1
|
Yan Z, Xia J, Cao Z, Zhang H, Wang J, Feng T, Shu Y, Zou L. Multi-omics integration reveals potential stage-specific druggable targets in T-cell acute lymphoblastic leukemia. Genes Dis 2024; 11:100949. [PMID: 39071111 PMCID: PMC11282411 DOI: 10.1016/j.gendis.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/11/2023] [Indexed: 07/30/2024] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL), a heterogeneous hematological malignancy, is caused by the developmental arrest of normal T-cell progenitors. The development of targeted therapeutic regimens is impeded by poor knowledge of the stage-specific aberrances in this disease. In this study, we performed multi-omics integration analysis, which included mRNA expression, chromatin accessibility, and gene-dependency database analyses, to identify potential stage-specific druggable targets and repositioned drugs for this disease. This multi-omics integration helped identify 29 potential pathological genes for T-ALL. These genes exhibited tissue-specific expression profiles and were enriched in the cell cycle, hematopoietic stem cell differentiation, and the AMPK signaling pathway. Of these, four known druggable targets (CDK6, TUBA1A, TUBB, and TYMS) showed dysregulated and stage-specific expression in malignant T cells and may serve as stage-specific targets in T-ALL. The TUBA1A expression level was higher in the early T cell precursor (ETP)-ALL cells, while TUBB and TYMS were mainly highly expressed in malignant T cells arrested at the CD4 and CD8 double-positive or single-positive stage. CDK6 exhibited a U-shaped expression pattern in malignant T cells along the naïve to maturation stages. Furthermore, mebendazole and gemcitabine, which target TUBA1A and TYMS, respectively, exerted stage-specific inhibitory effects on T-ALL cell lines, indicating their potential stage-specific antileukemic role in T-ALL. Collectively, our findings might aid in identifying potential stage-specific druggable targets and are promising for achieving more precise therapeutic strategies for T-ALL.
Collapse
Affiliation(s)
- Zijun Yan
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Jie Xia
- Bioinformatics and BioMedical Bigdata Mining Laboratory, School of Big Health, Guizhou Medical University, Guiyang, Guizhou 554300, China
| | - Ziyang Cao
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Hongyang Zhang
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Jinxia Wang
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Tienan Feng
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi Shu
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Lin Zou
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| |
Collapse
|
2
|
Klockner TC, Campbell CS. Selection forces underlying aneuploidy patterns in cancer. Mol Cell Oncol 2024; 11:2369388. [PMID: 38919375 PMCID: PMC11197905 DOI: 10.1080/23723556.2024.2369388] [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: 02/21/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024]
Abstract
Aneuploidy, the presence of an aberrant number of chromosomes, has been associated with tumorigenesis for over a century. More recently, advances in karyotyping techniques have revealed its high prevalence in cancer: About 90% of solid tumors and 50-70% of hematopoietic cancers exhibit chromosome gains or losses. When analyzed at the level of specific chromosomes, there are strong patterns that are observed in cancer karyotypes both pan-cancer and for specific cancer types. These specific aneuploidy patterns correlate strongly with outcomes for tumor initiation, progression, metastasis formation, immune evasion and resistance to therapeutic treatment. Despite their prominence, understanding the basis underlying aneuploidy patterns in cancer has been challenging. Advances in genetic engineering and bioinformatic analyses now offer insights into the genetic determinants of aneuploidy pattern selection. Overall, there is substantial evidence that expression changes of particular genes can act as the positive selective forces for adaptation through aneuploidy. Recent findings suggest that multiple genes contribute to the selection of specific aneuploid chromosomes in cancer; however, further research is necessary to identify the most impactful driver genes. Determining the genetic basis and accompanying vulnerabilities of specific aneuploidy patterns is an essential step in selectively targeting these hallmarks of tumors.
Collapse
Affiliation(s)
- Tamara C. Klockner
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Chromosome Biology, University of Vienna, Vienna, Austria
- A Doctoral School of the University of Vienna and the Medical University of Vienna, Vienna, Austria
| | - Christopher S. Campbell
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Center for Molecular Biology, Department of Chromosome Biology, University of Vienna, Vienna, Austria
| |
Collapse
|
3
|
Carey-Smith SL, Kotecha RS, Cheung LC, Malinge S. Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer. Int J Mol Sci 2024; 25:6815. [PMID: 38999925 PMCID: PMC11241182 DOI: 10.3390/ijms25136815] [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: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.
Collapse
Affiliation(s)
- Shannon L. Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Rishi S. Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Laurence C. Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
4
|
Chukwu W, Lee S, Crane A, Zhang S, Webster S, Mittra I, Imielinski M, Beroukhim R, Dubois F, Dalin S. Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.09.561462. [PMID: 38106141 PMCID: PMC10723258 DOI: 10.1101/2023.10.09.561462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Although several recent studies have characterized structural variants (SVs) in germline and cancer genomes, the features of SVs in these different contexts have not been directly compared. We examined similarities and differences between 2 million germline and 115 thousand tumor SVs from a cohort of 963 patients from The Cancer Genome Atlas (TCGA). We found significant differences in features related to their genomic sequences and localization that suggest differences between SV-generating processes and selective pressures. For example, we found that transposon-mediated processes shape germline much more than somatic SVs, while somatic SVs more frequently show features characteristic of chromoanagenesis. These differences were extensive enough to enable us to develop a classifier - "the great GaTSV" - that accurately distinguishes between germline and cancer SVs in tumor samples that lack a matched normal sample.
Collapse
Affiliation(s)
- Wolu Chukwu
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Siyun Lee
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Crane
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shu Zhang
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sophie Webster
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ipsa Mittra
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; Department of Pathology and Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Frank Dubois
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin; Humboldt-Universität zu Berlin, Institute of Pathology
| | - Simona Dalin
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cancer Biology and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| |
Collapse
|
5
|
Zhao J, Wang Q, Tan AF, Loh CJL, Toh HC. Sex differences in cancer and immunotherapy outcomes: the role of androgen receptor. Front Immunol 2024; 15:1416941. [PMID: 38863718 PMCID: PMC11165033 DOI: 10.3389/fimmu.2024.1416941] [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: 04/13/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
Across the wide range of clinical conditions, there exists a sex imbalance where biological females are more prone to autoimmune diseases and males to some cancers. These discrepancies are the combinatory consequence of lifestyle and environmental factors such as smoking, alcohol consumption, obesity, and oncogenic viruses, as well as other intrinsic biological traits including sex chromosomes and sex hormones. While the emergence of immuno-oncology (I/O) has revolutionised cancer care, the efficacy across multiple cancers may be limited because of a complex, dynamic interplay between the tumour and its microenvironment (TME). Indeed, sex and gender can also influence the varying effectiveness of I/O. Androgen receptor (AR) plays an important role in tumorigenesis and in shaping the TME. Here, we lay out the epidemiological context of sex disparity in cancer and then review the current literature on how AR signalling contributes to such observation via altered tumour development and immunology. We offer insights into AR-mediated immunosuppressive mechanisms, with the hope of translating preclinical and clinical evidence in gender oncology into improved outcomes in personalised, I/O-based cancer care.
Collapse
Affiliation(s)
- Junzhe Zhao
- Duke-NUS Medical School, Singapore, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Qian Wang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Medical Oncology Cancer Hospital of China Medical University/Liaoning Cancer Hospital & Institute, Shenyang, Liaoning, China
| | | | - Celestine Jia Ling Loh
- Duke-NUS Medical School, Singapore, Singapore
- Sengkang General Hospital, Singapore, Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| |
Collapse
|
6
|
Wójcik M, Juhas U, Mohammadi E, Mattisson J, Drężek-Chyła K, Rychlicka-Buniowska E, Bruhn-Olszewska B, Davies H, Chojnowska K, Olszewski P, Bieńkowski M, Jankowski M, Rostkowska O, Hellmann A, Pęksa R, Kowalski J, Zdrenka M, Kobiela J, Zegarski W, Biernat W, Szylberg Ł, Remiszewski P, Mieczkowski J, Filipowicz N, Dumanski JP. Loss of Y in regulatory T lymphocytes in the tumor micro-environment of primary colorectal cancers and liver metastases. Sci Rep 2024; 14:9458. [PMID: 38658633 PMCID: PMC11043399 DOI: 10.1038/s41598-024-60049-y] [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: 08/24/2023] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
Male sex is a risk factor for colorectal cancer (CRC) with higher illness burden and earlier onset. Thus, we hypothesized that loss of chromosome Y (LOY) in the tumor micro-environment (TME) might be involved in oncogenesis. Previous studies show that LOY in circulating leukocytes of aging men was associated with shorter survival and non-hematological cancer, as well as higher LOY in CD4 + T-lymphocytes in men with prostate cancer vs. controls. However, nothing is known about LOY in leukocytes infiltrating TME and we address this aspect here. We studied frequency and functional effects of LOY in blood, TME and non-tumorous tissue. Regulatory T-lymphocytes (Tregs) in TME had the highest frequency of LOY (22%) in comparison to CD4 + T-lymphocytes and cytotoxic CD8 + T-lymphocytes. LOY score using scRNA-seq was also linked to higher expression of PDCD1, TIGIT and IKZF2 in Tregs. PDCD1 and TIGIT encode immune checkpoint receptors involved in the regulation of Tregs function. Our study sets the direction for further functional research regarding a probable role of LOY in intensifying features related to the suppressive phenotype of Tregs in TME and consequently a possible influence on immunotherapy response in CRC patients.
Collapse
Affiliation(s)
- Magdalena Wójcik
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Ulana Juhas
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland
| | - Elyas Mohammadi
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | | | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Katarzyna Chojnowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Paweł Olszewski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Olga Rostkowska
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Andrzej Hellmann
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Jacek Kowalski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Jarek Kobiela
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Piotr Remiszewski
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jakub Mieczkowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland.
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland.
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| |
Collapse
|
7
|
Chen CC, Silberman RE, Ma D, Perry JA, Khalid D, Pikman Y, Amon A, Hemann MT, Rowe RG. Inherent genome instability underlies trisomy 21-associated myeloid malignancies. Leukemia 2024; 38:521-529. [PMID: 38245602 DOI: 10.1038/s41375-024-02151-8] [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: 08/11/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
Constitutional trisomy 21 (T21) is a state of aneuploidy associated with high incidence of childhood acute myeloid leukemia (AML). T21-associated AML is preceded by transient abnormal myelopoiesis (TAM), which is triggered by truncating mutations in GATA1 generating a short GATA1 isoform (GATA1s). T21-associated AML emerges due to secondary mutations in hematopoietic clones bearing GATA1s. Since aneuploidy generally impairs cellular fitness, the paradoxically elevated risk of myeloid malignancy in T21 is not fully understood. We hypothesized that individuals with T21 bear inherent genome instability in hematopoietic lineages that promotes leukemogenic mutations driving the genesis of TAM and AML. We found that individuals with T21 show increased chromosomal copy number variations (CNVs) compared to euploid individuals, suggesting that genome instability could be underlying predisposition to TAM and AML. Acquisition of GATA1s enforces myeloid skewing and maintenance of the hematopoietic progenitor state independently of T21; however, GATA1s in T21 hematopoietic progenitor cells (HPCs) further augments genome instability. Increased dosage of the chromosome 21 (chr21) gene DYRK1A impairs homology-directed DNA repair as a mechanism of elevated mutagenesis. These results posit a model wherein inherent genome instability in T21 drives myeloid malignancy in concert with GATA1s mutations.
