1
|
Xu S, Zhao J, Gao F, Zhang Y, Luo J, Zhang C, Tian R, Zhi E, Zhang J, Bai F, Sun H, Zhao F, Huang Y, Li P, Jiang L, Li Z, Yao C, Zhou Z. A bi-allelic REC114 loss-of-function variant causes meiotic arrest and nonobstructive azoospermia. Clin Genet 2024; 105:440-445. [PMID: 38148155 DOI: 10.1111/cge.14473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/14/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023]
Abstract
Nonobstructive azoospermia (NOA), the most severe manifestation of male infertility, lacks a comprehensive understanding of its genetic etiology. Here, a bi-allelic loss-of-function variant in REC114 (c.568C > T: p.Gln190*) were identified through whole exome sequencing (WES) in a Chinese NOA patient. Testicular histopathological analysis and meiotic chromosomal spread analysis were conducted to assess the stage of spermatogenesis arrested. Co-immunoprecipitation (Co-IP) and Western blot (WB) were used to investigate the influence of variant in vitro. In addition, our results revealed that the variant resulted in truncated REC114 protein and impaired interaction with MEI4, which was essential for meiotic DNA double-strand break (DSB) formation. As far as we know, this study presents the first report that identifies REC114 as the causative gene for male infertility. Furthermore, our study demonstrated indispensability of the REC114-MEI4 complex in maintaining DSB homoeostasis, and highlighted that the disruption of the complex due to the REC114 variant may underline the mechanism of NOA.
Collapse
Affiliation(s)
- Shuai Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingpeng Zhao
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Feng Gao
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuxiang Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiaqiang Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenwang Zhang
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Ruhui Tian
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Erlei Zhi
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiong Zhang
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Furong Bai
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongfang Sun
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fujun Zhao
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhua Huang
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Li
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liren Jiang
- Pathology Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng Li
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Chencheng Yao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Andrology, Center for Men's Health, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of ART, Institute of Urology, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Zhi Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| |
Collapse
|
2
|
Lee JY, Bhandare RR, Boddu SHS, Shaik AB, Saktivel LP, Gupta G, Negi P, Barakat M, Singh SK, Dua K, Chellappan DK. Molecular mechanisms underlying the regulation of tumour suppressor genes in lung cancer. Biomed Pharmacother 2024; 173:116275. [PMID: 38394846 DOI: 10.1016/j.biopha.2024.116275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Tumour suppressor genes play a cardinal role in the development of a large array of human cancers, including lung cancer, which is one of the most frequently diagnosed cancers worldwide. Therefore, extensive studies have been committed to deciphering the underlying mechanisms of alterations of tumour suppressor genes in governing tumourigenesis, as well as resistance to cancer therapies. In spite of the encouraging clinical outcomes demonstrated by lung cancer patients on initial treatment, the subsequent unresponsiveness to first-line treatments manifested by virtually all the patients is inherently a contentious issue. In light of the aforementioned concerns, this review compiles the current knowledge on the molecular mechanisms of some of the tumour suppressor genes implicated in lung cancer that are either frequently mutated and/or are located on the chromosomal arms having high LOH rates (1p, 3p, 9p, 10q, 13q, and 17p). Our study identifies specific genomic loci prone to LOH, revealing a recurrent pattern in lung cancer cases. These loci, including 3p14.2 (FHIT), 9p21.3 (p16INK4a), 10q23 (PTEN), 17p13 (TP53), exhibit a higher susceptibility to LOH due to environmental factors such as exposure to DNA-damaging agents (carcinogens in cigarette smoke) and genetic factors such as chromosomal instability, genetic mutations, DNA replication errors, and genetic predisposition. Furthermore, this review summarizes the current treatment landscape and advancements for lung cancers, including the challenges and endeavours to overcome it. This review envisages inspired researchers to embark on a journey of discovery to add to the list of what was known in hopes of prompting the development of effective therapeutic strategies for lung cancer.
Collapse
Affiliation(s)
- Jia Yee Lee
- School of Health Sciences, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Richie R Bhandare
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates.
| | - Sai H S Boddu
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada, Chebrolu, Guntur, Andhra Pradesh 522212, India; Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India
| | - Lakshmana Prabu Saktivel
- Department of Pharmaceutical Technology, University College of Engineering (BIT Campus), Anna University, Tiruchirappalli 620024, India
| | - Gaurav Gupta
- Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; School of Pharmacy, Suresh Gyan Vihar University, Jaipur, Rajasthan 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University, PO Box 9, Solan, Himachal Pradesh 173229, India
| | - Muna Barakat
- Department of Clinical Pharmacy & Therapeutics, Applied Science Private University, Amman-11937, Jordan
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara 144411, India; Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Kamal Dua
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia.
| |
Collapse
|
3
|
Chen X, Zhang W. [Analysis of X chromosome inactivation and prenatal diagnosis for a Chinese pedigree with loss of heterozygosity at Xq22.1q22.3]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2024; 41:326-330. [PMID: 38448023 DOI: 10.3760/cma.j.cn511374-20221224-00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
OBJECTIVE To explore the correlation between skewed X chromosome inactivation (XCI) and clinical phenotype of a Chinese pedigree with loss of heterozygosity at Xq22.1q22.3. METHODS A pedigree diagnosed at Taizhou Hospital on November 10, 2021 was selected as the study subject. G-banded chromosomal karyotyping and copy number variation sequencing (CNV-seq) were carried out to analyze the amniotic fluid and peripheral blood samples from the couple. XCI was detected by PCR amplification of CAG repeats in exon 1 of androgen receptor gene before and after the digestion with methylation-sensitive restriction enzyme Hpa II. Correlation between the genotype and clinical phenotype was analyzed. RESULTS The karyotypes of the pregnant woman and the fetus were both determined as 46,X,del(X)(q22), and the result of CNV-seq was seq[hg19]del(X)(q22.1q22.3) chrX: g.10046000_105740000del, suggesting that both had harbored a 5.28 Mb deletion on the X chromosome. No obvious abnormality was found in the husband. XCI analysis showed that the activity ratio of the two X chromosomes of the pregnant woman and her fetus was 0 : 100. The X chromosome harboring the q22.1q22.3 deletion was completely inactivated, and the inactivated X chromosome of the fetus was derived from its mother. CONCLUSION The fetus has harbored a maternally derived inactivated X chromosome del(X)(q22) , and its phenotype is closely associated with the activity of the abnormal X chromosome. Pedigree XCI analysis combined with the clinical phenotype has facilitated recognition of the maternal phenotype and prognosis of female fetus with loss of heterozygosity at Xq22.1q22.3.
Collapse
Affiliation(s)
- Xuejun Chen
- Reproductive Center of Taizhou Hospital, Taizhou, Zhejiang 317000, China.
| | | |
Collapse
|
4
|
Jia C, Yao XF, Zhang M, Guan XX, Wang JW, Song HC, He LJ. [Correlation of 1p/16q loss of heterozygosity and 1p gain with clinicopathological characteristics and prognosis in Wilms tumor]. Zhonghua Bing Li Xue Za Zhi 2024; 53:257-263. [PMID: 38433053 DOI: 10.3760/cma.j.cn112151-20230814-00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Objective: To investigate the relationship between 1p/16q loss of heterozygosity (LOH) and 1p gain in Wilms tumor and their clinicopathologic characteristics and prognosis. Methods: A total of 175 Wilms tumor samples received from the Department of Pathology, Beijing Children's Hospital from September 2019 to August 2022 were retrospectively analyzed. The histopathologic type and presence of lymph node involvement were evaluated by two pathologists. The clinical data including patients'gender, age, tumor location, preoperative chemotherapy, and tumor stage were summarized. Fluorescence in situ hybridization (FISH) was done to detect 1p/16q LOH and 1p gain and their correlation with the clinicopathological features and prognosis were analyzed. Results: Among the 175 samples, 86 cases (49.1%) were male and 89 (50.9%) were female. The mean age was (3.5±2.9) years, and the median age was 2.6 years. There were 26 (14.9%) cases with 1p LOH, 28 (16.0%) cases with 16q LOH, 10 (5.7%) cases of LOH at both 1p and 16q, and 53 (30.3%) cases with 1q gain. 1q gain was significantly associated with 1p LOH (P<0.01) and 16q LOH (P<0.01). There were significant differences (P<0.01) between 1q gain, 1p LOH and 16q LOH among different age groups. The rate of 16q LOH in the high-risk histopathological subtype (50.0%) was significantly higher than that in the intermediate-risk subtype (13.6%, P<0.05). The frequency of 1q gain, 1p LOH, and 16q LOH in children with advanced clinical stages (Ⅲ and Ⅳ) was significantly higher than that in children with early clinical stages (Ⅰ and Ⅱ). 1q gain, 1p LOH, and 16q LOH showed no significant correlation with gender, unilateral or bilateral disease, chemotherapy, or lymph node metastasis. The progression-free survival (PFS) time for patients with 1q gain and 1p LOH was significantly shorter than those without these aberrations (P<0.05). Additionally, the PFS time of patients with 16q LOH was slightly shorter than those with normal 16q, although the difference was not statistically significant. Patients with stage Ⅲ to Ⅳ disease exhibiting 1q gain or 1p LOH had a significantly higher relative risk of recurrence, metastasis, and mortality. Conclusions: 1p/16q LOH and 1q gain are associated with age, high-risk histological type, and clinical stage in Wilms tumor. 1q gain and 1p LOH are significantly correlated with the prognosis of Wilms tumor.
