoracic Oncology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
| | - Dongmei Lin
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, 100142, China.
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Ognibene M, De Marco P, Amoroso L, Fragola M, Zara F, Parodi S, Pezzolo A. Neuroblastoma Patients' Outcome and Chromosomal Instability. Int J Mol Sci 2023; 24:15514. [PMID: 37958497 PMCID: PMC10648898 DOI: 10.3390/ijms242115514] [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: 09/07/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Chromosomal instability (CIN) induces a high rate of losses or gains of whole chromosomes or parts of chromosomes. It is a hallmark of most human cancers and one of the causes of aneuploidy and intra-tumor heterogeneity. The present study aimed to evaluate the potential prognostic role of CIN in NB patients at diagnosis. We performed array comparative genomic hybridization analyses on 451 primary NB patients at the onset of the disease. To assess global chromosomal instability with high precision, we focused on the total number of DNA breakpoints of gains or losses of chromosome arms. For each tumor, an array-CGH-based breakpoint instability index (BPI) was assigned which defined the total number of chromosomal breakpoints per genome. This approach allowed us to quantify CIN related to whole genome disruption in all NB cases analyzed. We found differences in chromosomal breakages among the NB clinical risk groups. High BPI values are negatively associated with survival of NB patients. This association remains significant when correcting for stage, age, and MYCN status in the Cox model. Stratified analysis confirms the prognostic effect of BPI index in low-risk NB patients with non-amplified MYCN and with segmental chromosome aberrations.
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Affiliation(s)
- Marzia Ognibene
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Patrizia De Marco
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Loredana Amoroso
- U.O.C. Oncologia Pediatrica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy;
| | - Martina Fragola
- Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.F.); (S.P.)
| | - Federico Zara
- U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (P.D.M.); (F.Z.)
| | - Stefano Parodi
- Epidemiologia e Biostatistica, Direzione Scientifica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; (M.F.); (S.P.)
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Barrio L, Gaspar AE, Muzzopappa M, Ghosh K, Romao D, Clemente-Ruiz M, Milán M. Chromosomal instability-induced cell invasion through caspase-driven DNA damage. Curr Biol 2023; 33:4446-4457.e5. [PMID: 37751744 DOI: 10.1016/j.cub.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/28/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023]
Abstract
Chromosomal instability (CIN), an increased rate of changes in chromosome structure and number, is observed in most sporadic human carcinomas with high metastatic activity. Here, we use a Drosophila epithelial model to show that DNA damage, as a result of the production of lagging chromosomes during mitosis and aneuploidy-induced replicative stress, contributes to CIN-induced invasiveness. We unravel a sub-lethal role of effector caspases in invasiveness by enhancing CIN-induced DNA damage and identify the JAK/STAT signaling pathway as an activator of apoptotic caspases through transcriptional induction of pro-apoptotic genes. We provide evidence that an autocrine feedforward amplification loop mediated by Upd3-a cytokine with homology to interleukin-6 and a ligand of the JAK/STAT signaling pathway-contributes to amplifying the activation levels of the apoptotic pathway in migrating cells, thus promoting CIN-induced invasiveness. This work sheds new light on the chromosome-signature-independent effects of CIN in metastasis.
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Affiliation(s)
- Lara Barrio
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ana-Elena Gaspar
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Mariana Muzzopappa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Kaustuv Ghosh
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Daniela Romao
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marta Clemente-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marco Milán
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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Wang N, Xu S, Egli D. Replication stress in mammalian embryo development, differentiation, and reprogramming. Trends Cell Biol 2023; 33:872-886. [PMID: 37202286 DOI: 10.1016/j.tcb.2023.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/20/2023]
Abstract
Duplicating a genome of 3 billion nucleotides is challenged by a variety of obstacles that can cause replication stress and affect the integrity of the genome. Recent studies show that replication fork slowing and stalling is prevalent in early mammalian development, resulting in genome instability and aneuploidy, and constituting a barrier to development in human reproduction. Genome instability resulting from DNA replication stress is a barrier to the cloning of animals and to the reprogramming of differentiated cells to induced pluripotent stem cells, as well as a barrier to cell transformation. Remarkably, the regions most impacted by replication stress are shared in these different cellular contexts, affecting long genes and flanking intergenic areas. In this review we integrate our knowledge of DNA replication stress in mammalian embryos, in programming, and in reprogramming, and we discuss a potential role for fragile sites in sensing replication stress and restricting cell cycle progression in health and disease.