Collapse
Affiliation(s)
- Chun-Chin Chen
- Stem Cell Transplantation Program, Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca E Silberman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- RA Capital, Boston, MA, USA
| | - Duanduan Ma
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility, Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Delan Khalid
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Hemann
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - R Grant Rowe
- Stem Cell Transplantation Program, Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
8
|
Bhatia S, Khanna KK, Duijf PHG. Targeting chromosomal instability and aneuploidy in cancer. Trends Pharmacol Sci 2024; 45:210-224. [PMID: 38355324 DOI: 10.1016/j.tips.2024.01.009] [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: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Cancer development and therapy resistance are driven by chromosomal instability (CIN), which causes chromosome gains and losses (i.e., aneuploidy) and structural chromosomal alterations. Technical limitations and knowledge gaps have delayed therapeutic targeting of CIN and aneuploidy in cancers. However, our toolbox for creating and studying aneuploidy in cell models has greatly expanded recently. Moreover, accumulating evidence suggests that seven conventional antimitotic chemotherapeutic drugs achieve clinical response by inducing CIN instead of mitotic arrest, although additional anticancer activities may also contribute in vivo. In this review, we discuss these recent developments. We also highlight new discoveries, which together show that 25 chromosome arm aneuploidies (CAAs) may be targetable by 36 drugs across 14 types of cancer. Collectively, these advances offer many new opportunities to improve cancer treatment.
Collapse
Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia; Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Pascal H G Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
9
|
Stępień K, Skoneczna A, Kula-Maximenko M, Jurczyk Ł, Mołoń M. Disorders in the CMG helicase complex increase the proliferative capacity and delay chronological aging of budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119621. [PMID: 37907194 DOI: 10.1016/j.bbamcr.2023.119621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/08/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023]
Abstract
The replication of DNA requires specialized and intricate machinery. This machinery is known as a replisome and is highly evolutionarily conserved, from simple unicellular organisms such as yeast to human cells. The replisome comprises multiple protein complexes responsible for various steps in the replication process. One crucial component of the replisome is the Cdc45-MCM-GINS (CMG) helicase complex, which unwinds double-stranded DNA and coordinates the assembly and function of other replisome components, including DNA polymerases. The genes encoding the CMG helicase components are essential for initiating DNA replication. In this study, we aimed to investigate how the absence of one copy of the CMG complex genes in heterozygous Saccharomyces cerevisiae cells impacts the cells' physiology and aging. Our data revealed that these cells exhibited a significant reduction in transcript levels for the respective CMG helicase complex proteins, as well as disruptions in the cell cycle, extended doubling times, and alterations in their biochemical profile. Notably, this study provided the first demonstration that cells heterozygous for genes encoding subunits of the CMG helicase exhibited a significantly increased reproductive potential and delayed chronological aging. Additionally, we observed a noteworthy correlation between RNA and polysaccharide levels in yeast and their reproductive potential, as well as a correlation between fatty acid levels and cell doubling times. Our findings also shed new light on the potential utility of yeast in investigating potential therapeutic targets for cancer treatment.
Collapse
Affiliation(s)
- Karolina Stępień
- Institute of Medical Sciences, Rzeszów University, 35-959 Rzeszów, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Monika Kula-Maximenko
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland
| | - Łukasz Jurczyk
- Institute of Agricultural Sciences, Rzeszów University, 35-601 Rzeszów, Poland
| | - Mateusz Mołoń
- Institute of Biology, Rzeszów University, 35-601 Rzeszów, Poland.
| |
Collapse
|
10
|
Molina O, Ortega-Sabater C, Thampi N, Fernández-Fuentes N, Guerrero-Murillo M, Martínez-Moreno A, Vinyoles M, Velasco-Hernández T, Bueno C, Trincado JL, Granada I, Campos D, Giménez C, Boer JM, den Boer ML, Calvo GF, Camós M, Fuster JL, Velasco P, Ballerini P, Locatelli F, Mullighan CG, Spierings DCJ, Foijer F, Pérez-García VM, Menéndez P. Chromosomal instability in aneuploid acute lymphoblastic leukemia associates with disease progression. EMBO Mol Med 2024; 16:64-92. [PMID: 38177531 PMCID: PMC10897411 DOI: 10.1038/s44321-023-00006-w] [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: 08/05/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
Chromosomal instability (CIN) lies at the core of cancer development leading to aneuploidy, chromosomal copy-number heterogeneity (chr-CNH) and ultimately, unfavorable clinical outcomes. Despite its ubiquity in cancer, the presence of CIN in childhood B-cell acute lymphoblastic leukemia (cB-ALL), the most frequent pediatric cancer showing high frequencies of aneuploidy, remains unknown. Here, we elucidate the presence of CIN in aneuploid cB-ALL subtypes using single-cell whole-genome sequencing of primary cB-ALL samples and by generating and functionally characterizing patient-derived xenograft models (cB-ALL-PDX). We report higher rates of CIN across aneuploid than in euploid cB-ALL that strongly correlate with intraclonal chr-CNH and overall survival in mice. This association was further supported by in silico mathematical modeling. Moreover, mass-spectrometry analyses of cB-ALL-PDX revealed a "CIN signature" enriched in mitotic-spindle regulatory pathways, which was confirmed by RNA-sequencing of a large cohort of cB-ALL samples. The link between the presence of CIN in aneuploid cB-ALL and disease progression opens new possibilities for patient stratification and offers a promising new avenue as a therapeutic target in cB-ALL treatment.
Collapse
Affiliation(s)
- Oscar Molina
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain.
| | - Carmen Ortega-Sabater
- Mathematical Oncology Laboratory, Department of Mathematics & Institute of Applied Mathematics in Science and Engineering, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Namitha Thampi
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Narcís Fernández-Fuentes
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Mercedes Guerrero-Murillo
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Alba Martínez-Moreno
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Meritxell Vinyoles
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Talía Velasco-Hernández
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Juan L Trincado
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain
| | - Isabel Granada
- Hematology Service, Institut Català d'Oncologia (ICO)-Hospital Germans Trias i Pujol, Badalona, Spain
- Josep Carreras Leukemia Research Institute, Autonomous University of Barcelona, Badalona, Spain
| | | | | | - Judith M Boer
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Monique L den Boer
- Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology and Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Gabriel F Calvo
- Mathematical Oncology Laboratory, Department of Mathematics & Institute of Applied Mathematics in Science and Engineering, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Mireia Camós
- Hematology Laboratory, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumor Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose-Luis Fuster
- Pediatric Hematology and Oncology Department, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Pablo Velasco
- Pediatric Oncology and Hematology Department, Hospital Vall d'Hebrón, Barcelona, Spain
| | - Paola Ballerini
- AP-HP, Service of Pediatric Hematology, Hopital Armand Trousseau, Paris, France
| | - Franco Locatelli
- Bambino Gesù Children's Hospital, Catholic University of Sacred Heart, Rome, Italy
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Diana C J Spierings
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Víctor M Pérez-García
- Mathematical Oncology Laboratory, Department of Mathematics & Institute of Applied Mathematics in Science and Engineering, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
- Red Española de Terápias Avanzadas (TERAV), Instituto de Salud Carlos III, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Department of Biomedicine. School of Medicine, University of Barcelona, Barcelona, Spain.
- Spanish Cancer Research Network (CIBERONC), ISCIII, Barcelona, Spain.
| |
Collapse
|
11
|
Hormann FM, Mooij EJ, van de Mheen M, Beverloo HB, den Boer ML, Boer JM. The impact of an additional copy of chromosome 21 in B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2024; 63:e23217. [PMID: 38087879 DOI: 10.1002/gcc.23217] [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: 09/12/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/04/2024] Open
Abstract
A common finding in pediatric B-cell precursor acute lymphoblastic leukemia (BCPALL) is that chromosome 21 is never lost and an extra chromosome 21 is often gained. This implies an important role for chromosome 21 in the pathobiology of BCPALL, emphasized by the increased risk of BCPALL in children with Down syndrome. However, model systems of chromosome 21 gain are lacking. We therefore developed a BCPALL cell line (Nalm-6, DUX4-rearranged) with an additional chromosome 21 by means of microcell-mediated chromosome transfer. FISH, PCR, multiplex ligation-dependent probe amplification, and whole exome sequencing showed that an additional chromosome 21 was successfully transferred to the recipient cells. Transcription of some but not all genes on chromosome 21 was increased, indicating tight transcriptional regulation. Nalm-6 cells with an additional chromosome 21 proliferated slightly slower compared with parental Nalm-6 and sensitivity to induction chemotherapeutics was mildly increased. The extra copy of chromosome 21 did not confer sensitivity to targeted signaling inhibitors. In conclusion, a BCPALL cell line with an additional human chromosome 21 was developed, validated, and subjected to functional studies, which showed a minor but potentially relevant effect in vitro. This cell line offers the possibility to study further the role of chromosome 21 in ALL.
Collapse
Affiliation(s)
- Femke M Hormann
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Eva J Mooij
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Monique L den Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Judith M Boer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| |
Collapse
|
12
|
Wang M, Phan S, Hayes BH, Discher DE. Genetic heterogeneity in p53-null leukemia increases transiently with spindle assembly checkpoint inhibition and is not rescued by p53. Chromosoma 2024; 133:77-92. [PMID: 37256347 PMCID: PMC10828900 DOI: 10.1007/s00412-023-00800-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/01/2023]
Abstract
Chromosome gains or losses often lead to copy number variations (CNV) and loss of heterozygosity (LOH). Both quantities are low in hematologic "liquid" cancers versus solid tumors in data of The Cancer Genome Atlas (TCGA) that also shows the fraction of a genome affected by LOH is ~ one-half of that with CNV. Suspension cultures of p53-null THP-1 leukemia-derived cells conform to these trends, despite novel evidence here of genetic heterogeneity and transiently elevated CNV after perturbation. Single-cell DNAseq indeed reveals at least 8 distinct THP-1 aneuploid clones with further intra-clonal variation, suggesting ongoing genetic evolution. Importantly, acute inhibition of the mitotic spindle assembly checkpoint (SAC) produces CNV levels that are typical of high-CNV solid tumors, with subsequent cell death and down-selection to novel CNV. Pan-cancer analyses show p53 inactivation associates with aneuploidy, but leukemias exhibit a weaker trend even though p53 inactivation correlates with poor survival. Overexpression of p53 in THP-1 does not rescue established aneuploidy or LOH but slightly increases cell death under oxidative or confinement stress, and triggers p21, a key p53 target, but without affecting net growth. Our results suggest that factors other than p53 exert stronger pressures against aneuploidy in liquid cancers, and identifying such CNV suppressors could be useful across liquid and solid tumor types.
Collapse
Affiliation(s)
- Mai Wang
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Phan
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brandon H Hayes
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Dennis E Discher
- Molecular & Cell Biophysics Lab, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
13
|
Mall R, Kanneganti TD. Comparative analysis identifies genetic and molecular factors associated with prognostic clusters of PANoptosis in glioma, kidney and melanoma cancer. Sci Rep 2023; 13:20962. [PMID: 38017056 PMCID: PMC10684528 DOI: 10.1038/s41598-023-48098-1] [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: 05/27/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
The importance of inflammatory cell death, PANoptosis, in cancer is increasingly being recognized. PANoptosis can promote or inhibit tumorigenesis in context-dependent manners, and a computational approach leveraging transcriptomic profiling of genes involved in PANoptosis has shown that patients can be stratified into PANoptosis High and PANoptosis Low clusters that have significant differences in overall survival for low grade glioma (LGG), kidney renal cell carcinoma (KIRC) and skin cutaneous melanoma (SKCM). However, the molecular mechanisms that contribute to differential prognosis between PANoptosis clusters require further elucidation. Therefore, we performed a comprehensive comparison of genetic, genomic, tumor microenvironment, and pathway characteristics between the PANoptosis High and PANoptosis Low clusters to determine the relevance of each component in driving the differential associations with prognosis for LGG, KIRC and SKCM. Across these cancer types, we found that activation of the proliferation pathway was significantly different between PANoptosis High and Low clusters. In LGG and SKCM, we also found that aneuploidy and immune cell densities and activations contributed to differences in PANoptosis clusters. In individual cancers, we identified important roles for barrier gene pathway activation (in SKCM) and the somatic mutation profiles of driver oncogenes as well as hedgehog signaling pathway activation (in LGG). By identifying these genetic and molecular factors, we can possibly improve the prognosis for at risk-stratified patient populations based on the PANoptosis phenotype in LGG, KIRC and SKCM. This not only advances our mechanistic understanding of cancer but will allow for the selection of optimal treatment strategies.