Collapse
Affiliation(s)
- C Jia
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - X F Yao
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - M Zhang
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - X X Guan
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - J W Wang
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - H C Song
- Department of Urology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - L J He
- Department of Pathology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| |
Collapse
|
5
|
Evageliou N, Renfro LA, Geller J, Perlman E, Kalapurakal J, Paulino A, Dix D, Eklund MJ, Murphy AJ, Romao RLP, Ehrlich PF, Varela CR, Vallance K, Fernandez CV, Dome JS, Mullen EA. Prognostic impact of lymph node involvement and loss of heterozygosity of 1p or 16q in stage III favorable histology Wilms tumor: A report from Children's Oncology Group Studies AREN03B2 and AREN0532. Cancer 2024; 130:792-802. [PMID: 37902955 DOI: 10.1002/cncr.35084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 11/01/2023]
Abstract
INTRODUCTION The prognostic impact of positive lymph nodes (LN+) and/or singular loss of heterozygosity (LOH) of 1p or 16q were assessed in children with stage III favorable histology Wilms tumor (FHWT) enrolled on AREN0532 or AREN03B2 alone. PATIENTS AND METHODS A total of 635 stage III FHWT vincristine/dactinomycin/doxorubicin (DD4A)-treated patients met inclusion criteria. Event-free survival (EFS) and overall survival are reported overall and by LN sampling, LN status, LOH 1p, LOH 16q, and a combination of LN status and singular LOH. Patients with unknown or positive combined LOH of 1p and 16q status and AREN03B2-only patients with unknown outcomes or treatment other than DD4A were excluded. RESULTS EFS did not differ by study, supporting pooling. Lack of LN sampling (hazard ratio [HR], 2.12; p = .0037), LN positivity (HR, 2.78; p = .0002), LOH 1p (HR, 2.18; p = .0067), and LOH 16q (HR, 1.72; p = .042) were associated with worse EFS. Compared with patients with both LN- and LOH-, those with negative nodes but positive LOH 1p or 16q and those with LN+ but LOH- for 1p or 16q had significantly worse EFS (HR, 3.05 and 3.57, respectively). Patients positive for both LN and LOH had the worst EFS (HR, 6.33; overall group factor, p < .0001). CONCLUSION Findings confirm LN+ status as an adverse prognostic factor amplified by presence of singular LOH 1p or 16q, supporting study of intensified therapy for patients with LN+ in combination with singular LOH in a prospective clinical trial.
Collapse
Affiliation(s)
- Nicholas Evageliou
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lindsay A Renfro
- Division of Biostatistics, University of Southern California and Children's Oncology Group, Monrovia, California, USA
| | - James Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
| | - Elizabeth Perlman
- Department of Pathology and Laboratory Medicine, The Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University, Chicago, Illinois, USA
| | - John Kalapurakal
- Department of Radiation Oncology, Robert H. Lurie Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Arnold Paulino
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - David Dix
- Division of Oncology, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Meryle J Eklund
- Department of Radiology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rodrigo L P Romao
- Departments of Surgery and Urology, IWK Health, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Peter F Ehrlich
- Section of Pediatric Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Carly R Varela
- Division of Oncology, Children's National Hospital, Washington, District of Columbia, USA
- Divisions of Pediatric Hematology and Oncology, Inova Fairfax Hospital, Fairfax, Virginia, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Kelly Vallance
- Division of Hematology and Oncology, Cook Children's Hospital, Fort Worth, Texas, USA
| | - Conrad V Fernandez
- Department of Pediatrics, IWK Health Centre and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jeffrey S Dome
- Division of Oncology, Children's National Hospital, Washington, District of Columbia, USA
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Elizabeth A Mullen
- Dana-Farber/Boston Children's Blood Disorders and Cancer Center, Boston, Massachusetts, USA
| |
Collapse
|
6
|
Krishna C, Tervi A, Saffern M, Wilson EA, Yoo SK, Mars N, Roudko V, Cho BA, Jones SE, Vaninov N, Selvan ME, Gümüş ZH, Lenz TL, Merad M, Boffetta P, Martínez-Jiménez F, Ollila HM, Samstein RM, Chowell D. An immunogenetic basis for lung cancer risk. Science 2024; 383:eadi3808. [PMID: 38386728 DOI: 10.1126/science.adi3808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 01/16/2024] [Indexed: 02/24/2024]
Abstract
Cancer risk is influenced by inherited mutations, DNA replication errors, and environmental factors. However, the influence of genetic variation in immunosurveillance on cancer risk is not well understood. Leveraging population-level data from the UK Biobank and FinnGen, we show that heterozygosity at the human leukocyte antigen (HLA)-II loci is associated with reduced lung cancer risk in smokers. Fine-mapping implicated amino acid heterozygosity in the HLA-II peptide binding groove in reduced lung cancer risk, and single-cell analyses showed that smoking drives enrichment of proinflammatory lung macrophages and HLA-II+ epithelial cells. In lung cancer, widespread loss of HLA-II heterozygosity (LOH) favored loss of alleles with larger neopeptide repertoires. Thus, our findings nominate genetic variation in immunosurveillance as a critical risk factor for lung cancer.
Collapse
Affiliation(s)
- Chirag Krishna
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anniina Tervi
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
| | - Miriam Saffern
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric A Wilson
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nina Mars
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
| | - Vladimir Roudko
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Byuri Angela Cho
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samuel Edward Jones
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
| | - Natalie Vaninov
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, Universität Hamburg, 20146 Hamburg, Germany
| | - Miriam Merad
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paolo Boffetta
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy
- Stony Brook Cancer Center, Stony Brook University, New York, NY 11794, USA
| | - Francisco Martínez-Jiménez
- Vall d'Hebron Institute of Oncology, Barcelona 08035, Spain
- Hartwig Medical Foundation, Amsterdam 1098 XH, the Netherlands
| | - Hanna M Ollila
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland
- Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert M Samstein
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Radiation Oncology, Mount Sinai Hospital, New York, NY 10029, USA
| | - Diego Chowell
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Immunology and Immunotherapy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
7
|
McMahon JN, Gaffney EF, Aliaga-Kelly WJ, Stephens JF, Jalali A, Curran B. P53 loss of heterozygosity (LOH) in formalin-fixed paraffin-embedded leiomyosarcoma (LMS): a novel report. Ir J Med Sci 2024; 193:65-71. [PMID: 37468695 DOI: 10.1007/s11845-023-03370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/05/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND The occurrence of p53 loss of heterozygosity (LOH) is a common genetic event in malignancy. LOH occurs when a heterozygous locus loses one of its two parental alleles, becoming homozygous at that locus, by either copy number loss (CNL-LOH) or by becoming copy number neutral (CNN-LOH). A role for CNL-LOH (cnLOH) has been postulated in cancer aetiology. Loss of heterozygosity (LOH) results in irreversible genetic loss. AIMS LOH was determined in DNA extracted from formalin-fixed paraffin-embedded (FFPE) leiomyosarcoma (LMS) specimens in a retrospective study from 30 patients, to assess the prognostic significance of LOH. The findings were analysed and their validity assessed. LOH was an adverse prognostic factor in LMS. Prospective uniform standardisation of formalin-fixation techniques is required. METHODS DNA was extracted from 169 formalin-fixed paraffin blocks of 30 patients with LMS, following extensive tissue microdissection. Genomic DNA was amplified using the polymerase chain reaction (PCR) technique. Fluorescence-based microsatellite PCR was used to detect and quantitate heterozygosity loss. RESULTS LOH was detected at gene locus 17p13 in 16 LMS (Four grade 2 and 12 grade 3 LMS). LOH was not detected in 14 LMS cases (one grade 1, five grade 2 and eight grade 3 LMS). LOH was associated with shorter patient survival. CONCLUSIONS The results reported herein endorse the value of utilizing FFPE DNA in identifying LOH as a prognostic factor in LMS. The results have implications for tumour biobanking and precision medicine in patients with sarcomas.