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Affiliation(s)
- Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Weiner AC, Williams MJ, Shi H, Vázquez-García I, Salehi S, Rusk N, Aparicio S, Shah SP, McPherson A. Single-cell DNA replication dynamics in genomically unstable cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536250. [PMID: 37090647 PMCID: PMC10120671 DOI: 10.1101/2023.04.10.536250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Dysregulated DNA replication is both a cause and a consequence of aneuploidy, yet the dynamics of DNA replication in aneuploid cell populations remains understudied. We developed a new method, PERT, for inferring cell-specific DNA replication states from single-cell whole genome sequencing, and investigated clone-specific DNA replication dynamics in >50,000 cells obtained from a collection of aneuploid and clonally heterogeneous cell lines, xenografts and primary cancer tissues. Clone replication timing (RT) profiles correlated with future copy number changes in serially passaged cell lines. Cell type was the strongest determinant of RT heterogeneity, while whole genome doubling and mutational process were associated with accumulation of late S-phase cells and weaker RT associations. Copy number changes affecting chromosome X had striking impact on RT, with loss of the inactive X allele shifting replication earlier, and loss of inactive Xq resulting in reactivation of Xp. Finally, analysis of time series xenografts illustrate how cell cycle distributions approximate clone proliferation, recapitulating expected relationships between proliferation and fitness in treatment-naive and chemotherapeutic contexts.
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Affiliation(s)
- Adam C Weiner
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab Salehi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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44
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Liu A, Gao Y, Wang Q, Lin W, Ma Z, Yang X, Chen L, Xu D. The heterogeneity and clonal evolution analysis of the advanced prostate cancer with castration resistance. J Transl Med 2023; 21:641. [PMID: 37726835 PMCID: PMC10510184 DOI: 10.1186/s12967-023-04320-2] [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: 04/08/2023] [Accepted: 07/01/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Nowadays, the incidence rate of advanced and metastatic prostate cancer at the first time of diagnosis grows higher in China yearly. At present, androgen deprivation therapy (ADT) is the primary treatment of advanced prostate cancer. However, after several years of ADT, most patients will ultimately progress to castration-resistant prostate cancer (CRPC). Previous studies mainly focus on Caucasian and very few on East Asian patients. METHODS In this study, the pre- and post-ADT tumor samples were collected from five Chinese patients with advanced prostate cancer. The whole-exome sequencing, tumor heterogeneity, and clonal evolution pattern were analyzed. RESULTS The results showed that the gene mutation pattern and heterogeneity changed significantly after androgen deprivation therapy. Tumor Mutational Burden (TMB) and Copy Number Alteration (CNA) were substantially reduced in the post-treatment group, but the Mutant-allele tumor heterogeneity (MATH), Socio-Demographic Index (SDI), Intratumor heterogeneity (ITH), and weighted Genome Instability Index (wGII) had no significant difference. According to the clone types and characteristics, the presence of main clones in five pre-and post-treatment samples, the clonal evolution pattern can be further classified into two sub-groups (the Homogeneous origin clonal model or the Heterogeneous origin clonal model). The Progression-free survival (PFS) of the patients with the "Homogeneous origin clonal model" was shorter than the "Heterogeneous origin clonal model". The longer PFS might relate to MUC7 and MUC5B mutations repaired. ZNF91 mutation might be responsible for resistance to ADT resistance. CONCLUSION Our findings revealed potential genetic regulators to predict the castration resistance and provide insights into the castration resistance processes in advanced prostate cancer. The crosstalk between clonal evolution patterns and tumor microenvironment may also play a role in castration resistance. A multicenter-research including larger populations with different background are needed to confirm our conclusion in the future.