Collapse
Affiliation(s)
- Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-2794, USA
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Thirumala-Devi Kanneganti
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-2794, USA.
| |
Collapse
|
14
|
Thierry AR, Sanchez C, Colinge J, Pisareva E. Circulating DNA reveals a specific and higher fragmentation of the Y chromosome. Hum Genet 2023; 142:1603-1609. [PMID: 37743368 DOI: 10.1007/s00439-023-02600-x] [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: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Chromosome stability is a key point in genome evolution, particularly that of the Y chromosome. The Y chromosome loss in blood and tumor cells is well established. Through processes that are common to other chromosomes too, the Y chromosome undergoes degradation and fragmentation in the blood stream before elimination. This process gives rise to circulating DNA (cirDNA) fragments, whose examination may provide potential insight into the role of DNA fragmentation in blood for the Y chromosome elimination. In this study, we employed shallow whole genome sequencing (sWGS) to comprehensively assess the total cirDNA and the individual chromosome fragment size profiles in the plasma of healthy male individuals. Here, we show that (i) the fragment size profiles of total circulating DNA (cirDNA) and DNA fragments originating from autosomes and the X chromosome in blood plasma are homogeneous, and have a remarkably low variability (mean CV = 7%) among healthy individuals, (ii) the Y chromosome has a distinct fragment size profile with the accumulation of the fragment < 145 bp and depletion of the dinucleosome-associated fragments (290-390 bp), and its fragment fraction in blood decreases with age. These results indicate a higher fragmentation of the Y chromosome compared to other chromosomes and this in turn might be due to its increased susceptibility to degradation. Our findings pave the way for an elucidation of the impact of chromosomal origin on DNA degradation and the Y chromosome biology.
Collapse
Affiliation(s)
- Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
- ICM, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France.
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Jacques Colinge
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
| |
Collapse
|
15
|
Kuznetsova IL, Uralsky LI, Tyazhelova TV, Andreeva TV, Rogaev EI. Mosaic loss of the Y chromosome in human neurodegenerative and oncological diseases. Vavilovskii Zhurnal Genet Selektsii 2023; 27:502-511. [PMID: 37808213 PMCID: PMC10551935 DOI: 10.18699/vjgb-23-61] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 10/10/2023] Open
Abstract
The development of new biomarkers for prediction and early detection of human diseases, as well as for monitoring the response to therapy is one of the most relevant areas of modern human genetics and genomics. Until recently, it was believed that the function of human Y chromosome genes was limited to determining sex and controlling spermatogenesis. Thanks to occurance of large databases of the genome-wide association study (GWAS), there has been a transition to the use of large samples for analyzing genetic changes in both normal and pathological conditions. This has made it possible to assess the association of mosaic aneuploidy of the Y chromosome in somatic cells with a shorter lifespan in men compared to women. Based on data from the UK Biobank, an association was found between mosaic loss of the Y chromosome (mLOY) in peripheral blood leukocytes and the age of men over 70, as well as a number of oncological, cardiac, metabolic, neurodegenerative, and psychiatric diseases. As a result, mLOY in peripheral blood cells has been considered a potential marker of biological age in men and as a marker of certain age-related diseases. Currently, numerous associations have been identified between mLOY and genes based on GWAS and transcriptomes in affected tissues. However, the exact cause of mLOY and the impact and consequences of this phenomenon at the whole organism level have not been established. In particular, it is unclear whether aneuploidy of the Y chromosome in blood cells may affect the development of pathologies that manifest in other organs, such as the brain in Alzheimer's disease, or whether it is a neutral biomarker of general genomic instability. This review examines the main pathologies and genetic factors associated with mLOY, as well as the hypotheses regarding their interplay. Special attention is given to recent studies on mLOY in brain cells in Alzheimer's disease.
Collapse
Affiliation(s)
- I L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - L I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - T V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia
| | - T V Andreeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
| | - E I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
| |
Collapse
|
16
|
Truong MA, Cané-Gasull P, Lens SMA. Modeling specific aneuploidies: from karyotype manipulations to biological insights. Chromosome Res 2023; 31:25. [PMID: 37640903 PMCID: PMC10462580 DOI: 10.1007/s10577-023-09735-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
An abnormal chromosome number, or aneuploidy, underlies developmental disorders and is a common feature of cancer, with different cancer types exhibiting distinct patterns of chromosomal gains and losses. To understand how specific aneuploidies emerge in certain tissues and how they contribute to disease development, various methods have been developed to alter the karyotype of mammalian cells and mice. In this review, we provide an overview of both classic and novel strategies for inducing or selecting specific chromosomal gains and losses in human and murine cell systems. We highlight how these customized aneuploidy models helped expanding our knowledge of the consequences of specific aneuploidies to (cancer) cell physiology.
Collapse
Affiliation(s)
- My Anh Truong
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Paula Cané-Gasull
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Susanne M A Lens
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands.
| |
Collapse
|
17
|
Fischer GM, Gliem TJ, Greipp PT, Rosenberg AE, Folpe AL, Hornick JL. Anaplastic Kaposi Sarcoma: A Clinicopathologic and Molecular Genetic Analysis. Mod Pathol 2023; 36:100191. [PMID: 37080393 DOI: 10.1016/j.modpat.2023.100191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/22/2023]
Abstract
Kaposi sarcoma (KS) is a human herpesvirus 8 (HHV8)-associated vascular proliferation that most often involves the skin. Rarely, KS shows marked nuclear atypia or pleomorphism; such examples are known as "anaplastic" KS. This poorly characterized variant often pursues an aggressive course; little is known of its genetic landscape. This study evaluated the clinicopathologic and genomic features of anaplastic KS. We identified 9 anaplastic KS cases from 7 patients and 8 conventional KS cases, including a matched conventional KS and primary metastasis anaplastic KS pair from a single patient (anaplastic KS diagnosed 9 years after conventional KS). All patients with anaplastic KS were men, aged 51 to 82 years, who had locally aggressive tumors predominantly affecting the soft tissue and bone of the lower extremities (5/7 patients). Four patients were known to be HIV positive (all on antiretrovirals), 2 were HIV negative, and 1 was of unknown HIV status. The tumors showed angiosarcoma-like or pleomorphic spindle cell sarcoma morphology. Plasma cell-rich chronic inflammation and hemosiderin deposition were commonly present. Single-nucleotide polymorphism-based chromosomal microarray analysis showed the anaplastic KS cohort to demonstrate highly recurrent whole chromosome (chr) gains of chr 7, 11, 19, and 21, which primarily affected olfactory and G protein-coupled receptor signaling and losses of chr6_q and chrY. Compared with conventional KS, anaplastic KS cases showed significantly more total copy number alterations and more frequent gains of chr7 and chr11_q13.1 (MARK2, RELA, and ESRRA, including high copy number gain in 1 case). Pathway analysis demonstrated that these gains preferentially affected genes that facilitate cyclin-dependent cell signaling. Furthermore, anaplastic KS cases were phylogenetically distinct from conventional KS cases, including the patient-matched primary metastasis anaplastic KS pair and conventional KS. Our study is the first to demonstrate that a more complex genome and distinct copy number alterations distinguish anaplastic KS from conventional KS. Gains of chr7 and chr11_q13.1 appear central to biological transformation.
Collapse
Affiliation(s)
- Grant M Fischer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Troy J Gliem
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew E Rosenberg
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| |
Collapse
|
18
|
Qi M, Pang J, Mitsiades I, Lane AA, Rheinbay E. Loss of chromosome Y in primary tumors. Cell 2023; 186:S0092-8674(23)00646-3. [PMID: 37385248 DOI: 10.1016/j.cell.2023.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/17/2023] [Accepted: 06/08/2023] [Indexed: 07/01/2023]
Abstract
Certain cancer types afflict female and male patients disproportionately. The reasons include differences in male/female physiology, effect of sex hormones, risk behavior, environmental exposures, and genetics of the sex chromosomes X and Y. Loss of Y (LOY) is common in peripheral blood cells in aging men, and this phenomenon is associated with several diseases. However, the frequency and role of LOY in tumors is little understood. Here, we present a comprehensive catalog of LOY in >5,000 primary tumors from male patients in the TCGA. We show that LOY rates vary by tumor type and provide evidence for LOY being either a passenger or driver event depending on context. LOY in uveal melanoma specifically is associated with age and survival and is an independent predictor of poor outcome. LOY creates common dependencies on DDX3X and EIF1AX in male cell lines, suggesting that LOY generates unique vulnerabilities that could be therapeutically exploited.
Collapse
Affiliation(s)
- Meifang Qi
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiali Pang
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Irene Mitsiades
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Andrew A Lane
- Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Esther Rheinbay
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital Department of Pathology, Boston, MA 02114, USA.
| |
Collapse
|
19
|
Wang P, Ma J, Li W, Wang Q, Xiao Y, Jiang Y, Gu X, Wu Y, Dong S, Guo H, Li M. Profiling the metabolome of uterine fluid for early detection of ovarian cancer. Cell Rep Med 2023:101061. [PMID: 37267943 DOI: 10.1016/j.xcrm.2023.101061] [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: 09/15/2022] [Revised: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/04/2023]
Abstract
Ovarian cancer (OC) causes high mortality in women because of ineffective biomarkers for early diagnosis. Here, we perform metabolomics analysis on an initial training set of uterine fluid from 96 gynecological patients. A seven-metabolite-marker panel consisting of vanillylmandelic acid, norepinephrine, phenylalanine, beta-alanine, tyrosine, 12-S-hydroxy-5,8,10-heptadecatrienoic acid, and crithmumdiol is established for detecting early-stage OC. The panel is further validated in an independent sample set from 123 patients, discriminating early OC from controls with an area under the curve (AUC) of 0.957 (95% confidence interval [CI], 0.894-1). Interestingly, we find elevated norepinephrine and decreased vanillylmandelic acid in most OC cells, resulting from excess 4-hydroxyestradiol that antagonizes the catabolism of norepinephrine by catechol-O-methyltransferase. Moreover, exposure to 4-hydroxyestradiol induces cellular DNA damage and genomic instability that could lead to tumorigenesis. Thus, this study not only reveals metabolic features in uterine fluid of gynecological patients but also establishes a noninvasive approach for the early diagnosis of OC.