Collapse
Affiliation(s)
- John N McMahon
- Research Laboratory, St Vincent's University Hospital, University College Dublin, PathologyDublin, Ireland.
| | - Eoin F Gaffney
- Department of Histopathology, St James's Hospital and Trinity College Dublin, Dublin, Ireland
| | | | - John F Stephens
- Research Laboratory, St Vincent's University Hospital, University College Dublin, PathologyDublin, Ireland
| | | | - Bernadette Curran
- Department of Biochemistry, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
8
|
Collins K, Acosta AM, Siegmund SE, Cheng L, Hirsch MS, Idrees MT. Genetic Profiling Uncovers Genome-Wide Loss of Heterozygosity and Provides Insight into Mechanisms of Sarcomatoid Transformation in Chromophobe Renal Cell Carcinoma. Mod Pathol 2024; 37:100396. [PMID: 38043790 DOI: 10.1016/j.modpat.2023.100396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/07/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Sarcomatoid transformation occurs in ∼8% of chromophobe renal cell carcinoma (chRCC) and is associated with aggressive clinical behavior. In recent years, several studies have identified genomic, transcriptomic, and epigenomic correlates of aggressive behavior in chRCC; however, the molecular mechanisms associated with sarcomatoid transformation remain incompletely understood. In this study, we analyzed paired conventional and sarcomatoid histologic components of individual chRCC to elucidate the genomic alterations that underlie sarcomatoid transformation in this tumor type. Massively parallel sequencing was performed on paired (conventional and sarcomatoid) components from 8 chRCCs. All cases harbored TP53 variants (87.5% showing TP53 variants in both components and 12.5% only in the sarcomatoid component). Intratumor comparisons revealed that TP53 variants were concordant in 71% and discordant in 29% of cases. Additional recurrent single-nucleotide variants were found in RB1 (37.5% of cases) and PTEN (25% of cases), with the remaining single-nucleotide variants detected in these tumors (PBRM1, NF1, and ASXL1) being nonrecurrent. Copy number variant analysis showed the characteristic pattern of chromosomal losses associated with chRCC (1, 2, 6, 10, 13, 17, and 21) in the conventional histologic components only. Interestingly, the sarcomatoid components of these tumors demonstrated widespread loss of heterozygosity but lacked the above chromosomal losses, likely as a consequence of whole-genome duplication/imbalanced chromosomal duplication events. Overall, the findings suggest that TP53 variants followed by whole-genome duplication/imbalanced chromosomal duplication events underlie sarcomatoid transformation in chRCC.
Collapse
Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Andres M Acosta
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Liang Cheng
- Department of Pathology, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, Rhode Island
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| |
Collapse
|
9
|
Katagiri T, Iwasaki H, Fujieda A, Kasashima S, Ozaki S, Uemori M, Ogawa S, Nakao S. A case of hepatitis-associated aplastic anaemia following living-donor liver transplantation for fulminant hepatitis showing loss of heterozygosity in the 6p chromosome in the affected liver. Br J Haematol 2024; 204:623-627. [PMID: 38011365 DOI: 10.1111/bjh.19219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/16/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
The mechanisms underlying hepatitis-associated aplastic anaemia (HAAA) that occurs several weeks after the development of acute hepatitis are unknown. A 20-year-old male developed HAAA following living-donor liver transplantation for fulminant hepatitis. The patient's leucocytes lacked HLA-class I due to loss of heterozygosity in the short arm of chromosome 6p (6pLOH). Interestingly, the patient's liver cells resected during the transplantation also exhibited 6pLOH that affected the same HLA haplotype as the leucocytes, suggesting that CD8+ T cells recognizing antigens presented by specific HLA molecules on liver cells may have attacked the haematopoietic stem cells of the patient, leading to the HAAA development.
Collapse
Affiliation(s)
- Takamasa Katagiri
- Department of Clinical Laboratory Science, Graduate School of Medical Science, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hiroka Iwasaki
- Department of Clinical Laboratory Science, Graduate School of Medical Science, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Atsushi Fujieda
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
- Department of Hematology, Japanese Red Cross Ise Hospital, Ise, Mie, Japan
| | - Satomi Kasashima
- Department of Clinical Laboratory Science, Graduate School of Medical Science, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Satoru Ozaki
- Department of Clinical Laboratory Science, Graduate School of Medical Science, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Mizuho Uemori
- Department of Clinical Laboratory Science, Graduate School of Medical Science, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Centre for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Shinji Nakao
- Department of Hematology, Faculty of Medicine, Institute of Medical Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| |
Collapse
|
10
|
Xue H, Yu A, Zhang L, Chen L, Guo Q, Lin M, Lin N, Chen X, Xu L, Huang H. Genetic testing for fetal loss of heterozygosity using single nucleotide polymorphism array and whole-exome sequencing. Sci Rep 2024; 14:2190. [PMID: 38273042 PMCID: PMC10810965 DOI: 10.1038/s41598-024-52812-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
The study explored the clinical significance of fetal loss of heterozygosity (LOH) identified by single-nucleotide polymorphism array (SNP array). We retrospectively reviewed data from pregnant women who underwent invasive diagnostic procedures at prenatal diagnosis centers in southeastern China from December 2016 to December 2021. SNP array was performed by the Affymetrix CytoScan 750 K array platform. Fetuses with LOH were further identified by parental verification, MS-MLPA, and/or trio whole-exome sequencing (trio-WES). The genetic results, fetal clinical manifestations, and perinatal outcome were analyzed. Of 11,062 fetuses, 106 (0.96%) had LOH exhibiting a neutral copy number, 88 (83.0%) had LOH in a single chromosome, whereas 18 (17.0%) had multiple LOHs on different chromosomes. Sixty-six fetuses had ultrasound anomalies (UAs), most frequently fetal growth restriction (18/66 (27.3%)). Parental SNP array verification was performed in 21 cases and trio-WES in 21 cases. Twelve cases had clinically relevant uniparental disomy, five had pathogenic variants, four had likely pathogenic variants, six had variants of unknown significance, and eight had identity by descent. The rate of adverse pregnancy outcomes in fetuses with LOH and UAs (24/66 (36.4%)) was higher than in those without UAs (6/40 (15.0%)) (p < 0.05). LOH is not uncommon. Molecular genetic testing techniques, including parental SNP array verification, trio-WES, methylation-specific multiplex ligation-dependent probe amplification, regular and systematic ultrasonic monitoring, and placental study, can accurately assess the prognosis and guide the management of the affected pregnancy.
Collapse
Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Lin Zhang
- Fujian Medical University, No. 88 Jiaotong Road, Cangshan District, Fuzhou City, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001, Fujian Province, China.
| |
Collapse
|
11
|
Brown J, Su TT. E2F1, DIAP1, and the presence of a homologous chromosome promote while JNK inhibits radiation-induced loss of heterozygosity in Drosophila melanogaster. Genetics 2024; 226:iyad192. [PMID: 37874851 PMCID: PMC10763536 DOI: 10.1093/genetics/iyad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 08/25/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
Loss of heterozygosity (LOH) can occur when a heterozygous mutant cell loses the remaining wild-type allele to become a homozygous mutant. LOH can have physiological consequences if, for example, the affected gene encodes a tumor suppressor. We used fluorescent reporters to study the mechanisms of LOH induction by X-rays, a type of ionizing radiation (IR), in Drosophila melanogaster larval wing discs. IR is used to treat more than half of patients with cancer, so understanding its effects is of biomedical relevance. Quantitative analysis of IR-induced LOH at different positions between the telomere and the centromere on the X chromosome showed a strong sex dependence and the need for a recombination-proficient homologous chromosome, whereas, paradoxically, position along the chromosome made little difference in LOH incidence. We propose that published data documenting high recombination frequency within centromeric heterochromatin on the X chromosome can explain these data. Using a focused screen, we identified E2F1 as a key promotor of LOH and further testing suggests a mechanism involving its role in cell-cycle regulation. We leveraged the loss of a transcriptional repressor through LOH to express transgenes specifically in cells that have already acquired LOH. This approach identified JNK signaling and apoptosis as key determinants of LOH maintenance. These studies reveal previously unknown mechanisms for the generation and elimination of cells with chromosome aberrations after exposure to IR.