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Affiliation(s)
- Ao Liu
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yi Gao
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Qi Wang
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Wenhao Lin
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Zhiyang Ma
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xiaoqun Yang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Lu Chen
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Danfeng Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
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Andrade JR, Gallagher AD, Maharaj J, McClelland SE. Disentangling the roles of aneuploidy, chromosomal instability and tumour heterogeneity in developing resistance to cancer therapies. Chromosome Res 2023; 31:28. [PMID: 37721639 PMCID: PMC10506951 DOI: 10.1007/s10577-023-09737-5] [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: 05/01/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Aneuploidy is defined as the cellular state of having a number of chromosomes that deviates from a multiple of the normal haploid chromosome number of a given organism. Aneuploidy can be present in a static state: Down syndrome individuals stably maintain an extra copy of chromosome 21 in their cells. In cancer cells, however, aneuploidy is usually present in combination with chromosomal instability (CIN) which leads to a continual generation of new chromosomal alterations and the development of intratumour heterogeneity (ITH). The prevalence of cells with specific chromosomal alterations is further shaped by evolutionary selection, for example, during the administration of cancer therapies. Aneuploidy, CIN and ITH have each been individually associated with poor prognosis in cancer, and a wealth of evidence suggests they contribute, either alone or in combination, to cancer therapy resistance by providing a reservoir of potential resistant states, or the ability to rapidly evolve resistance. A full understanding of the contribution and interplay between aneuploidy, CIN and ITH is required to tackle therapy resistance in cancer patients. However, these characteristics often co-occur and are intrinsically linked, presenting a major challenge to defining their individual contributions. Moreover, their accurate measurement in both experimental and clinical settings is a technical hurdle. Here, we attempt to deconstruct the contribution of the individual and combined roles of aneuploidy, CIN and ITH to therapy resistance in cancer, and outline emerging approaches to measure and disentangle their roles as a step towards integrating these principles into cancer therapeutic strategy.
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Affiliation(s)
- Joana Reis Andrade
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Annie Dinky Gallagher
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Jovanna Maharaj
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
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Gao M, Liu W, Li T, Song Z, Wang X, Zhang X. Identifying Genetic Signatures Associated with Oncogene-Induced Replication Stress in Osteosarcoma and Screening for Potential Targeted Drugs. Biochem Genet 2023:10.1007/s10528-023-10497-4. [PMID: 37672187 DOI: 10.1007/s10528-023-10497-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 08/07/2023] [Indexed: 09/07/2023]
Abstract
Osteosarcoma is the most common type of primary malignant bone tumor. Due to the lack of selectivity and sensitivity of chemotherapy drugs to tumor cells, coupled with the use of large doses, chemotherapy drugs often have systemic toxicity. The use of modern sequencing technology to screen tumor markers in a large number of tumor samples is a common method for screening highly specific and selective anti-tumor drugs. This study aims to identify potential biomarkers using the latest reported gene expression signatures of oncogene-induced replication stress (ORS) in aggressive cancers, and potential anti-osteosarcoma drugs were screened in different drug databases. In this study, we obtained 89 osteosarcoma-related samples in the TARGET database, all of which included survival information. According to the median expression of each of six reported ORS gene markers (NAT10/DDX27/ZNF48/C8ORF33/MOCS3/MPP6), we divided 89 osteosarcoma gene expression datasets into a high expression group and a low expression group and then performed a differentially expressed gene (DEG) analysis. The coexisting genes of 6 groups of DEGs were used as replication stress-related genes (RSGs) of osteosarcoma. Then, key RSGs were screened using LASSO regression, a Cox risk proportional regression prognostic model and a tenfold cross-validation test. GSE21257 datasets collected from the Gene Expression Omnibus (GEO) database were used to verify the prognostic model. The final key RSGs selected were used in the L1000PWD and DGIdb databases to mine potential drugs. After further validation by the prognostic model, we identified seven genes associated with ORS in osteosarcoma as key RSGs, including transcription factor 7 like 2 (TCF7L2), solute carrier family 27 member 4 (SLC27A4), proprotein convertase subtilisin/kexin type 5 (PCSK5), nucleolar protein 6 (NOL6), coiled-coil-coil-coil-coil-helix domain containing 4 (CHCHD4), eukaryotic translation initiation factor 3 subunit B (EIF3B), and synthesis of cytochrome C oxidase 1 (SCO1). Then, we screened the seven key RSGs in two drug databases and found six potential anti-osteosarcoma drugs (D GIdb database: repaglinide, tacrolimus, sirolimus, cyclosporine, and hydrochlorothiazide; L1000PWD database: the small molecule VU-0365117-1). Seven RSGs (TCF7L2, SLC27A4, PCSK5, NOL6, CHCHD4, EIF3B, and SCO1) may be associated with the ORS gene signatures in osteosarcoma. Repaglinide, tacrolimus, sirolimus, cyclosporine, hydrochlorothiazide and the small molecule VU-0365117-1 are potential therapeutic drugs for osteosarcoma.
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Affiliation(s)
- Meng Gao
- School of Medicine, Nankai University, Tianjin, China
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - Weibo Liu
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - Teng Li
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - ZeLong Song
- School of Medicine, Nankai University, Tianjin, China
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - XiangYu Wang
- Department of Pain Medicine, First Medical Center, PLA General Hospital, Beijing, 100000, China.
| | - XueSong Zhang
- School of Medicine, Nankai University, Tianjin, China.