Collapse
Affiliation(s)
- Pan Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China
| | - Jihong Ma
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China
| | - Wenjing Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China
| | - Qilong Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yinan Xiao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China
| | - Yuening Jiang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China
| | - Xiaoyang Gu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China
| | - Yu Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China; Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China.
| | - Mo Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing 100191, China.
| |
Collapse
|
20
|
Gialesaki S, Bräuer-Hartmann D, Issa H, Bhayadia R, Alejo-Valle O, Verboon L, Schmell AL, Laszig S, Regényi E, Schuschel K, Labuhn M, Ng M, Winkler R, Ihling C, Sinz A, Glaß M, Hüttelmaier S, Matzk S, Schmid L, Strüwe FJ, Kadel SK, Reinhardt D, Yaspo ML, Heckl D, Klusmann JH. RUNX1 isoform disequilibrium promotes the development of trisomy 21-associated myeloid leukemia. Blood 2023; 141:1105-1118. [PMID: 36493345 PMCID: PMC10023736 DOI: 10.1182/blood.2022017619] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/08/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Gain of chromosome 21 (Hsa21) is among the most frequent aneuploidies in leukemia. However, it remains unclear how partial or complete amplifications of Hsa21 promote leukemogenesis and why children with Down syndrome (DS) (ie, trisomy 21) are particularly at risk of leukemia development. Here, we propose that RUNX1 isoform disequilibrium with RUNX1A bias is key to DS-associated myeloid leukemia (ML-DS). Starting with Hsa21-focused CRISPR-CRISPR-associated protein 9 screens, we uncovered a strong and specific RUNX1 dependency in ML-DS cells. Expression of the RUNX1A isoform is elevated in patients with ML-DS, and mechanistic studies using murine ML-DS models and patient-derived xenografts revealed that excess RUNX1A synergizes with the pathognomonic Gata1s mutation during leukemogenesis by displacing RUNX1C from its endogenous binding sites and inducing oncogenic programs in complex with the MYC cofactor MAX. These effects were reversed by restoring the RUNX1A:RUNX1C equilibrium in patient-derived xenografts in vitro and in vivo. Moreover, pharmacological interference with MYC:MAX dimerization using MYCi361 exerted strong antileukemic effects. Thus, our study highlights the importance of alternative splicing in leukemogenesis, even on a background of aneuploidy, and paves the way for the development of specific and targeted therapies for ML-DS, as well as for other leukemias with Hsa21 aneuploidy or RUNX1 isoform disequilibrium.
Collapse
Affiliation(s)
- Sofia Gialesaki
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Daniela Bräuer-Hartmann
- Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Hasan Issa
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Raj Bhayadia
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Oriol Alejo-Valle
- Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Lonneke Verboon
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anna-Lena Schmell
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephanie Laszig
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Enikő Regényi
- Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Konstantin Schuschel
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maurice Labuhn
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Michelle Ng
- Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Robert Winkler
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Markus Glaß
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Sören Matzk
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lena Schmid
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | | | - Sofie-Katrin Kadel
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Dirk Reinhardt
- Pediatric Hematology and Oncology, Pediatrics III, University Hospital Essen, Essen, Germany
| | | | - Dirk Heckl
- Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Halle, Germany
- Dirk Heckl, Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, Ernst-Grube-Str. 40, 06120 Halle, Germany;
| | - Jan-Henning Klusmann
- Department of Pediatrics, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Correspondence: Jan-Henning Klusmann, Department of Pediatrics, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany;
| |
Collapse
|
21
|
van den Bosch T, Derks S, Miedema DM. Chromosomal Instability, Selection and Competition: Factors That Shape the Level of Karyotype Intra-Tumor Heterogeneity. Cancers (Basel) 2022; 14:cancers14204986. [PMID: 36291770 PMCID: PMC9600040 DOI: 10.3390/cancers14204986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Each cancer consists of billions of cells. These cells are far from identical; hence, the population of cells that constitute a tumor is heterogeneous. A salient property that varies between cells in a tumor is their karyotype, the number and configuration of the chromosomes. The level of karyotype heterogeneity can be used to predict the survival of a patient. In this review, we describe the processes that shape the level of karyotype heterogeneity in a cancer. Abstract Intra-tumor heterogeneity (ITH) is a pan-cancer predictor of survival, with high ITH being correlated to a dismal prognosis. The level of ITH is, hence, a clinically relevant characteristic of a malignancy. ITH of karyotypes is driven by chromosomal instability (CIN). However, not all new karyotypes generated by CIN are viable or competitive, which limits the amount of ITH. Here, we review the cellular processes and ecological properties that determine karyotype ITH. We propose a framework to understand karyotype ITH, in which cells with new karyotypes emerge through CIN, are selected by cell intrinsic and cell extrinsic selective pressures, and propagate through a cancer in competition with other malignant cells. We further discuss how CIN modulates the cell phenotype and immune microenvironment, and the implications this has for the subsequent selection of karyotypes. Together, we aim to provide a comprehensive overview of the biological processes that shape the level of karyotype heterogeneity.
Collapse
Affiliation(s)
- Tom van den Bosch
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
| | - Sarah Derks
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Department of Medical Oncology, Amsterdam University Medical Centers—Location VUmc, 1081 HV Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
| | - Daniël M. Miedema
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers—Location AMC, 1105 AZ Amsterdam, The Netherlands
- Oncode Institute, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (S.D.); (D.M.M.)
| |
Collapse
|
22
|
Audrey A, de Haan L, van Vugt MATM, de Boer HR. Processing DNA lesions during mitosis to prevent genomic instability. Biochem Soc Trans 2022; 50:1105-1118. [PMID: 36040211 PMCID: PMC9444068 DOI: 10.1042/bst20220049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022]
Abstract
Failure of cells to process toxic double-strand breaks (DSBs) constitutes a major intrinsic source of genome instability, a hallmark of cancer. In contrast with interphase of the cell cycle, canonical repair pathways in response to DSBs are inactivated in mitosis. Although cell cycle checkpoints prevent transmission of DNA lesions into mitosis under physiological condition, cancer cells frequently display mitotic DNA lesions. In this review, we aim to provide an overview of how mitotic cells process lesions that escape checkpoint surveillance. We outline mechanisms that regulate the mitotic DNA damage response and the different types of lesions that are carried over to mitosis, with a focus on joint DNA molecules arising from under-replication and persistent recombination intermediates, as well as DNA catenanes. Additionally, we discuss the processing pathways that resolve each of these lesions in mitosis. Finally, we address the acute and long-term consequences of unresolved mitotic lesions on cellular fate and genome stability.
Collapse
Affiliation(s)
- Anastasia Audrey
- Department of Medical Oncology, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands
| | - Lauren de Haan
- Department of Medical Oncology, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands
| | - H Rudolf de Boer
- Department of Medical Oncology, University Medical Center Groningen, Hanzeplein 1, 9713GZ Groningen, The Netherlands
| |
Collapse
|
23
|
Li M, Gao F, Ren X, Dong G, Chen H, Lin AY, Wang DD, Liu M, Lin PP, Shen S, Jiang H, Yang C, Zhang X, Zhao X, Zhu Q, Li M, Cui Y, Lin S. Non‐hematogenic circulating aneuploid cells confer inferior prognosis and therapeutic resistance in gliomas. Cancer Sci 2022; 113:3535-3546. [PMID: 35940591 PMCID: PMC9530864 DOI: 10.1111/cas.15516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/27/2022] Open
Abstract
Aneuploidy is the hallmark of malignancy. Our previous study successfully detected nonhematogenic circulating aneuploidy cells (CACs) in types of gliomas. The current prospective clinical study aims to further precisely subcategorize aneuploid CACs, including CD31− circulating tumor cells (CTCs) and CD31+ circulating tumor endothelial cells, and thoroughly investigate the clinical utilities of these different subtypes of cells. Co‐detection and analysis of CTCs and circulating tumor‐derived endothelial cells (CTECs) expressing CD133, glial fibrillary acidic protein (GFAP), or epidermal growth factor receptor variant III (EGFR vIII) were performed by integrated subtraction enrichment and immunostaining fluorescence in situ hybridization (SE‐iFISH) in 111 preoperative primary diffuse glioma patients. Aneuploid CACs could be detected in most de novo glioma patients. Among detected CACs, 45.6% were CD31−/CD45− aneuploid CTCs and the remaining 54.4% were CD31+/CD45− aneuploid CTECs. Positive detection of CTECs significantly correlated with disruption of the blood–brain barrier. The median number of large CTCs (LCTCs, >5 μm, 2) in low‐grade glioma (WHO grade 2) was less than high‐grade glioma (WHO grades 3 and 4) (3, p = 0.044), but this difference was not observed in small CTCs (SCTCs, ≤5 μm), CTECs or CACs (CTCs + CTECs). The numbers of CTCs, CTECs, or CACs in patients with contrast‐enhancing (CE) lesions considerably exceeded that of non‐CE lesions (p < 0.05). Receiver operating characteristic curves demonstrated that CD31+ CTECs, especially LCTECs, exhibited a close positive relationship with CE lesions. Survival analysis revealed that the high number of CD31− CTCs could be an adverse factor for compromised progression‐free survival and overall survival. Longitudinal surveillance of CD31− CTCs was suitable for evaluating the therapeutic response and for monitoring potential emerging treatment resistance.
Collapse
Affiliation(s)
- Mingxiao Li
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Faliang Gao
- Department of Neurosurgery, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou, People’s Hospital of Hangzhou Medical College Hangzhou Zhejiang China
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province Hangzhou Zhejiang China
| | - Xiaohui Ren
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital Capital Medical University Beijing China
| | - Hongyan Chen
- Department of Radiology, Beijing Tiantan Hospital Capital Medical University Beijing China
| | | | | | - Mingyang Liu
- Department of Medicine University of Oklahoma Health Science Center Oklahoma City OK USA
| | | | - Shaoping Shen
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Haihui Jiang
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Chuanwei Yang
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Xiaokang Zhang
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Xuzhe Zhao
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Qinghui Zhu
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Ming Li
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Yong Cui
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
| | - Song Lin
- Department of Neuro‐surgical Oncology, National Clinical Research Center for Neurological Diseases Capital Medical University Beijing China
- Department of Neurosurgery, Beijing Neurosurgical Institute Capital Medical University Beijing China
- Center of Brain Tumor Beijing Institute for Brain Disorders Beijing China
- Beijing Key Laboratory of Brain Tumor Beijing China
| |
Collapse
|
24
|
Klaasen SJ, Truong MA, van Jaarsveld RH, Koprivec I, Štimac V, de Vries SG, Risteski P, Kodba S, Vukušić K, de Luca KL, Marques JF, Gerrits EM, Bakker B, Foijer F, Kind J, Tolić IM, Lens SMA, Kops GJPL. Nuclear chromosome locations dictate segregation error frequencies. Nature 2022; 607:604-609. [PMID: 35831506 PMCID: PMC9300461 DOI: 10.1038/s41586-022-04938-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 06/07/2022] [Indexed: 12/25/2022]
Abstract
Chromosome segregation errors during cell divisions generate aneuploidies and micronuclei, which can undergo extensive chromosomal rearrangements such as chromothripsis1-5. Selective pressures then shape distinct aneuploidy and rearrangement patterns-for example, in cancer6,7-but it is unknown whether initial biases in segregation errors and micronucleation exist for particular chromosomes. Using single-cell DNA sequencing8 after an error-prone mitosis in untransformed, diploid cell lines and organoids, we show that chromosomes have different segregation error frequencies that result in non-random aneuploidy landscapes. Isolation and sequencing of single micronuclei from these cells showed that mis-segregating chromosomes frequently also preferentially become entrapped in micronuclei. A similar bias was found in naturally occurring micronuclei of two cancer cell lines. We find that segregation error frequencies of individual chromosomes correlate with their location in the interphase nucleus, and show that this is highest for peripheral chromosomes behind spindle poles. Randomization of chromosome positions, Cas9-mediated live tracking and forced repositioning of individual chromosomes showed that a greater distance from the nuclear centre directly increases the propensity to mis-segregate. Accordingly, chromothripsis in cancer genomes9 and aneuploidies in early development10 occur more frequently for larger chromosomes, which are preferentially located near the nuclear periphery. Our findings reveal a direct link between nuclear chromosome positions, segregation error frequencies and micronucleus content, with implications for our understanding of tumour genome evolution and the origins of specific aneuploidies during development.
Collapse
Affiliation(s)
- Sjoerd J Klaasen
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - My Anh Truong
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | | | - Sippe G de Vries
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | | | | | - Kim L de Luca
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Joana F Marques
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Elianne M Gerrits
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Bjorn Bakker
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Floris Foijer
- Department of Ageing Biology/ERIBA, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Jop Kind
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | - Susanne M A Lens
- Oncode Institute, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute-KNAW (Royal Academy of Arts and Sciences) and University Medical Centre Utrecht, Utrecht, the Netherlands.
| |
Collapse
|
25
|
Schukken KM, Sheltzer JM. Extensive protein dosage compensation in aneuploid human cancers. Genome Res 2022; 32:1254-1270. [PMID: 35701073 PMCID: PMC9341510 DOI: 10.1101/gr.276378.121] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/01/2022] [Indexed: 01/03/2023]
Abstract
Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we conducted an analysis of hundreds of human cancer cell lines and tumors with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins show dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has a moderate effect on the expression of oncogenes and tumor suppressors, showing that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.