Collapse
Affiliation(s)
- Jeremy Brown
- Department of Molecular, Cellular and Developmental Biology, 347 UCB, University of Colorado, Boulder, CO 80309-0347, USA
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, 13001 E. 17th Pl., Aurora, CO 80045, USA
| | - Tin Tin Su
- Department of Molecular, Cellular and Developmental Biology, 347 UCB, University of Colorado, Boulder, CO 80309-0347, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, 13001 E. 17th Pl., Aurora, CO 80045, USA
| |
Collapse
|
12
|
Al Zouabi L, Stefanutti M, Roumeliotis S, Le Meur G, Boumard B, Riddiford N, Rubanova N, Bohec M, Gervais L, Servant N, Bardin AJ. Molecular underpinnings and environmental drivers of loss of heterozygosity in Drosophila intestinal stem cells. Cell Rep 2023; 42:113485. [PMID: 38032794 DOI: 10.1016/j.celrep.2023.113485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/29/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023] Open
Abstract
During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes within tissue compartments. This phenomenon occurs in normal human tissues and is prevalent in pathological genetic conditions and cancers. While studies in yeast have defined DNA repair mechanisms that can promote LOH, the predominant pathways and environmental triggers in somatic tissues of multicellular organisms are not well understood. Here, we investigate mechanisms underlying LOH in intestinal stem cells in Drosophila. Infection with the pathogenic bacteria, Erwinia carotovora carotovora 15, but not Pseudomonas entomophila, increases LOH frequency. Using whole genome sequencing of somatic LOH events, we demonstrate that they arise primarily via mitotic recombination. Molecular features and genetic evidence argue against a break-induced replication mechanism and instead support cross-over via double Holliday junction-based repair. This study provides a mechanistic understanding of mitotic recombination, an important mediator of LOH, and its effects on stem cells in vivo.
Collapse
Affiliation(s)
- Lara Al Zouabi
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Marine Stefanutti
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Spyridon Roumeliotis
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Gwenn Le Meur
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Benjamin Boumard
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Nick Riddiford
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Natalia Rubanova
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France; Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, 75005 Paris, France
| | - Mylène Bohec
- ICGex Next-Generation Sequencing Platform, Institut Curie, PSL Research University, 75005 Paris, France
| | - Louis Gervais
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France
| | - Nicolas Servant
- Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, 75005 Paris, France
| | - Allison J Bardin
- Genetics and Developmental Biology Department, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, 75248 Paris, France.
| |
Collapse
|
13
|
Risinskaya N, Gladysheva M, Abdulpatakhov A, Chabaeva Y, Surimova V, Aleshina O, Yushkova A, Dubova O, Kapranov N, Galtseva I, Kulikov S, Obukhova T, Sudarikov A, Parovichnikova E. DNA Copy Number Alterations and Copy Neutral Loss of Heterozygosity in Adult Ph-Negative Acute B-Lymphoblastic Leukemia: Focus on the Genes Involved. Int J Mol Sci 2023; 24:17602. [PMID: 38139431 PMCID: PMC10744257 DOI: 10.3390/ijms242417602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The landscape of chromosomal aberrations in the tumor cells of the patients with B-ALL is diverse and can influence the outcome of the disease. Molecular karyotyping at the onset of the disease using chromosomal microarray (CMA) is advisable to identify additional molecular factors associated with the prognosis of the disease. Molecular karyotyping data for 36 patients with Ph-negative B-ALL who received therapy according to the ALL-2016 protocol are presented. We analyzed copy number alterations and their prognostic significance for CDKN2A/B, DMRTA, DOCK8, TP53, SMARCA2, PAX5, XPA, FOXE1, HEMGN, USP45, RUNX1, NF1, IGF2BP1, ERG, TMPRSS2, CRLF2, FGFR3, FLNB, IKZF1, RUNX2, ARID1B, CIP2A, PIK3CA, ATM, RB1, BIRC3, MYC, IKZF3, ETV6, ZNF384, PTPRJ, CCL20, PAX3, MTCH2, TCF3, IKZF2, BTG1, BTG2, RAG1, RAG2, ELK3, SH2B3, EP300, MAP2K2, EBI3, MEF2D, MEF2C, CEBPA, and TBLXR1 genes, choosing t(4;11) and t(7;14) as reference events. Of the 36 patients, only 5 (13.8%) had a normal molecular karyotype, and 31 (86.2%) were found to have various molecular karyotype abnormalities-104 deletions, 90 duplications or amplifications, 29 cases of cnLOH and 7 biallelic/homozygous deletions. We found that 11q22-23 duplication involving the BIRC3, ATM and MLL genes was the most adverse prognostic event in the study cohort.
Collapse
Affiliation(s)
- Natalya Risinskaya
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Maria Gladysheva
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Abdulpatakh Abdulpatakhov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Yulia Chabaeva
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Valeriya Surimova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Olga Aleshina
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Anna Yushkova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Olga Dubova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
- Institute of Biodesign and Modeling of Complex Systems, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Nikolay Kapranov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Irina Galtseva
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Sergey Kulikov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Tatiana Obukhova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Andrey Sudarikov
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| | - Elena Parovichnikova
- National Medical Research Center for Hematology, 125167 Moscow, Russia; (M.G.); (A.A.); (Y.C.); (V.S.); (O.A.); (A.Y.); (O.D.); (N.K.); (I.G.); (S.K.); (A.S.); (E.P.)
| |
Collapse
|
14
|
Engal E, Oja KT, Maroofian R, Geminder O, Le TL, Marzin P, Guimier A, Mor E, Zvi N, Elefant N, Zaki MS, Gleeson JG, Muru K, Pajusalu S, Wojcik MH, Pachat D, Elmaksoud MA, Chan Jeong W, Lee H, Bauer P, Zifarelli G, Houlden H, Daana M, Elpeleg O, Amiel J, Lyonnet S, Gordon CT, Harel T, Õunap K, Salton M, Mor-Shaked H. Bi-allelic loss-of-function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental syndrome. Am J Hum Genet 2023; 110:2112-2119. [PMID: 37963460 PMCID: PMC10716347 DOI: 10.1016/j.ajhg.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Over two dozen spliceosome proteins are involved in human diseases, also referred to as spliceosomopathies. WW domain-binding protein 4 (WBP4) is part of the early spliceosomal complex and has not been previously associated with human pathologies in the Online Mendelian Inheritance in Man (OMIM) database. Through GeneMatcher, we identified ten individuals from eight families with a severe neurodevelopmental syndrome featuring variable manifestations. Clinical manifestations included hypotonia, global developmental delay, severe intellectual disability, brain abnormalities, musculoskeletal, and gastrointestinal abnormalities. Genetic analysis revealed five different homozygous loss-of-function variants in WBP4. Immunoblotting on fibroblasts from two affected individuals with different genetic variants demonstrated a complete loss of protein, and RNA sequencing analysis uncovered shared abnormal splicing patterns, including in genes associated with abnormalities of the nervous system, potentially underlying the phenotypes of the probands. We conclude that bi-allelic variants in WBP4 cause a developmental disorder with variable presentations, adding to the growing list of human spliceosomopathies.
Collapse
Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Department of Military Medicine and "Tzameret," Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kaisa Teele Oja
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reza Maroofian
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; Department of Military Medicine and "Tzameret," Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Thuy-Linh Le
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France
| | - Pauline Marzin
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Anne Guimier
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Evyatar Mor
- Department of Computer Science, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Naama Zvi
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Naama Elefant
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, Cairo, Egypt
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, USA; Rady Children's Institute for Genomic Medicine, San Diego, La Jolla, USA
| | - Kai Muru
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | - Divya Pachat
- Department of Medical Genetics, Aster MIMS (Malabar Institute of Medical Sciences)-Calicut, Kerala, India
| | - Marwa Abd Elmaksoud
- Neurology Unit, Department of Pediatrics, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | | | | | - Peter Bauer
- CENTOGENE GmbH, Am Strande 7, 18055 Rostock, Germany
| | | | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Muhannad Daana
- Child Development Centers, Clalit Health Care Services, Jerusalem, Israel
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France; Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, 75015 Paris, France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de La Santé et de La Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, 75015 Paris, France
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Katrin Õunap
- Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hagar Mor-Shaked
- Department of Genetics, Hadassah Medical Organization, Jerusalem, Israel; Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
15
|
Feng Y, Yuan Q, Newsome RC, Robinson T, Bowman RL, Zuniga AN, Hall KN, Bernsten CM, Shabashvili DE, Krajcik KI, Gunaratne C, Zaroogian ZJ, Venugopal K, Casellas Roman HL, Levine RL, Chatila WK, Yaeger R, Riva A, Jobin C, Kopinke D, Avram D, Guryanova OA. Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer. J Exp Med 2023; 220:e20230011. [PMID: 37615936 PMCID: PMC10450614 DOI: 10.1084/jem.20230011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/12/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations of DNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer. In a mouse model that combines colitis-associated colon cancer (CAC) with experimental CH driven by Dnmt3a+/Δ, we found higher tumor penetrance and increased tumor burden compared with controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia, and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven by Dnmt3a haploinsufficiency and rebalanced hematopoiesis. This study provides conceptually novel insights into non-tumor-cell-autonomous effects of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies.