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China.
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Sokač M, Kjær A, Dyrskjøt L, Haibe-Kains B, JWL Aerts H, Birkbak NJ. Spatial transformation of multi-omics data unlocks novel insights into cancer biology. eLife 2023; 12:RP87133. [PMID: 37669321 PMCID: PMC10479962 DOI: 10.7554/elife.87133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023] Open
Abstract
The application of next-generation sequencing (NGS) has transformed cancer research. As costs have decreased, NGS has increasingly been applied to generate multiple layers of molecular data from the same samples, covering genomics, transcriptomics, and methylomics. Integrating these types of multi-omics data in a combined analysis is now becoming a common issue with no obvious solution, often handled on an ad hoc basis, with multi-omics data arriving in a tabular format and analyzed using computationally intensive statistical methods. These methods particularly ignore the spatial orientation of the genome and often apply stringent p-value corrections that likely result in the loss of true positive associations. Here, we present GENIUS (GEnome traNsformatIon and spatial representation of mUltiomicS data), a framework for integrating multi-omics data using deep learning models developed for advanced image analysis. The GENIUS framework is able to transform multi-omics data into images with genes displayed as spatially connected pixels and successfully extract relevant information with respect to the desired output. We demonstrate the utility of GENIUS by applying the framework to multi-omics datasets from the Cancer Genome Atlas. Our results are focused on predicting the development of metastatic cancer from primary tumors, and demonstrate how through model inference, we are able to extract the genes which are driving the model prediction and are likely associated with metastatic disease progression. We anticipate our framework to be a starting point and strong proof of concept for multi-omics data transformation and analysis without the need for statistical correction.
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Affiliation(s)
- Mateo Sokač
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
- Bioinformatics Research Center, Aarhus UniversityAarhusDenmark
| | - Asbjørn Kjær
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
- Bioinformatics Research Center, Aarhus UniversityAarhusDenmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Temerty Faculty of Medicine, University of TorontoTorontoCanada
| | - Hugo JWL Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical SchoolBostonUnited States
- Departments of Radiation Oncology and Radiology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical SchoolBostonUnited States
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht UniversityMaastrichtNetherlands
| | - Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
- Bioinformatics Research Center, Aarhus UniversityAarhusDenmark
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48
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Parisis N, Dans PD, Jbara M, Singh B, Schausi-Tiffoche D, Molina-Serrano D, Brun-Heath I, Hendrychová D, Maity SK, Buitrago D, Lema R, Nait Achour T, Giunta S, Girardot M, Talarek N, Rofidal V, Danezi K, Coudreuse D, Prioleau MN, Feil R, Orozco M, Brik A, Wu PYJ, Krasinska L, Fisher D. Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair. Nat Commun 2023; 14:5104. [PMID: 37607906 PMCID: PMC10444856 DOI: 10.1038/s41467-023-40843-4] [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: 11/10/2018] [Accepted: 08/12/2023] [Indexed: 08/24/2023] Open
Abstract
Histone post-translational modifications promote a chromatin environment that controls transcription, DNA replication and repair, but surprisingly few phosphorylations have been documented. We report the discovery of histone H3 serine-57 phosphorylation (H3S57ph) and show that it is implicated in different DNA repair pathways from fungi to vertebrates. We identified CHK1 as a major human H3S57 kinase, and disrupting or constitutively mimicking H3S57ph had opposing effects on rate of recovery from replication stress, 53BP1 chromatin binding, and dependency on RAD52. In fission yeast, mutation of all H3 alleles to S57A abrogated DNA repair by both non-homologous end-joining and homologous recombination, while cells with phospho-mimicking S57D alleles were partly compromised for both repair pathways, presented aberrant Rad52 foci and were strongly sensitised to replication stress. Mechanistically, H3S57ph loosens DNA-histone contacts, increasing nucleosome mobility, and interacts with H3K56. Our results suggest that dynamic phosphorylation of H3S57 is required for DNA repair and recovery from replication stress, opening avenues for investigating the role of this modification in other DNA-related processes.