Collapse
|
26
|
Su J, Han X, Xu X, Ding W, Li M, Wang W, Tian M, Chen X, Xu B, Chen Z, Yuan J, Qin X, Lin D, Wang R, Gong Y, Pan L, Wang J, Wang M. Simultaneous Detection of Pathogens and Tumors in Patients With Suspected Infections by Next-Generation Sequencing. Front Cell Infect Microbiol 2022; 12:892087. [PMID: 35755839 PMCID: PMC9218804 DOI: 10.3389/fcimb.2022.892087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background Differential diagnosis of patients with suspected infections is particularly difficult, but necessary for prompt diagnosis and rational use of antibiotics. A substantial proportion of these patients have non-infectious diseases that include malignant tumors. This study aimed to explore the clinical value of metagenomic next-generation sequencing (mNGS) for tumor detection in patients with suspected infections. Methods A multicenter, prospective case study involving patients diagnosed with suspected infections was conducted in four hospitals in Shanghai, China between July 2019 and January 2020. Based upon mNGS technologies and chromosomal copy number variation (CNV) analysis on abundant human genome, a new procedure named Onco-mNGS was established to simultaneously detect pathogens and malignant tumors in all of the collected samples from patients. Results Of 140 patients screened by Onco-mNGS testing, 115 patients were diagnosed with infections; 17 had obvious abnormal CNV signals indicating malignant tumors that were confirmed clinically. The positive percent agreement and negative percent agreement of mNGS testing compared to clinical diagnosis was 53.0% (61/115) and 60% (15/25), vs. 20.9% (24/115) and 96.0% (24/25), respectively, for conventional microbiological testing (both P <0.01). Klebsiella pneumoniae (14.8%, 9/61) was the most common pathogen detected by mNGS, followed by Escherichia coli (11.5%, 7/61) and viruses (11.5%, 7/61). The chromosomal abnormalities of the 17 cases included genome-wide variations and local variations of a certain chromosome. Five of 17 patients had a final confirmed with malignant tumors, including three lung adenocarcinomas and two hematological tumors; one patient was highly suspected to have lymphoma; and 11 patients had a prior history of malignant tumor. Conclusion This preliminary study demonstrates the feasibility and clinical value of using Onco-mNGS to simultaneously search for potential pathogens and malignant tumors in patients with suspected infections.
Collapse
Affiliation(s)
- Jiachun Su
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xu Han
- Research and Development Department, MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,The National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai, China
| | - Wenchao Ding
- Research and Development Department, MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Ming Li
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiqin Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mi Tian
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiyuan Chen
- Department of Critical Care Medicine, Jing'an District Centre Hospital, Fudan University, Shanghai, China
| | - Binbin Xu
- Department of Neurosurgery, Putuo District People's Hospital, Tongji University, Shanghai, China
| | - Zhongqing Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinyi Yuan
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaohua Qin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Dongfang Lin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye Gong
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Liping Pan
- Department of Critical Care Medicine, Jing'an District Centre Hospital, Fudan University, Shanghai, China
| | - Jun Wang
- Research and Development Department, MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,The National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai, China
| |
Collapse
|
27
|
Zhou J, Ouyang G, Wu L, Zhang M, Weng R, Lin S, Wang Y, Li K, Yang X, Wu Y, Liang Z, Li F, Qu S, Yang X. Simulated confined placental mosaicism proportion (SCPMP) based on cell-free fetal DNA fraction enrichment can reduce false-positive results in non-invasive prenatal testing. Prenat Diagn 2022; 42:1008-1014. [PMID: 35441712 DOI: 10.1002/pd.6150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/25/2022] [Accepted: 04/14/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To decrease the false-positive rate of NIPT using cell-free fetal DNA (cffDNA) fraction enrichment and the simulated confined placental mosaicism proportion (SCPMP) threshold application via cffDNA quantification. METHOD Using a cffDNA enrichment method, 303 plasma samples with positive NIPT results (Z-score > 3.0; 200 true-positive and 103 false-positive cases) were re-sequenced. A method to calculate the SCPMP based on the quantified cffDNA fraction was developed; the SCPMP threshold between true- and false-positive NIPT results was determined and used for re-analyses. RESULTS With enrichment, the fetal fraction of the 303 samples was 26.9 ± 8.4%, compared to 11.0 ± 3.2% without enrichment. The optimized threshold method with double determination using the Z-value-defined SCPMP can reduce the false-positive rates for trisomies 21, 18, and 13 by 87%, 80%, and 88.9%, respectively. CONCLUSION Our optimized method can decrease the false-positive rate of NIPT results. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Junhua Zhou
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Guojun Ouyang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Long Wu
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Min Zhang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Rongtao Weng
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Shuman Lin
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Yuanli Wang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xu Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yingsong Wu
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Fenxia Li
- Department of obstetrics and Gynecology, Nanfang Hospital, Southern Medical university, Guangzhou, Guangdong, China
| | - Shoufang Qu
- National Institutes for Food and Drug Control, Beijing, 100050
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| |
Collapse
|
28
|
Köferle A, Schlattl A, Hörmann A, Thatikonda V, Popa A, Spreitzer F, Ravichandran MC, Supper V, Oberndorfer S, Puchner T, Wieshofer C, Corcokovic M, Reiser C, Wöhrle S, Popow J, Pearson M, Martinez J, Weitzer S, Mair B, Neumüller RA. Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes. Cell Rep 2022; 39:110636. [PMID: 35417719 DOI: 10.1016/j.celrep.2022.110636] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 03/16/2022] [Indexed: 02/07/2023] Open
Abstract
Genetic networks are characterized by extensive buffering. During tumor evolution, disruption of functional redundancies can create de novo vulnerabilities that are specific to cancer cells. Here, we systematically search for cancer-relevant paralog interactions using CRISPR screens and publicly available loss-of-function datasets. Our analysis reveals >2,000 candidate dependencies, several of which we validate experimentally, including CSTF2-CSTF2T, DNAJC15-DNAJC19, FAM50A-FAM50B, and RPP25-RPP25L. We provide evidence that RPP25L can physically and functionally compensate for the absence of RPP25 as a member of the RNase P/MRP complexes in tRNA processing. Our analysis also reveals unexpected redundancies between sex chromosome genes. We show that chrX- and chrY-encoded paralogs, such as ZFX-ZFY, DDX3X-DDX3Y, and EIF1AX-EIF1AY, are functionally linked. Tumor cell lines from male patients with loss of chromosome Y become dependent on the chrX-encoded gene. We propose targeting of chrX-encoded paralogs as a general therapeutic strategy for human tumors that have lost the Y chromosome.
Collapse
Affiliation(s)
- Anna Köferle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Andreas Schlattl
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Hörmann
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Venu Thatikonda
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Alexandra Popa
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Fiona Spreitzer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | | | - Verena Supper
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Sarah Oberndorfer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Corinna Wieshofer
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Maja Corcokovic
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Christoph Reiser
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Barbara Mair
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| | - Ralph A Neumüller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria.
| |
Collapse
|
29
|
Arpas T, Jelinkova H, Hrabovsky S, Orsulova M, Vrzalova Z, Navrkalova V, Brhelova E, Bryjova L, Bulikova A, Ondrouskova E, Sejnohova M, Folber F, Sedová P, Mayer J, Pospisilova S, Jarosova M, Doubek M. Very rare near-haploid acute lymphoblastic leukemia resistant to immunotherapy and CAR-T therapy in 19-year-old male patient. Clin Case Rep 2022; 10:e05545. [PMID: 35280086 PMCID: PMC8894580 DOI: 10.1002/ccr3.5545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/17/2022] [Accepted: 02/06/2022] [Indexed: 02/02/2023] Open
Abstract
Near-haploid acute lymphoblastic leukemia is rare subgroup of the disease, which is very important due to very poor prognosis and resistance to treatment including novel monoclonal antibodies and CAR-T therapy.
Collapse
Affiliation(s)
- Tomas Arpas
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Hana Jelinkova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Stepan Hrabovsky
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Martina Orsulova
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Zuzana Vrzalova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzechia
| | - Veronika Navrkalova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Eva Brhelova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Lenka Bryjova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Alena Bulikova
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
- Department of Clinical HematologyUniversity HospitalBrnoCzechia
| | - Eva Ondrouskova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Marketa Sejnohova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Frantisek Folber
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Petra Sedová
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Jiri Mayer
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Sarka Pospisilova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzechia
- Department of Medical Genetics and GenomicsUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Marie Jarosova
- Center of Molecular Biology and GeneticsDepartment of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
- Department of Medical Genetics and GenomicsUniversity Hospital and Faculty of MedicineBrnoCzechia
| | - Michael Doubek
- Department of Internal Medicine, Hematology and OncologyUniversity Hospital and Faculty of MedicineBrnoCzechia
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzechia
- Department of Medical Genetics and GenomicsUniversity Hospital and Faculty of MedicineBrnoCzechia
| |
Collapse
|
30
|
The spectrum of sex differences in cancer. Trends Cancer 2022; 8:303-315. [PMID: 35190302 PMCID: PMC8930612 DOI: 10.1016/j.trecan.2022.01.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
Sex differences in cellular and systems biology have been evolutionarily selected to optimize reproductive success in all species with little (sperm) and big (ova) gamete producers. They are evident from the time of fertilization and accrue throughout development through genetic, epigenetic, and circulating sex hormone-dependent mechanisms. Among other effects, they significantly impact on chromatin organization, metabolism, cell cycle regulation, immunity, longevity, and cancer risk and survival. Sex differences in cancer should be expected and accounted for in basic, translational, and clinical oncology research.
Collapse
|
31
|
Abstract
Aneuploidy, a genomic alternation characterized by deviations in the copy number of chromosomes, affects organisms from early development through to aging. Although it is a main cause of human pregnancy loss and a hallmark of cancer, how aneuploidy affects cellular function has been elusive. The last two decades have seen rapid advances in the understanding of the causes and consequences of aneuploidy at the molecular and cellular levels. These studies have uncovered effects of aneuploidy that can be beneficial or detrimental to cells and organisms in an environmental context-dependent and karyotype-dependent manner. Aneuploidy also imposes general stress on cells that stems from an imbalanced genome and, consequently, also an imbalanced proteome. These insights provide the fundamental framework for understanding the impact of aneuploidy in genome evolution, human pathogenesis and drug resistance.
Collapse
|
32
|
Shohat S, Vol E, Shifman S. Gene essentiality in cancer cell lines is modified by the sex chromosomes. Genome Res 2022; 32:1993-2002. [PMID: 36418059 PMCID: PMC9808629 DOI: 10.1101/gr.276488.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
Human sex differences arise from gonadal hormones and sex chromosomes. Studying the direct effects of sex chromosomes in humans is still challenging. Here we studied how the sex chromosomes can modulate gene expression and the outcome of mutations across the genome by exploiting the tendency of cancer cell lines to lose or gain sex chromosomes. We inferred the dosage of the sex chromosomes in 355 female and 408 male cancer cell lines and used it to dissect the contributions of the Y and X Chromosomes to sex-biased gene expression. Furthermore, based on genome-wide CRISPR screens, we identified genes whose essentiality is different between male and female cells depending on the sex chromosomes. The most significant genes were X-linked genes compensated by Y-linked paralogs. Our sex-based analysis identifies genes that, when mutated, can affect male and female cells differently and reinforces the roles of the X and Y Chromosomes in sex-specific cell function.