Collapse
Affiliation(s)
- Yang Feng
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Qingchen Yuan
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Rachel C. Newsome
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashley N. Zuniga
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kendra N. Hall
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Cassandra M. Bernsten
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Daniil E. Shabashvili
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kathryn I. Krajcik
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Chamara Gunaratne
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Zachary J. Zaroogian
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Heidi L. Casellas Roman
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K. Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Christian Jobin
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
- Immunology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Olga A. Guryanova
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| |
Collapse
|
16
|
Groves A, Ward A, Li YY, Lazo de la Vega L, Nag A, Forrest SJ, Gupta HV, Thorner AR, Meyerson M, Kamihara J, Cherniack AD, Janeway KA. Loss of heterozygosity does not occur in BRCA1/2 mutant pediatric solid and central nervous system tumors. Pediatr Blood Cancer 2023; 70:e30643. [PMID: 37596911 PMCID: PMC10883645 DOI: 10.1002/pbc.30643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Utilization of tumor-only sequencing has expanded in pediatric cancer patients, which can lead to identification of pathogenic variants in genes that may be germline and/or have uncertain relevance to the tumor in question, such as the homologous recombination (HR) pathway genes BRCA1/2. We identified patients with pathogenic BRCA1/2 mutations from somatic tumor sequencing, and performed additional germline sequencing to assess for the presence of loss of heterozygosity (LOH). Of seven patients identified, four (57.1%) mutations were found in the germline and none had associated LOH. Our data suggest that BRCA1/2 mutations identified in this context are likely incidental findings.
Collapse
Affiliation(s)
- Andrew Groves
- Division of Pediatric Hematology/Oncology, University of Iowa Stead Family Children's Hospital, Iowa City, Iowa, USA
| | - Abigail Ward
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Yvonne Y Li
- Dana-Farber Brigham and Women's Cancer Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Lorena Lazo de la Vega
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Anwesha Nag
- Dana-Farber Brigham and Women's Cancer Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne J Forrest
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hersh V Gupta
- Dana-Farber Brigham and Women's Cancer Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Aaron R Thorner
- Dana-Farber Brigham and Women's Cancer Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Dana-Farber Brigham and Women's Cancer Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Junne Kamihara
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew D Cherniack
- Dana-Farber Brigham and Women's Cancer Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Katherine A Janeway
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
17
|
Archetti M. Soft selection reduces loss of heterozygosity in asexual reproduction. J Evol Biol 2023; 36:1313-1327. [PMID: 37584223 DOI: 10.1111/jeb.14209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/27/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023]
Abstract
The adaptive value of sexual reproduction is still debated in evolutionary theory. It has been proposed that the advantage of sexual reproduction over asexual reproduction is to promote genetic diversity, to prevent the accumulation of harmful mutations or to preserve heterozygosity. Since these hypothetical advantages depend on the type of asexual reproduction, understanding how selection affects the taxonomic distribution of each type could help us discriminate between existing hypotheses. Here, I argue that soft selection, competition among embryos or offspring in selection arenas prior to the hard selection of the adult phase, reduces loss of heterozygosity in certain types of asexual reproduction. Since loss of heterozygosity leads to the unmasking of recessive deleterious mutations in the progeny of asexual individuals, soft selection facilitates the evolution of these types of asexual reproduction. Using a population genetics model, I calculate how loss of heterozygosity affects fitness for different types of apomixis and automixis, and I show that soft selection significantly reduces loss of heterozygosity, hence increases fitness, in apomixis with suppression of the first meiotic division and in automixis with central fusion, the most common types of asexual reproduction. Therefore, if sexual reproduction evolved to preserve heterozygosity, soft selection should be associated with these types of asexual reproduction. I discuss the evidence for this prediction and how this and other observations on the distribution of different types of asexual reproduction in nature is consistent with the heterozygosity hypothesis.
Collapse
Affiliation(s)
- Marco Archetti
- Department of Biology, W210 MSC, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
18
|
de Koster EJ, Corver WE, de Geus-Oei LF, Oyen WJG, Ruano D, Schepers A, Snel M, van Wezel T, Vriens D, Morreau H. A clinically applicable molecular classification of oncocytic cell thyroid nodules. Endocr Relat Cancer 2023; 30:e230047. [PMID: 37399519 PMCID: PMC10448578 DOI: 10.1530/erc-23-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Whole chromosome instability with near-whole genome haploidization (GH) and subsequent endoreduplication is considered a main genomic driver in the tumorigenesis of oncocytic cell thyroid neoplasms (OCN). These copy number alterations (CNA) occur less frequently in oncocytic thyroid adenoma (OA) than in oncocytic carcinoma (OCA), suggesting a continuous process. The current study described the CNA patterns in a cohort of 30 benign and malignant OCN, observed using a next-generation sequencing (NGS) panel that assesses genome-wide loss of heterozygosity (LOH) and chromosomal imbalances using 1500 single-nucleotide polymorphisms (SNPs) across all autosomes and the X chromosome in DNA derived from cytological and histological samples. Observed CNA patterns were verified using multiparameter DNA flow cytometry with or without whole-genome SNP array analysis and lesser-allele intensity-ratio (LAIR) analysis. On CNA-LOH analysis using the NGS panel, GH-type CNA were observed in 4 of 11 (36%) OA and in 14 of 16 OCA (88%). Endoreduplication was suspected in 8 of 16 (50%) OCA, all with more extensive GH-type CNA (P < 0.001). Reciprocal chromosomal imbalance type CNA, characterized by (imbalanced) chromosomal copy number gains and associated with benign disease, were observed in 6 of 11 (55%) OA and one equivocal case of OCA. CNA patterns were different between the histopathological subgroups (P < 0.001). By applying the structured interpretation and considerations provided by the current study, CNA-LOH analysis using an NGS panel that is feasible for daily practice may be of great added value to the widespread application of molecular diagnostics in the diagnosis and risk stratification of OCN.
Collapse
Affiliation(s)
- Elizabeth J de Koster
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Radiology, Section of Nuclear Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Willem E Corver
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lioe-Fee de Geus-Oei
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Radiology, Section of Nuclear Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Biomedical Photonic Imaging Group, University of Twente, Enschede, the Netherlands
| | - Wim J G Oyen
- Department of Medical Imaging, Nuclear Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Radiology and Nuclear Medicine, Rijnstate Hospital, Arnhem, the Netherlands
- Department of Biomedical Sciences and Humanitas Clinical and Research Centre, Department of Nuclear Medicine, Humanitas University, Milan, Italy
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Abbey Schepers
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke Snel
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dennis Vriens
- Department of Radiology, Section of Nuclear Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
19
|
Wang Y, Hou X, Liu Q, Wang D, Li S, Dang Z. Verification of a loss of heterozygosity at the D8S1179 locus in a paternity case by the MiSeq FGx system. Int J Legal Med 2023; 137:1407-1412. [PMID: 37338606 DOI: 10.1007/s00414-023-03043-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
Capillary electrophoresis is widely used to study short tandem repeats (STRs) in forensic genetics. However, next-generation sequencing platforms have become a new strategy for forensic DNA typing. In this study, we report a false four-step STR mutation between an alleged father (AF) and child in a paternity case. A total of 23 autosomal STR loci were evaluated using the Huaxia™ Platinum and Goldeneye™ 20A kits, revealing a single mismatch in D8S1179 between the AF (10/10) and the male child (14/14). Additional Y-STR typing of the AF and child was performed, and the results were consistent with those based on 27 Y-STR loci. To further confirm the experimental results, we sequenced the individuals using the MiSeq FGx system and detected 10/15 unbalanced alleles in the D8S1179 locus of the AF and 14/15 unbalanced alleles in the D8S1179 locus of the child. Sanger sequencing revealed that both the AF and child had the C→G point mutation in the primer binding region of D8S1179 resulting in allelic dropout. Therefore, the verification of STR typing by different sequencing systems is helpful for the interpretation of results in cases of multistep STR mutations.
Collapse
Affiliation(s)
- Yequan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China.