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Affiliation(s)
- Nikolaos Parisis
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
- BPMP, CNRS, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- Institut Jacques Monod, CNRS, University Paris Diderot, Paris, France
| | - Pablo D Dans
- IRB Barcelona, BIST, Barcelona, Spain
- Bioinformatics Unit, Institute Pasteur of Montevideo, Montevideo, Uruguay
- Department of Biological Sciences, CENUR North Riverside, University of the Republic (UdelaR), Salto, Uruguay
| | - Muhammad Jbara
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, Israel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | | | | | | | - Denisa Hendrychová
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Suman Kumar Maity
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, Israel
| | | | | | - Thiziri Nait Achour
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Simona Giunta
- The Rockefeller University, New York, NY, USA
- Laboratory of Genome Evolution, Department of Biology and Biotechnology "Charles Darwin", University of Rome Sapienza, Rome, Italy
| | - Michael Girardot
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Nicolas Talarek
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Valérie Rofidal
- BPMP, CNRS, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Katerina Danezi
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Damien Coudreuse
- IGDR, CNRS, University of Rennes, Rennes, France
- IBGC, CNRS, University of Bordeaux, Bordeaux, France
| | | | - Robert Feil
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France
| | | | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion Israel Institute of Technology, Haifa, Israel
| | - Pei-Yun Jenny Wu
- IGDR, CNRS, University of Rennes, Rennes, France
- IBGC, CNRS, University of Bordeaux, Bordeaux, France
| | - Liliana Krasinska
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France.
- Equipe labellisée Ligue contre le Cancer, Paris, France.
| | - Daniel Fisher
- IGMM, CNRS, INSERM, University of Montpellier, Montpellier, France.
- Equipe labellisée Ligue contre le Cancer, Paris, France.
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49
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Micheloni M, Petrolli L, Lattanzi G, Potestio R. Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations. Biophys J 2023; 122:3314-3322. [PMID: 37455429 PMCID: PMC10465705 DOI: 10.1016/j.bpj.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/16/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
Double-strand breaks (DSBs), i.e., the covalent cut of the DNA backbone over both strands, are a detrimental outcome of cell irradiation, bearing chromosomal aberrations and leading to cell apoptosis. In the early stages of the evolution of a DSB, the disruption of the residual interactions between the DNA moieties drives the fracture of the helical layout; in spite of its biological significance, the details of this process are still largely uncertain. Here, we address the mechanical rupture of DNA by DSBs via coarse-grained molecular dynamics simulations: the setup involves a 3855-bp DNA filament and diverse DSB motifs, i.e., within a range of distances between strand breaks (or DSB distance). By employing a coarse-grained model of DNA, we access the molecular details and characteristic timescales of the rupturing process. A sequence-nonspecific, linear correlation is observed between the DSB distance and the internal energy contribution to the disruption of the residual (Watson-Crick and stacking) contacts between DNA moieties, which is seemingly driven by an abrupt, cooperative process. Moreover, we infer an exponential dependence of the characteristic rupture times on the DSB distances, which we associate to an Arrhenius-like law of thermally-activated processes. This work lays the foundations of a detailed, mechanistic assessment of DSBs in silico as a benchmark to both numerical simulations and data from single-molecule experiments.
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Affiliation(s)
- Manuel Micheloni
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Lorenzo Petrolli
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Gianluca Lattanzi
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy.
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Chowdhury S, Kennedy JJ, Ivey RG, Murillo OD, Hosseini N, Song X, Petralia F, Calinawan A, Savage SR, Berry AB, Reva B, Ozbek U, Krek A, Ma W, da Veiga Leprevost F, Ji J, Yoo S, Lin C, Voytovich UJ, Huang Y, Lee SH, Bergan L, Lorentzen TD, Mesri M, Rodriguez H, Hoofnagle AN, Herbert ZT, Nesvizhskii AI, Zhang B, Whiteaker JR, Fenyo D, McKerrow W, Wang J, Schürer SC, Stathias V, Chen XS, Barcellos-Hoff MH, Starr TK, Winterhoff BJ, Nelson AC, Mok SC, Kaufmann SH, Drescher C, Cieslik M, Wang P, Birrer MJ, Paulovich AG. Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer. Cell 2023; 186:3476-3498.e35. [PMID: 37541199 PMCID: PMC10414761 DOI: 10.1016/j.cell.2023.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.
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Affiliation(s)
- Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Department of Population Health Science and Policy, Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Umut Ozbek
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jiayi Ji
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Uliana J Voytovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yajue Huang
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sun-Hee Lee
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Lindsay Bergan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David Fenyo
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua Wang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, Miller School of Medicine, and Institute for Data Science & Computing, University of Miami, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Mary Helen Barcellos-Hoff
- Helen Diller Family Comprehensive Cancer Center, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Timothy K Starr
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Boris J Winterhoff
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C Mok
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Charles Drescher
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Marcin Cieslik
- Department of Pathology, Department of Computational Medicine and Bioinformatics, Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Michael J Birrer
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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