Collapse
|
33
|
Rempfer C, Wiedemann G, Schween G, Kerres KL, Lucht JM, Horres R, Decker EL, Reski R. Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella. PLANT CELL REPORTS 2022; 41:153-173. [PMID: 34636965 PMCID: PMC8803787 DOI: 10.1007/s00299-021-02794-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
In Physcomitrella, whole-genome duplications affected the expression of about 3.7% of the protein-encoding genes, some of them relevant for DNA repair, resulting in a massively reduced gene-targeting frequency. Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome (WGD), might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant mosses. Whereas angiosperms repair DNA double-strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in the moss Physcomitrella homologous recombination (HR) is the main DNA-DSB repair pathway. HR facilitates the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in Physcomitrella using haploid plants and autodiploid plants, generated via an artificial WGD. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the WGD event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p < 0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.
Collapse
Affiliation(s)
- Christine Rempfer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Gabriele Schween
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Corteva Agriscience, Pioneer Hi-Bred Northern Europe, Münstertäler Strasse 26, 79427, Eschbach, Germany
| | - Klaus L Kerres
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jan M Lucht
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Scienceindustries, Nordstrasse 15, 8006, Zurich, Switzerland
| | - Ralf Horres
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, Schaenzlestr. 18, 79104, Freiburg, Germany.
| |
Collapse
|
34
|
Yu JE, Kim S, Hwang J, Hong JT, Hwang J, Soung N, Cha‐Molstad H, Kwon YT, Kim BY, Lee KH. Phosphorylation of β-catenin Ser60 by polo-like kinase 1 drives the completion of cytokinesis. EMBO Rep 2021; 22:e51503. [PMID: 34585824 PMCID: PMC8647012 DOI: 10.15252/embr.202051503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/31/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
β-Catenin is a multifunctional protein and participates in numerous processes required for embryonic development, cell proliferation, and homeostasis through various molecular interactions and signaling pathways. To date, however, there is no direct evidence that β-catenin contributes to cytokinesis. Here, we identify a novel p-S60 epitope on β-catenin generated by Plk1 kinase activity, which can be found at the actomyosin contractile ring of early telophase cells and at the midbody of late telophase cells. Depletion of β-catenin leads to cytokinesis-defective phenotypes, which eventually result in apoptotic cell death. In addition, phosphorylation of β-catenin Ser60 by Plk1 is essential for the recruitment of Ect2 to the midbody, activation of RhoA, and interaction between β-catenin, Plk1, and Ect2. Time-lapse image analysis confirmed the importance of β-catenin phospho-Ser60 in furrow ingression and the completion of cytokinesis. Taken together, we propose that phosphorylation of β-catenin Ser60 by Plk1 in cooperation with Ect2 is essential for the completion of cytokinesis. These findings may provide fundamental knowledge for the research of cytokinesis failure-derived human diseases.
Collapse
Affiliation(s)
- Ji Eun Yu
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
- Department of Drug Discovery and DevelopmentCollege of PharmacyChungbuk National UniversityCheongjuKorea
| | - Sun‐Ok Kim
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Jeong‐Ah Hwang
- Department of PhysiologyResearch Institute of Medical SciencesCollege of MedicineChungnam National UniversityDaejeonKorea
| | - Jin Tae Hong
- Department of Drug Discovery and DevelopmentCollege of PharmacyChungbuk National UniversityCheongjuKorea
| | - Joonsung Hwang
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Nak‐Kyun Soung
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Hyunjoo Cha‐Molstad
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| | - Yong Tae Kwon
- Protein Metabolism Medical Research Center and Department of Biomedical SciencesCollege of MedicineSeoul National UniversitySeoulKorea
| | - Bo Yeon Kim
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
- Department of Biomolecular ScienceUniversity of Science and TechnologyDaejeonKorea
| | - Kyung Ho Lee
- Anticancer Agent Research CenterKorea Research Institute of Bioscience and Biotechnology (KRIBB)OchangChungbukKorea
| |
Collapse
|
35
|
Mettman D, Saeed A, Shold J, Laury R, Ly A, Khan I, Golem S, Olyaee M, O'Neil M. Refined pancreatobiliary UroVysion criteria and an approach for further optimization. Cancer Med 2021; 10:5725-5738. [PMID: 34374212 PMCID: PMC8419786 DOI: 10.1002/cam4.4043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/12/2021] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
Pancreatobiliary strictures are a common source of false negatives for malignancy detection. UroVysion is more sensitive than any other method but remains underutilized because of conflicting sensitivities and specificities due to a lack of standardized cutoff criteria and confusion in interpreting results in the context of primary sclerosing cholangitis. We set out to determine the sensitivities and specificities of UroVysion, brushing cytology, forceps biopsies, and fine needle aspiration (FNAs) for pancreatobiliary stricture malignancy detection. A retrospective review was performed of all biopsied pancreatobiliary strictures at our institution over 5 years. UroVysion was unquestionably the most sensitive method and all methods were highly specific. Sensitivity was highest while maintaining specificity when a malignant interpretation was limited to cases with 5+ cells with the same polysomic signal pattern and/or loss of one or both 9p21 signals. Only UroVysion detected the metastases and a neuroendocrine tumor. In reviewing and analyzing the signal patterns, we noticed trends according to location and diagnosis. Herein we describe our method for analyzing signal patterns and propose cutoff criteria based upon observations gleaned from such analysis.
Collapse
Affiliation(s)
- Daniel Mettman
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Azhar Saeed
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Janna Shold
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Raquele Laury
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Andrew Ly
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Irfan Khan
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Shivani Golem
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Mojtaba Olyaee
- Department of Internal MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Maura O'Neil
- Department of Pathology and Laboratory MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| |
Collapse
|
36
|
Glenfield C, Innan H. Gene Duplication and Gene Fusion Are Important Drivers of Tumourigenesis during Cancer Evolution. Genes (Basel) 2021; 12:1376. [PMID: 34573358 PMCID: PMC8466788 DOI: 10.3390/genes12091376] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently observed in human malignancies and many of the products of these events are pathogenic, representing significant drivers of tumourigenesis and cancer evolution. In certain subsets of cancers duplicated and fused genes appear to be essential for initiation of tumour formation, and some even have the capability of transforming normal cells, highlighting the importance of understanding the events that result in their formation. The mechanisms that drive gene duplication and fusion are unregulated in cancer and they facilitate rapid evolution by selective forces akin to Darwinian survival of the fittest on a cellular level. In this review, we examine current knowledge of the landscape and prevalence of gene duplication and gene fusion in human cancers.
Collapse
Affiliation(s)
| | - Hideki Innan
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawar 240-0193, Japan;
| |
Collapse
|
37
|
Rafferty K, Archer KJ, Turner K, Brown R, Jackson-Cook C. Trisomy 21-associated increases in chromosomal instability are unmasked by comparing isogenic trisomic/disomic leukocytes from people with mosaic Down syndrome. PLoS One 2021; 16:e0254806. [PMID: 34283872 PMCID: PMC8291705 DOI: 10.1371/journal.pone.0254806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022] Open
Abstract
Down syndrome, which results from a trisomic imbalance for chromosome 21, has been associated with 80+ phenotypic traits. However, the cellular changes that arise in somatic cells due to this aneuploid condition are not fully understood. The primary aim of this study was to determine if germline trisomy 21 is associated with an increase in spontaneous somatic cell chromosomal instability frequencies (SCINF). To achieve this aim, we quantified SCINF in people with mosaic Down syndrome using a cytokinesis-blocked micronucleus assay. By comparing values in their isogenic trisomic/disomic cells, we obtained a measure of differences in SCINF that are directly attributable to a trisomy 21 imbalance, since differential effects attributable to "background" genetic factors and environmental exposures could be eliminated. A cross-sectional assessment of 69 people with mosaic Down syndrome (ages 1 to 44; mean age of 12.84 years) showed a significantly higher frequency of micronuclei in their trisomic (0.37 ± 0.35 [mean ± standard deviation]) compared to disomic cells (0.18 ± 0.11)(P <0.0001). The daughter binucleates also showed significantly higher levels of abnormal patterns in the trisomic (1.68 ± 1.21) compared to disomic (0.35 ± 0.45) cells (P <0.0001). Moreover, a significant Age x Cell Type interaction was noted (P = 0.0113), indicating the relationship between age and SCINF differed between the trisomic and disomic cells. Similarly, a longitudinal assessment (mean time interval of 3.9 years; range of 2 to 6 years) of 18 participants showed a mean 1.63-fold increase in SCINF within individuals over time for their trisomic cells (P = 0.0186), compared to a 1.13-fold change in their disomic cells (P = 0.0464). In summary, these results showed a trisomy 21-associated, age-related increase in SCINF. They also underscore the strength of the isogenic mosaic Down syndrome model system for "unmasking" cellular changes arising from a trisomy 21 imbalance.
Collapse
Affiliation(s)
- Kelly Rafferty
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kellie J. Archer
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Kristi Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Ruth Brown
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Colleen Jackson-Cook
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
| |
Collapse
|
38
|
Bai Y, Guan X, Wei W, Feng Y, Meng H, Li G, Li H, Li M, Wang C, Fu M, Jie J, Zhang X, He M, Guo H. Effects of polycyclic aromatic hydrocarbons and multiple metals co-exposure on the mosaic loss of chromosome Y in peripheral blood. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125519. [PMID: 33676251 DOI: 10.1016/j.jhazmat.2021.125519] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Mosaic loss of chromosome Y (mLOY) is an indicator of genome instability, but the environmental stressors of mLOY remained largely unknown. In this study, we detected the internal exposure levels of 11 polycyclic aromatic hydrocarbon (PAH) metabolites and 22 metals among 888 coke-oven workers, and calculated their blood mLOY based on genome-wide SNP genotyping data and presented as median log R ratio (mLRR-Y). The generalized linear model (GLM), LASSO, and Bayesian kernel machine regression (BKMR), were used to select mLOY-relevant chemicals. The results of these models consistently suggested the negative dose-response relationships of urinary 1-hydroxynaphthalene (1-OHNa), antimony (Sb), and molybdenum (Mo) with mLRR-Y. There were no pairwise interactions between these three chemicals (Pinteraction > 0.05), but subjects with high exposure to ≥ 2 kinds of these chemicals showed reducing mLRR-Y [β(95%CI) = - 0.015(- 0.023, - 0.008)], increasing oxidative DNA damage (marked by 8-hydroxydeoxyguanosine) [β(95%CI) = 0.625(0.454, 0.796)] and chromosome damage (marked by micronucleus frequency in lymphocytes) [frequency ratio (FR) and 95%CI = 1.146(1.047, 1.225)] than those with low exposure to all these chemicals. The combined effects of 1-OHNa, Sb, and Mo on elevating DNA damage may partly explain their joint effects on increased blood mLOY. These results provided a new insight into environmental hazards co-exposure on chromosome-Y deletions.