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China.
| | - Xiudi Hou
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Qi Liu
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Shuyue Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
- Forensic Science Center of Jining Medical University, Jining, Shandong, People's Republic of China
| | - Zhen Dang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China.
| |
Collapse
|
20
|
Schandl CA, Mazzoni S, Znoyko I, Nahhas GJ, Chung D, Ding Y, Hess B, Wolff DJ. Novel high-risk acute myeloid leukemia subgroup with ERG amplification and Biallelic loss of TP53. Cancer Genet 2023; 272-273:23-28. [PMID: 36657266 DOI: 10.1016/j.cancergen.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
ETS-related gene (ERG) amplification, observed in 4-6% of acute myeloid leukemia (AML), is associated with unfavorable prognosis. To determine coincident effects of additional genomic abnormalities in AML with ERG amplification (ERGamp), we examined 11 ERGamp cases of 205 newly diagnosed AML using chromosomal microarray analysis and next generation sequencing. ERGamp cases demonstrated a distinct pattern of high genetic complexity: loss of 5q, chromothripsis and TP53 loss of function variants. Remarkably, allelic TP53 loss or loss of heterozygosity (LOH) co-occurring with TP53 inactivating mutation dramatically effected ERGamp tumor patient outcome. In the presence of homozygous TP53 loss of function, ERGamp patients demonstrated no response to induction chemotherapy with median overall survival (OS) of 3.8 months (N = 9). Two patients with heterozygous loss of TP53 function underwent alloSCT without evidence of relapse at one year. Similarly, a validation TCGA cohort, 6 of the 8 ERGamp cases with TP53 loss of function demonstrated median OS of 2.5 months. This suggests that with TP53 mutant ERGamp AML, successive loss of the second TP53 allele, typically by 17p deletion or LOH identifies a specific high-risk subtype of AML patients who are resistant to standard induction chemotherapy and need novel approaches to avert the very poor prognosis.
Collapse
Affiliation(s)
- Cynthia A Schandl
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Sandra Mazzoni
- Departmant of Hematology and Oncology, Cleveland Clinic Taussig Cancer Center, Cleveland, OH, USA.
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Georges J Nahhas
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Dongjun Chung
- Department of Public Health-Division of Biostatistics and Bioinformatics, Medical University of South Carolina, Charleston, SC, USA
| | - Yanna Ding
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Brian Hess
- Department of Hematology and Oncology, Medical University of South Carolina Hollings Cancer Center, Charleston, SC, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| |
Collapse
|
21
|
Soloveva M, Solovev M, Nikulina E, Risinskaya N, Biderman B, Yakutik I, Obukhova T, Mendeleeva L. Loss of Heterozygosity in the Circulating Tumor DNA and CD138+ Bone Marrow Cells in Multiple Myeloma. Genes (Basel) 2023; 14:genes14020351. [PMID: 36833278 PMCID: PMC9957234 DOI: 10.3390/genes14020351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/21/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Multiple myeloma (MM) is characterized by heterogeneity of tumor cells. The study of tumor cells from blood, bone marrow, plasmacytoma, etc., allows us to identify similarities and differences in tumor lesions of various anatomical localizations. The aim of this study was to compare the loss of heterozygosity (LOH) by tumor cells by assessing STR profiles of different MM lesions. We examined paired samples of plasma circulating tumor DNA (ctDNA) and CD138+ bone marrow cells in MM patients. For patients with plasmacytomas (66% of 38 patients included), the STR profile of plasmacytomas was also studied when biopsy samples were available. Diverse patterns of LOH were found in lesions of different localization for most patients. LOH in plasma ctDNA, bone marrow, and plasmacytoma samples was found for 55%, 71%, and 100% of patients, respectively. One could expect a greater variety of STR profiles in aberrant loci for patients with plasmacytomas. This hypothesis was not confirmed-no difference in the frequency of LOH in MM patients with or without plasmacytomas was found. This indicates the genetic diversity of tumor clones in MM, regardless of the presence of extramedullar lesions. Therefore, we conclude that risk stratification based on molecular tests performed solely on bone marrow samples may not be sufficient for all MM patients, including those without plasmacytomas. Due to genetic heterogeneity of MM tumor cells from various lesions, the high diagnostic value of liquid biopsy approaches becomes obvious.
Collapse
|
22
|
Nakayama T, Sunaoshi M, Shang Y, Takahashi M, Saito T, Blyth BJ, Amasaki Y, Daino K, Shimada Y, Tachibana A, Kakinuma S. Calorie restriction alters the mechanisms of radiation-induced mouse thymic lymphomagenesis. PLoS One 2023; 18:e0280560. [PMID: 36662808 PMCID: PMC9858762 DOI: 10.1371/journal.pone.0280560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/29/2022] [Indexed: 01/21/2023] Open
Abstract
Calorie restriction (CR) suppresses not only spontaneous but also chemical- and radiation-induced carcinogenesis. Our previous study revealed that the cancer-preventive effect of CR is tissue dependent and that CR does not effectively prevent the development of thymic lymphoma (TL). We investigated the association between CR and the genomic alterations of resulting TLs to clarify the underlying resistance mechanism. TLs were obtained from previous and new experiments, in which B6C3F1 mice were exposed to radiation at 1 week of age and fed with a CR or standard (non-CR) diet from 7 weeks throughout their lifetimes. All available TLs were used for analysis of genomic DNA. In contrast to the TLs of the non-CR group, those of the CR group displayed suppression of copy-neutral loss of heterozygosity (LOH) involving relevant tumor suppressor genes (Cdkn2a, Ikzf1, Trp53, Pten), an event regarded as cell division-associated. However, CR did not affect interstitial deletions of those genes, which were observed in both groups. In addition, CR affected the mechanism of Ikzf1 inactivation in TLs: the non-CR group exhibited copy-neutral LOH with duplicated inactive alleles, whereas the CR group showed expression of dominant-negative isoforms accompanying a point mutation or an intragenic deletion. These results suggest that, even though CR reduces cell division-related genomic rearrangements by suppressing cell proliferation, tumors arise via diverse carcinogenic pathways including inactivation of tumor suppressors via interstitial deletions and other mutations. These findings provide a molecular basis for improved prevention strategies that overcome the CR resistance of lymphomagenesis.
Collapse
Affiliation(s)
- Takafumi Nakayama
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
- Graduate School of Science and Engineering, Ibaraki University, Mito, Japan
| | - Masaaki Sunaoshi
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yi Shang
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Mizuki Takahashi
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
- Graduate School of Science and Engineering, Ibaraki University, Mito, Japan
| | - Takato Saito
- Graduate School of Science and Engineering, Ibaraki University, Mito, Japan
| | - Benjamin J. Blyth
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yoshiko Amasaki
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Kazuhiro Daino
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yoshiya Shimada
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Akira Tachibana
- Graduate School of Science and Engineering, Ibaraki University, Mito, Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| |
Collapse
|
23
|
Pastorino L, Dalmasso B, Allavena E, Vanni I, Ugolini F, Baroni G, Croce M, Guadagno A, Cabiddu F, Andreotti V, Bruno W, Zoppoli G, Ferrando L, Tanda ET, Spagnolo F, Menin C, Gangemi R, Massi D, Ghiorzo P. Ataxia-Telangiectasia Mutated Loss of Heterozygosity in Melanoma. Int J Mol Sci 2022; 23:ijms232416027. [PMID: 36555667 PMCID: PMC9786167 DOI: 10.3390/ijms232416027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
ATM germline pathogenic variants were recently found enriched in high-risk melanoma patients. However, ATM loss of heterozygosity (LOH) has never been investigated in melanoma and, therefore, a causal association with melanoma development has not been established yet. The purpose of this study was to functionally characterize 13 germline ATM variants found in high-risk melanoma patients-and classified by in silico tools as pathogenic, uncertain significance, or benign-using multiple assays evaluating ATM/pATM expression and/or LOH in melanoma tissues and cell lines. We assessed ATM status by Immunohistochemistry (IHC), Western Blot, Whole-Exome Sequencing/Copy Number Variation analysis, and RNA sequencing, supported by Sanger sequencing and microsatellite analyses. For most variants, IHC results matched those obtained with in silico classification and LOH analysis. Two pathogenic variants (p.Ser1135_Lys1192del and p.Ser1993ArgfsTer23) showed LOH and complete loss of ATM activation in melanoma. Two variants of unknown significance (p.Asn358Ile and p.Asn796His) showed reduced expression and LOH, suggestive of a deleterious effect. This study, showing a classic two-hit scenario in a well-known tumor suppressor gene, supports the inclusion of melanoma in the ATM-related cancer spectrum.
Collapse
Affiliation(s)
- Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Bruna Dalmasso
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Eleonora Allavena
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
| | - Irene Vanni
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Filippo Ugolini
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Gianna Baroni
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Michela Croce
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Antonio Guadagno
- Anatomia Patologica, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Cabiddu
- Anatomia Patologica, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Virginia Andreotti
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - William Bruno
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Lorenzo Ferrando
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Clinica di Medicina Interna a Indirizzo Oncologico, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Enrica Teresa Tanda
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Francesco Spagnolo
- Oncologia Medica 2, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Chiara Menin
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padua, Italy
| | - Rosaria Gangemi
- Bioterapie, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Daniela Massi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, 50134 Florence, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
- Genetica dei Tumori Rari, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Correspondence:
| |
Collapse
|
24
|
Wu B, Ellisen LW. Loss of p53 and genetic evolution in pancreatic cancer: Ordered chaos after the guardian is gone. Cancer Cell 2022; 40:1276-1278. [PMID: 36379206 DOI: 10.1016/j.ccell.2022.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A recent Nature study delineates a stepwise genomic evolution during pancreatic cancer development, employing an engineered mutant Kras and heterozygous Trp53 mouse model that identifies cells undergoing Trp53 loss of heterozygosity (LOH). Genetic progression post-Trp53 LOH involves clonal deletions, then genome doubling and subsequent accumulation of subclonal gains and amplifications.