Collapse
Affiliation(s)
- Yansen Bai
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Guan
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Wei
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yue Feng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hua Meng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guyanan Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hang Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengying Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chenming Wang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ming Fu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiali Jie
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Meian He
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huan Guo
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| |
Collapse
|
39
|
Wagenblast E, Araújo J, Gan OI, Cutting SK, Murison A, Krivdova G, Azkanaz M, McLeod JL, Smith SA, Gratton BA, Marhon SA, Gabra M, Medeiros JJF, Manteghi S, Chen J, Chan-Seng-Yue M, Garcia-Prat L, Salmena L, De Carvalho DD, Abelson S, Abdelhaleem M, Chong K, Roifman M, Shannon P, Wang JCY, Hitzler JK, Chitayat D, Dick JE, Lechman ER. Mapping the cellular origin and early evolution of leukemia in Down syndrome. Science 2021; 373:eabf6202. [PMID: 34244384 DOI: 10.1126/science.abf6202] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/09/2021] [Accepted: 05/21/2021] [Indexed: 12/14/2022]
Abstract
Children with Down syndrome have a 150-fold increased risk of developing myeloid leukemia, but the mechanism of predisposition is unclear. Because Down syndrome leukemogenesis initiates during fetal development, we characterized the cellular and developmental context of preleukemic initiation and leukemic progression using gene editing in human disomic and trisomic fetal hematopoietic cells and xenotransplantation. GATA binding protein 1 (GATA1) mutations caused transient preleukemia when introduced into trisomy 21 long-term hematopoietic stem cells, where a subset of chromosome 21 microRNAs affected predisposition to preleukemia. By contrast, progression to leukemia was independent of trisomy 21 and originated in various stem and progenitor cells through additional mutations in cohesin genes. CD117+/KIT proto-oncogene (KIT) cells mediated the propagation of preleukemia and leukemia, and KIT inhibition targeted preleukemic stem cells.
Collapse
MESH Headings
- Animals
- Antigens, CD34/analysis
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Lineage
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Disease Models, Animal
- Disease Progression
- Down Syndrome/complications
- Down Syndrome/genetics
- Female
- GATA1 Transcription Factor/genetics
- GATA1 Transcription Factor/metabolism
- Hematopoiesis
- Hematopoietic Stem Cell Transplantation
- Hematopoietic Stem Cells/physiology
- Heterografts
- Humans
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Leukemia, Myeloid/pathology
- Liver/embryology
- Male
- Megakaryocytes/physiology
- Mice
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Mutation
- Preleukemia/genetics
- Preleukemia/metabolism
- Preleukemia/pathology
- Protein Kinase Inhibitors/pharmacology
- Proto-Oncogene Mas
- Proto-Oncogene Proteins c-kit/analysis
- Proto-Oncogene Proteins c-kit/antagonists & inhibitors
- Cohesins
Collapse
Affiliation(s)
- Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | - Joana Araújo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Hematology, Centro Hospitalar Universitário de São João, Porto, 4200-319, Portugal
- Faculty of Medicine, University of Porto, Porto, 4200-319, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, 4200-135, Portugal
- Instituto Nacional de Investigação Biomédica, University of Porto, Porto, 4200-135, Portugal
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sarah K Cutting
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Gabriela Krivdova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maria Azkanaz
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jessica L McLeod
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sabrina A Smith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Blaise A Gratton
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Martino Gabra
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessie J F Medeiros
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Sanaz Manteghi
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada
| | - Jian Chen
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada
| | - Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Leonardo Salmena
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sagi Abelson
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Mohamed Abdelhaleem
- Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maian Roifman
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Johann K Hitzler
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
- Division of Hematology and Oncology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| |
Collapse
|
40
|
Kurtenbach S, Cruz AM, Rodriguez DA, Durante MA, Harbour JW. Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data. BMC Genomics 2021; 22:419. [PMID: 34090344 PMCID: PMC8180062 DOI: 10.1186/s12864-021-07739-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies are ideal to identify tumor sub-clones, they remain expensive and in contrast to single cell RNA-seq (scRNA-seq) methods are more limited in the data they generate. However, CNV data can be inferred from scRNA-seq and bulk RNA-seq, for which several tools have been developed, including inferCNV, CaSpER, and HoneyBADGER. Inferences regarding tumor clonality from CNV data (and other sources) are frequently visualized using phylogenetic plots, which previously required time-consuming and error-prone, manual analysis. RESULTS Here, we present Uphyloplot2, a python script that generates phylogenetic plots directly from inferred RNA-seq data, or any Newick formatted dendrogram file. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/ . CONCLUSIONS Uphyloplot2 is an easy-to-use tool to generate phylogenetic plots to depict tumor clonality from scRNA-seq data and other sources.
Collapse
Affiliation(s)
- Stefan Kurtenbach
- Sylvester Comprehensive Cancer Center, Interdisciplinary Stem Cell Institute, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA.
| | - Anthony M Cruz
- Sylvester Comprehensive Cancer Center, Interdisciplinary Stem Cell Institute, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Daniel A Rodriguez
- Sylvester Comprehensive Cancer Center, Interdisciplinary Stem Cell Institute, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A Durante
- Sylvester Comprehensive Cancer Center, Interdisciplinary Stem Cell Institute, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - J William Harbour
- Sylvester Comprehensive Cancer Center, Interdisciplinary Stem Cell Institute, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
41
|
Cáceres A, Jene A, Esko T, Pérez-Jurado LA, González JR. Extreme Downregulation of Chromosome Y and Cancer Risk in Men. J Natl Cancer Inst 2021; 112:913-920. [PMID: 31945786 DOI: 10.1093/jnci/djz232] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/31/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Understanding the biological differences between sexes in cancer is essential for personalized treatment and prevention. We hypothesized that the extreme downregulation of chromosome Y gene expression (EDY) is a signature of cancer risk in men and the functional mediator of the reported association between the mosaic loss of chromosome Y (LOY) and cancer. METHODS We advanced a method to measure EDY from transcriptomic data. We studied EDY across 47 nondiseased tissues from the Genotype Tissue-Expression Project (n = 371) and its association with cancer status across 12 cancer studies from The Cancer Genome Atlas (n = 1774) and seven other studies (n = 7562). Associations of EDY with cancer status and presence of loss-off function mutations in chromosome X were tested with logistic regression models, and a Fisher's test was used to assess genome-wide association of EDY with the proportion of copy number gains. All statistical tests were two-sided. RESULTS EDY was likely to occur in multiple nondiseased tissues (P < .001) and was statistically significantly associated with the EGFR tyrosine kinase inhibitor resistance pathway (false discovery rate = 0.028). EDY strongly associated with cancer risk in men (odds ratio [OR] = 3.66, 95% confidence interval [CI] = 1.58 to 8.46, P = .002), adjusted by LOY and age, and its variability was largely explained by several genes of the nonrecombinant region whose chromosome X homologs showed loss-of-function mutations that co-occurred with EDY during cancer (OR = 2.82, 95% CI = 1.32 to 6.01, P = .007). EDY associated with a high proportion of EGFR amplifications (OR = 5.64, 95% CI = 3.70 to 8.59, false discovery rate < 0.001) and EGFR overexpression along with SRY hypomethylation and nonrecombinant region hypermethylation, indicating alternative causes of EDY in cancer other than LOY. EDY associations were independently validated for different cancers and exposure to smoking, and its status was accurately predicted from individual methylation patterns. CONCLUSIONS EDY is a male-specific signature of cancer susceptibility that supports the escape from X-inactivation tumor suppressor hypothesis for genes that protect women compared with men from cancer risk.
Collapse
Affiliation(s)
- Alejandro Cáceres
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Aina Jene
- Center for Genomics Regulation, Barcelona, Spain
| | - Tonu Esko
- Estonian Genome Centre Science Centre, University of Tartu, Tartu, Estonia
| | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain.,Women's and Children's Hospital, South Australian Health and Medical Research Institute & University of Adelaide, Adelaide, Australia
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra, Spain
| |
Collapse
|
42
|
Qiao Y, Pei Y, Luo M, Rajasekaran M, Hui KM, Chen J. Cytokinesis regulators as potential diagnostic and therapeutic biomarkers for human hepatocellular carcinoma. Exp Biol Med (Maywood) 2021; 246:1343-1354. [PMID: 33899543 DOI: 10.1177/15353702211008380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cytokinesis, the final step of mitosis, is critical for maintaining the ploidy level of cells. Cytokinesis is a complex, highly regulated process and its failure can lead to genetic instability and apoptosis, contributing to the development of cancer. Human hepatocellular carcinoma is often accompanied by a high frequency of aneuploidy and the DNA ploidy pattern observed in human hepatocellular carcinoma results mostly from impairments in cytokinesis. Many key regulators of cytokinesis are abnormally expressed in human hepatocellular carcinoma, and their expression levels are often correlated with patient prognosis. Moreover, preclinical studies have demonstrated that the inhibition of key cytokinesis regulators can suppress the growth of human hepatocellular carcinoma. Here, we provide an overview of the current understanding of the signaling networks regulating cytokinesis, the key cytokinesis regulators involved in the initiation and development of human hepatocellular carcinoma, and their applications as potential diagnostic and therapeutic biomarkers.
Collapse
Affiliation(s)
- Yiting Qiao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, P. R. China
| | - Yunxin Pei
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Miao Luo
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Muthukumar Rajasekaran
- Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore
| | - Kam M Hui
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jianxiang Chen
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore
| |
Collapse
|
43
|
Montero-Mateos E, Del Carmen S, Sanz J, Rodriguez-García R, Alcázar JA, Sayagués JM, Abad M. Endoluminal tumor implant of a colorectal cancer in an anal fistula detected by FISH techniques: a case report. J Gastrointest Oncol 2021; 12:900-905. [PMID: 34012678 DOI: 10.21037/jgo-20-281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intraluminal shedding of tumor cells is a rare infrequent sporadic colorectal cancer (sCRC) mechanism of spreading. Less than 30 cases of sCRC metastasis into anal fistula have been reported. Here, we study a 72-year-old male with an adenocarcinoma arising in an anal fistula. Subsequent studies revealed another tumor in the rectum without distant metastatic disease; therefore, a curative-intent abdominoperineal resection was performed. The histologic study showed a moderately differentiated adenocarcinoma in both locations. No perineural or lymphovascular invasion was observed, and all the lymphatic nodes resected were negative for malignancy. Both tumors showed positive CK20 and negative CK7 immunostaining, but KRAS G12D mutation was only detected in the rectal tumor. After those conventional studies, a cytogenetic profile of both tumors was performed by interphase fluorescence in situ hybridization (iFISH) techniques. The FISH study displayed an identical genetic profile in both tumors, loss of the chromosomes 8 and 18q, and no alteration in chromosome 7 and 13q. Based on pathological and genetic findings, we established the same clonal origin of both tumors. Currently, the diagnosis of an intraluminal CRC metastasis relies on histologic and immunohistochemistry findings. We suggest that genetic studies at the individual cell level by FISH techniques may be useful in order to differentiate synchronous from intraluminal metastasis.
Collapse
Affiliation(s)
- Enrique Montero-Mateos
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Sofía Del Carmen
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Julia Sanz
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Raquel Rodriguez-García
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - José Antonio Alcázar
- Servicio de Cirugía General y del Aparato Digestivo, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - José María Sayagués
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| | - Mar Abad
- Servicio de Anatomía Patológica, Hospital Clínico Universitario de Salamanca e Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca, Salamanca, Spain
| |
Collapse
|
44
|
Will Castro LSEP, Pieters W, Alemdehy MF, Aslam MA, Buoninfante OA, Raaijmakers JA, Pilzecker B, van den Berk PCM, Te Riele H, Medema RH, Pedrosa RC, Jacobs H. The Widely Used Antihelmintic Drug Albendazole is a Potent Inducer of Loss of Heterozygosity. Front Pharmacol 2021; 12:596535. [PMID: 33679394 PMCID: PMC7935534 DOI: 10.3389/fphar.2021.596535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The antihelmintic drug ABZ and its metabolites belong to the chemical family of benzimidazoles (BZM) that act as potent tubulin polymerization inhibitors, suggesting a potential re-direction of BZMs for cancer therapy. Applying UV-Vis spectrometry we here demonstrate ABZ as a DNA intercalator. This insight led us to determine the primary mode of ABZ action in mammalian cells. As revealed by RNA sequencing, ABZ did neither grossly affect replication as analyzed by survival and replication stress signaling, nor the transcriptome. Actually, unbiased transcriptome analysis revealed a marked cell cycle signature in ABZ exposed cells. Indeed, short-term exposure to ABZ arrested mammalian cells in G2/M cell cycle stages associated with frequent gains and losses of chromatin. Cellular analyses revealed ABZ as a potent mammalian spindle poison for normal and malignant cells, explaining the serious chromosome segregation defects. Since chromosomal aberrations promote both cancer development and cell death, we determined if besides its general cytotoxicity, ABZ could predispose to tumor development. As measured by loss of heterozygosity (LOH) in vitro and in vivo ABZ was found as a potent inducer of LOH and accelerator of chromosomal missegregation.