Collapse
Affiliation(s)
- Bogang Wu
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Leif W Ellisen
- Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA.
| |
Collapse
|
25
|
Du J, Wan X, Zhang H, Cao J, Zhao W, Li Z. [Association of genomic instability of CDH1 gene with clinicopathological characteristics of gastric cancer]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2022; 39:1279-1282. [PMID: 36317219 DOI: 10.3760/cma.j.cn511374-20210304-00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
OBJECTIVE To assess the association of genomic instability of epithelial cadherin 1 (CDH1) gene and clinicopathological characteristics of gastric cancer. METHODS In total 120 paraffin-embedded gastric cancer tissue specimen were prepared, and genomic DNA was extracted. The genomic instability of the CDH1 gene was analyzed by immunohistochemistry and silver staining PCR-single-strand conformation polymorphism. RESULTS The number of information individuals (heterozygotes) was 98 for the D16S752 locus. The detection rates for microsatellite instability (MSI) and loss of heterozygosity (LOH) at the D16S752 locus and the positive rate of CDH1 protein were 19.39%, 16.33% and 51.02%, respectively. The detection rate of MSI in TNM stages I or II was significantly higher than that in stages III or IV (P<0.05) while the detection rate of LOH was significantly lower than that in stages III or IV (P<0.05). The positive rate of CDH1 protein in TNM stages III or IV was significantly lower than that in stages I or II (P<0.05). The detection rate of MSI of cases with lymph node metastasis was significantly lower than that of without lymph node metastasis (P<0.05) while the detection rate of LOH was significantly higher than that without lymph node metastasis (P<0.05). The positive rate of CDH1 protein in patients with lymph node metastasis was significantly lower than that in patients without lymph node metastasis (P<0.05). The positive rate of CDH1 protein in MSI-positive group was significantly higher than that in MSI-negative group (P<0.05), and the positive rate of CDH1 protein in the LOH-positive group was significantly lower than that the LOH-negative group (P<0.05). CONCLUSION The genomic instability of the CDH1 gene is associated with the progression of gastric cancer. MSI at the D16S752 locus may be used as a molecular marker for early gastric cancer, while LOH at this locus mostly occurs in advanced gastric cancer and can be regarded as an effective indicators for malignancy evaluation and prognosis.
Collapse
Affiliation(s)
- Jitao Du
- Department of General Surgery, the Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan 450000, China.
| | | | | | | | | | | |
Collapse
|
26
|
Dermawan JK, Hwang S, Wexler L, Tap WD, Singer S, Vanderbilt CM, Antonescu CR. Myxoid pleomorphic liposarcoma is distinguished from other liposarcomas by widespread loss of heterozygosity and significantly worse overall survival: a genomic and clinicopathologic study. Mod Pathol 2022; 35:1644-1655. [PMID: 35672466 PMCID: PMC9613513 DOI: 10.1038/s41379-022-01107-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 12/21/2022]
Abstract
Myxoid pleomorphic liposarcoma (MPLPS) is a recently described and extremely rare subtype of liposarcoma with a predilection for the mediastinum. However, the genomic features of MPLPS remain poorly understood. We performed comprehensive genomic profiling of MPLPS in comparison with pleomorphic liposarcoma (PLPS) and myxoid/round cell liposarcoma (MRLPS). Of the 8 patients with MPLPS, 5 were female and 3 were male, with a median age of 32 years old (range 10-68). All except one were located in the mediastinum, with invasion of surrounding anatomic structures, including chest wall, pleura, spine, and large vessels. All cases showed an admixture of morphologies reminiscent of PLPS and MRLPS, including myxoid areas with plexiform vasculature admixed with uni- and/or multivacuolated pleomorphic lipoblasts. Less common features included well-differentiated liposarcoma-like areas, and in one case fascicular spindle cell sarcoma reminiscent of dedifferentiated LPS. Clinically, 4 experienced local recurrence, 4 had distant metastases and 5 died of disease. Compared to PLPS and MRLPS, patients with MPLPS had worse overall and progression-free survival. Recurrent TP53 mutations were present in all 8 MPLPS cases. In contrast, in PLPS, which also showed recurrent TP53 mutations (83%), RB1 and ATRX losses were more common. MRLPS was highly enriched in TERT promoter mutations (88%) and PI3K/AKT pathway mutations. Copy number profiling in MPLPS revealed multiple chromosomal gains with recurrent amplifications of chromosomes 1, 19 and 21. Importantly, allele-specific copy number analysis revealed widespread loss of heterozygosity (80% of the genome on average) in MPLPS, but not in PLPS or MRLPS. Our findings revealed genome-wide loss of heterozygosity co-existing with TP53 mutations as a characteristic genomic signature distinct from other liposarcoma subtypes, which supports the current classification of MPLPS as a stand-alone pathologic entity. These results further expand the clinicopathologic features of MPLPS, including older age, extra-mediastinal sites, and a highly aggressive outcome.
Collapse
Affiliation(s)
- Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sinchun Hwang
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonard Wexler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
27
|
Deshpande M, Paniza T, Jalloul N, Nanjangud G, Twarowski J, Koren A, Zaninovic N, Zhan Q, Chadalavada K, Malkova A, Khiabanian H, Madireddy A, Rosenwaks Z, Gerhardt J. Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells. Mol Cell 2022; 82:3781-3793.e7. [PMID: 36099913 DOI: 10.1016/j.molcel.2022.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/21/2022] [Accepted: 08/16/2022] [Indexed: 01/05/2023]
Abstract
Germline mutations in the BRCA genes are associated with a higher risk of carcinogenesis, which is linked to an increased mutation rate and loss of the second unaffected BRCA allele (loss of heterozygosity, LOH). However, the mechanisms triggering mutagenesis are not clearly understood. The BRCA genes contain high numbers of repetitive DNA sequences. We detected replication forks stalling, DNA breaks, and deletions at these sites in haploinsufficient BRCA cells, thus identifying the BRCA genes as fragile sites. Next, we found that stalled forks are repaired by error-prone pathways, such as microhomology-mediated break-induced replication (MMBIR) in haploinsufficient BRCA1 breast epithelial cells. We detected MMBIR mutations in BRCA1 tumor cells and noticed deletions-insertions (>50 bp) at the BRCA1 genes in BRCA1 patients. Altogether, these results suggest that under stress, error-prone repair of stalled forks is upregulated and induces mutations, including complex genomic rearrangements at the BRCA genes (LOH), in haploinsufficient BRCA1 cells.
Collapse
Affiliation(s)
- Madhura Deshpande
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Theodore Paniza
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nahed Jalloul
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08903, USA
| | - Gouri Nanjangud
- Molecular Cytogenetics Core Facility, Sloan Kettering Institute, New York, NY 10065, USA
| | - Jerzy Twarowski
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Nikica Zaninovic
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Qiansheng Zhan
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kalyani Chadalavada
- Molecular Cytogenetics Core Facility, Sloan Kettering Institute, New York, NY 10065, USA
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08903, USA
| | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers University, New Brunswick, NJ 08903, USA
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10021, USA.
| |
Collapse
|
28
|
Anno M, Izawa S, Fujioka Y, Matsuzawa K, Saito K, Hikita K, Makishima K, Nosaka K, Takenaka A, Usui T, Yamamoto K. Retroperitoneal paraganglioma with loss of heterozygosity of the von Hippel-Lindau gene: a case report and review of the literature. Endocr J 2022; 69:1137-1147. [PMID: 35466127 DOI: 10.1507/endocrj.ej21-0611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Von Hippel-Lindau (VHL) disease is an autosomal dominant disease related to germline mutations in VHL. In VHL disease, pheochromocytoma develops in 10%-20% of patients because of germline mutations and loss of heterozygosity of VHL. However, the rate of paraganglioma associated with VHL is low compared with that of pheochromocytoma, and the reason is unknown. In this study, we performed germline and somatic mutation analyses of retroperitoneal paraganglioma that developed in a patient with clinically diagnosed VHL disease and investigated the tumorigenic mechanism of paraganglioma. The patient was a 25-year-old woman who was considered to have VHL disease on the basis of her family history. She was referred to our clinic to investigate a tumor at the bifurcation of the common iliac artery. The tumor was diagnosed as retroperitoneal paraganglioma by clinical evaluations. A left renal cell carcinoma was also suspected. Polymerase chain reaction direct sequencing analysis and polymorphic microsatellite analysis within the VHL locus suggested that loss of heterozygosity of VHL was associated with paraganglioma and renal cell carcinoma. Multiplex ligation-dependent probe amplification analysis showed a loss of the copy number of VHL exons in paraganglioma. These results suggest that VHL disease contributes to the development of paraganglioma. A literature review showed no reported common missense variants involved in the progression of paraganglioma. The loss of heterozygosity of VHL can be a tumorigenic mechanism of retroperitoneal paraganglioma in VHL disease. However, the low rate of paraganglioma compared with pheochromocytoma is not explained by their genetic background alone.