Collapse
Affiliation(s)
- Luiza S E P Will Castro
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Wietske Pieters
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mir Farshid Alemdehy
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Muhammad A Aslam
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.,Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Jonne A Raaijmakers
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bas Pilzecker
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Paul C M van den Berk
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Rozangela C Pedrosa
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| |
Collapse
|
45
|
Ouseph MM, Hasserjian RP, Dal Cin P, Lovitch SB, Steensma DP, Nardi V, Weinberg OK. Genomic alterations in patients with somatic loss of the Y chromosome as the sole cytogenetic finding in bone marrow cells. Haematologica 2021; 106:555-564. [PMID: 32193254 PMCID: PMC7849577 DOI: 10.3324/haematol.2019.240689] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/19/2020] [Indexed: 01/23/2023] Open
Abstract
Loss of the Y chromosome (LOY) is one of the most common somatic genomic alterations in hematopoietic cells in men. However, due to the high prevalence of LOY as the sole cytogenetic finding in the healthy older population, differentiating isolated LOY associated with clonal hematologic processes from aging-associated mosaicism can be difficult in the absence of definitive morphological features of disease. In the past, various investigators have proposed that a high percentage of metaphases with LOY is more likely to represent expansion of a clonal myeloid disease-associated population. It is unknown whether the proportion of metaphases with LOY is associated with the incidence of myeloid neoplasia-associated genomic alterations. To address this question, we identified bone marrow samples with LOY as an isolated cytogenetic finding and used targeted next generation sequencing-based molecular analysis to identify common myeloid neoplasia-associated somatic mutations. Among 73 patients with a median age of 75 years (range, 29-90), the percentage of metaphases with LOY was <25% in 23 patients, 25-49% in 10, 50-74% in 8 and ≥75% in 32. A threshold of ≥75% LOY was significantly associated with a morphological diagnosis of myeloid neoplasm (P=0.004). Furthermore, ≥75% LOY was associated with a higher lifetime incidence of a diagnosis of myelodysplastic syndromes (MDS) (P<0.0001), and in multivariate analysis ≥75% LOY was a statistically significant independent predictor of myeloid neoplasia (odds ratio 6.17; 95% confidence interval: 2.15-17.68; P=0.0007]. Higher LOY percentage (≥75%) was associated with greater likelihood of having somatic mutations (P=0.0009) and a higher number of these mutations (P=0.0002). Our findings indicate that ≥75% LOY in bone marrow cells is associated with an increased likelihood of molecular aberrations in genes commonly seen to be altered in myeloid neoplasia and with morphological features of MDS. These observations suggest that ≥75% LOY in bone marrow should be considered an MDS-associated cytogenetic aberration.
Collapse
Affiliation(s)
- Madhu M Ouseph
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | | | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - Scott B Lovitch
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - David P Steensma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, USA
| | - Olga K Weinberg
- Department of Pathology, Boston Children Hospital, Boston, USA
| |
Collapse
|
46
|
Genomic instability-derived plasma extracellular vesicle-microRNA signature as a minimally invasive predictor of risk and unfavorable prognosis in breast cancer. J Nanobiotechnology 2021; 19:22. [PMID: 33436002 PMCID: PMC7802300 DOI: 10.1186/s12951-020-00767-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background Breast cancer (BC) is the most frequently diagnosed cancer and the leading cause of cancer-associated deaths in women. Recent studies have indicated that microRNA (miRNA) regulation in genomic instability (GI) is associated with disease risk and clinical outcome. Herein, we aimed to identify the GI-derived miRNA signature in extracellular vesicles (EVs) as a minimally invasive biomarker for early diagnosis and prognostic risk stratification. Experimental design Integrative analysis of miRNA expression and somatic mutation profiles was performed to identify GI-associated miRNAs. Then, we constructed a discovery and validation study with multicenter prospective cohorts. The GI-derived miRNA signature (miGISig) was developed in the TCGA discovery cohort (n = 261), and was subsequently independently validated in internal TCGA validation (n = 261) and GSE22220 (n = 210) cohorts for prognosis prediction, and in GSE73002 (n = 3966), GSE41922 (n = 54), and in-house clinical exosome (n = 30) cohorts for diagnostic performance. Results We identified a GI-derived three miRNA signature (MIR421, MIR128-1 and MIR128-2) in the serum extracellular vesicles of BC patients, which was significantly associated with poor prognosis in all the cohorts tested and remained as an independent prognostic factor using multivariate analyses. When integrated with the clinical characteristics, the composite miRNA-clinical prognostic indicator showed improved prognostic performance. The miGISig also showed high accuracy in differentiating BC from healthy controls with the area under the receiver operating characteristics curve (ROC) with 0.915, 0.794 and 0.772 in GSE73002, GSE41922 and TCGA cohorts, respectively. Furthermore, circulating EVs from BC patients in the in-house cohort harbored elevated levels of miGISig, with effective diagnostic accuracy. Conclusions We report a novel GI-derived three miRNA signature in EVs, as an excellent minimally invasive biomarker for the early diagnosis and unfavorable prognosis in BC.
Collapse
|
47
|
Acute systemic loss of Mad2 leads to intestinal atrophy in adult mice. Sci Rep 2021; 11:68. [PMID: 33420244 PMCID: PMC7794249 DOI: 10.1038/s41598-020-80169-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/15/2020] [Indexed: 11/08/2022] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer, leading to aneuploid cells. To study the role that CIN plays in tumor evolution, several mouse models have been engineered over the last 2 decades. These models have unequivocally shown that systemic high-grade CIN is embryonic lethal. We and others have previously shown that embryonic lethality can be circumvented by provoking CIN in a tissue-specific fashion. In this study, we provoke systemic high-grade CIN in adult mice as an alternative to circumvent embryonic lethality. For this, we disrupt the spindle assembly checkpoint (SAC) by alleviating Mad2 or truncating Mps1, both essential genes for SAC functioning, with or without p53 inactivation. We find that disruption of the SAC leads to rapid villous atrophy, atypia and apoptosis of the epithelia of the jejunum and ileum, substantial weight loss, and death within 2-3 weeks after the start of the CIN insult. Despite this severe intestinal phenotype, most other tissues are unaffected, except for minor abnormalities in spleen, presumably due to the lower proliferation rate in these tissues. We conclude that high-grade CIN in vivo in adult mice is most toxic to the high cell turnover intestinal epithelia.
Collapse
|
48
|
Aneuploidy in Cancer: Lessons from Acute Lymphoblastic Leukemia. Trends Cancer 2021; 7:37-47. [PMID: 32952102 DOI: 10.1016/j.trecan.2020.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 11/22/2022]
Abstract
Aneuploidy, the gain or loss of chromosomes in a cell, is a hallmark of cancer. Although our understanding of the contribution of aneuploidy to cancer initiation and progression is incomplete, significant progress has been made in uncovering the cellular consequences of aneuploidy and how aneuploid cancer cells self-adapt to promote tumorigenesis. Aneuploidy is physiologically associated with significant cellular stress but, paradoxically, it favors tumor progression. Although more common in solid tumors, different forms of aneuploidy represent the initiating oncogenic lesion in patients with B cell acute lymphoblastic leukemia (B-ALL), making B-ALL an excellent model for studying the role of aneuploidy in tumorigenesis. We review the molecular mechanisms underlying aneuploidy and discuss its contributions to B-ALL initiation and progression.
Collapse
|
49
|
Funk LC, Wan J, Ryan SD, Kaur C, Sullivan R, Roopra A, Weaver BA. p53 Is Not Required for High CIN to Induce Tumor Suppression. Mol Cancer Res 2021; 19:112-123. [PMID: 32948674 PMCID: PMC7810023 DOI: 10.1158/1541-7786.mcr-20-0488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/14/2020] [Accepted: 09/13/2020] [Indexed: 11/16/2022]
Abstract
Chromosomal instability (CIN) is a hallmark of cancer. While low levels of CIN can be tumor promoting, high levels of CIN cause cell death and tumor suppression. The widely used chemotherapeutic, paclitaxel (Taxol), exerts its anticancer effects by increasing CIN above a maximally tolerated threshold. One significant outstanding question is whether the p53 tumor suppressor is required for the cell death and tumor suppression caused by high CIN. Both p53 loss and reduction of the mitotic kinesin, centromere-associated protein-E, cause low CIN. Combining both genetic insults in the same cell leads to high CIN. Here, we test whether high CIN causes cell death and tumor suppression even in the absence p53. Despite a surprising sex-specific difference in tumor spectrum and latency in p53 heterozygous animals, these studies demonstrate that p53 is not required for high CIN to induce tumor suppression. Pharmacologic induction of high CIN results in equivalent levels of cell death due to loss of essential chromosomes in p53+/+ and p53-/- cells, further demonstrating that high CIN elicits cell death independently of p53 function. IMPLICATIONS: These results provide support for the efficacy of anticancer therapies that induce high CIN, even in tumors that lack functional p53.
Collapse
Affiliation(s)
- Laura C Funk
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Jun Wan
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sean D Ryan
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Charanjeet Kaur
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ruth Sullivan
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Avtar Roopra
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Neuroscience, University of Wisconsin-Madison, Madison, Wisconsin
| | - Beth A Weaver
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin.
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin
| |
Collapse
|
50
|
Asim A, Agarwal S, Avasthi KK, Sureka S, Rastogi N, Dean DD, Mohindra S. Investigation of LOY in Prostate, Pancreatic, and Colorectal Cancers in males: A case-control study. Expert Rev Mol Diagn 2020; 20:1259-1263. [PMID: 33210965 DOI: 10.1080/14737159.2020.1853528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background: LOY is associated with ageing and increase the incidence of cancers. Aims: To elucidate the role of LOY in various cancer types, namely, prostate (PRT), pancreatic (PC), and colorectal (CRC) cancers in males. Material and Methods: Fifty CRC patients [mean age = 44.58±11.2 years], fifty PRT [mean age= 60.48± 17.07 years] and fifty PC [mean age = 48.74 ±16.45 years] along with 100 healthy controls [mean age= 54.06 ±15.04 years] were recruited. DNA was isolated from peripheral blood and was subjected to multiplex QF-PCR. The Y/X ratio was calculated from the peak height. Results: The mean Y/X ratio was lower in all patients with cancers (0.875333± 0.086; p value˂ 0.0001) than in controls (1.11 ± 0.071), as well as, in CRC (0.926±0.192; p value˂0.0001), PC (0.85 ± 0.0311; p value˂0.0001) and PRT (0.85±0.122; p value˂0.0001) when calculated separately. Multivariate logistic regression analysis was used to analyze the strength of the presence of cancer prediction using the percentage of LOY and age showed that LOY (p= 0.001) is a better predictor of cancer presence than age (p= 0.359). Conclusion: LOY in blood could be a predictive biomarker in the carcinogenesis of males.
Collapse
Affiliation(s)
- Ambreen Asim
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS) , Lucknow, India
| | - Sarita Agarwal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS) , Lucknow, India
| | - Kapil Kumar Avasthi
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS) , Lucknow, India
| | - Sanjoy Sureka
- Department of Urology, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS) , Lucknow, India
| | - Neeraj Rastogi
- Department of Radiotherapy, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS) , Lucknow, India
| | - Deepika Delsa Dean
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS) , Lucknow, India
| | - Samir Mohindra
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS) , Lucknow, India
| |
Collapse
|