Collapse
Affiliation(s)
- Mari Anno
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Shoichiro Izawa
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Yohei Fujioka
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kazuhiko Matsuzawa
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kohei Saito
- Center for Diabetes, Endocrinology and Metabolism, Shizuoka Prefectural Hospital, Shizuoka 420-8527, Japan
| | - Katsuya Hikita
- Division of Urology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Karen Makishima
- Division of Pathology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kanae Nosaka
- Division of Pathology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Atsushi Takenaka
- Division of Urology, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Takeshi Usui
- Research Support Center, Shizuoka Prefectural Hospital, Shizuoka 420-8527, Japan
- Shizuoka Graduate University of Public Health, Shizuoka 420-0881, Japan
| | - Kazuhiro Yamamoto
- Division of Endocrinology and Metabolism, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| |
Collapse
|
29
|
Chun SK, Fortin BM, Fellows RC, Habowski AN, Verlande A, Song WA, Mahieu AL, Lefebvre AEYT, Sterrenberg JN, Velez LM, Digman MA, Edwards RA, Pannunzio NR, Seldin MM, Waterman ML, Masri S. Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer. Sci Adv 2022; 8:eabo2389. [PMID: 35947664 PMCID: PMC9365282 DOI: 10.1126/sciadv.abo2389] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
An alarming rise in young onset colorectal cancer (CRC) has been reported; however, the underlying molecular mechanism remains undefined. Suspected risk factors of young onset CRC include environmental aspects, such as lifestyle and dietary factors, which are known to affect the circadian clock. We find that both genetic disruption and environmental disruption of the circadian clock accelerate Apc-driven CRC pathogenesis in vivo. Using an intestinal organoid model, we demonstrate that clock disruption promotes transformation by driving Apc loss of heterozygosity, which hyperactivates Wnt signaling. This up-regulates c-Myc, a known Wnt target, which drives heightened glycolytic metabolism. Using patient-derived organoids, we show that circadian rhythms are lost in human tumors. Last, we identify that variance between core clock and Wnt pathway genes significantly predicts the survival of patients with CRC. Overall, our findings demonstrate a previously unidentified mechanistic link between clock disruption and CRC, which has important implications for young onset cancer prevention.
Collapse
Affiliation(s)
- Sung Kook Chun
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Bridget M. Fortin
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel C. Fellows
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Amber N. Habowski
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA
| | - Amandine Verlande
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Wei A. Song
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Alisa L. Mahieu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | | | - Leandro M. Velez
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Michelle A. Digman
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Robert A. Edwards
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Marcus M. Seldin
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Marian L. Waterman
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA 92697, USA
| | - Selma Masri
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author.
| |
Collapse
|
30
|
Ma Y, Ling S, Li Y, Hu M, Kong B, Huang P, Liu H. Loss of Heterozygosity for KrasG12D Promotes Malignant Phenotype of Pancreatic Ductal Adenocarcinoma by Activating HIF-2α-c-Myc-Regulated Glutamine Metabolism. Int J Mol Sci 2022; 23:6697. [PMID: 35743139 PMCID: PMC9224498 DOI: 10.3390/ijms23126697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 01/27/2023] Open
Abstract
Loss of heterozygosity (LOH) for KRAS, in which a wild-type KRAS allele is progressively lost, promotes invasive and migratory abilities of pancreatic ductal adenocarcinoma (PDAC) cells and tissues. Moreover, the occurrence of KrasG12D-LOH activates nonclassical glutamine metabolism, which is related to the malignant behavior of PDAC cells. Herein, we aim to demonstrate the regulatory link between hypoxia-inducible factor-2α (HIF-2α) and glutamine metabolism that mediates malignant phenotypes in KrasG12D-LOH PDAC cells. HIF-2α-shRNA knockdown lentivirus transfection and metabolite analysis were performed in KrasG12D-LOH and KrasG12D cell lines, respectively. Cell proliferation, migration, and invasion were examined using Cell Counting Kit-8, colony formation, and Transwell assays. Cell cycle phase and apoptosis were determined using flow cytometry. Western blotting and real-time quantitative PCR were also performed. Additionally, a subcutaneous xenograft mouse model was established. LOH stimulated HIF-2α activity and transactivated c-Myc, which has a central regulatory effect on glutamine metabolism independent of hypoxia. Meanwhile, HIF-2α silencing repressed KrasG12D-LOH PDAC cell proliferation, invasion, and migration. HIF-2α knockdown inhibited glutamine uptake and GOT1 expression via a c-Myc-dependent pathway. Collectively, KrasG12D-LOH can activate HIF-2α to regulate c-Myc-mediated glutamine metabolism and promote malignant phenotypes. Moreover, targeting HIF-2α-c-Myc regulated nonclassical glutamine metabolism, providing a new therapeutic perspective for KrasG12D-LOH PDAC.
Collapse
Affiliation(s)
- Yu Ma
- Department of Pathology, Xuzhou Medical University, Xuzhou 221004, China;
| | - Sunkai Ling
- School of Medicine, Southeast University, Nanjing 210009, China; (S.L.); (Y.L.); (M.H.); (P.H.)
| | - Yuan Li
- School of Medicine, Southeast University, Nanjing 210009, China; (S.L.); (Y.L.); (M.H.); (P.H.)
| | - Mingyue Hu
- School of Medicine, Southeast University, Nanjing 210009, China; (S.L.); (Y.L.); (M.H.); (P.H.)
| | - Bo Kong
- Department of Surgery, Klinikumrechts der Isar, School of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany;
| | - Peilin Huang
- School of Medicine, Southeast University, Nanjing 210009, China; (S.L.); (Y.L.); (M.H.); (P.H.)
| | - Hui Liu
- Department of Pathology, Xuzhou Medical University, Xuzhou 221004, China;
| |
Collapse
|
31
|
Parilla M, Chapel D, Hechtman JF, Wanjari P, Jabbour TE, Sharma A, Ritterhouse L, Segal J, Vanderbilt C, Klimstra DS, Setia N, Tang L. Recurrent Loss of Heterozygosity in Pancreatic Neuroendocrine Tumors. Am J Surg Pathol 2022; 46:823-831. [PMID: 35125451 PMCID: PMC9106831 DOI: 10.1097/pas.0000000000001860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chromosomal aneuploidies are prognostic markers across a wide variety of tumor types, and recent literature suggests that pancreatic neuroendocrine tumors are no different. In this study 214 patients with grade 1, 2, or 3 pancreatic neuroendocrine tumors had their tissue examined for chromosomal copy number alterations using next-generation sequencing. Univariate and multivariate statistical analyses were performed with all-cause mortality and disease-specific mortality as the end comparators. As such, the cohort stratified into 3 different clinically relevant chromosomal subgroups: an indolent subgroup characterized by loss of chromosome 11 in relative isolation, an aggressive subgroup characterized by losses of chromosomes 1, 2, 3, 6, 10, 11, 16, and 22 and with no loss of chromosomes 4, 5, 7, 12, 14, 17, 19, and 20, and finally a heterogeneous third group with a subset of cases that behave even more aggressively than the aforementioned.
Collapse
Affiliation(s)
- Megan Parilla
- Department of Pathology, University of Chicago, Chicago, IL
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Loyola Univesity, Maywood, IL
| | - David Chapel
- Department of Pathology, University of Chicago, Chicago, IL
- Department of Pathology, University of Michigan - Michigan Medicine, Ann Arbor, MI
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Neogenomics Laboratories, Fort Myers, FL
| | | | - Tony El Jabbour
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Aarti Sharma
- Department of Pathology, University of Chicago, Chicago, IL
| | - Lauren Ritterhouse
- Department of Pathology, University of Chicago, Chicago, IL
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jeremy Segal
- Department of Pathology, University of Chicago, Chicago, IL
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Namrata Setia
- Department of Pathology, University of Chicago, Chicago, IL
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
32
|
Tuveri S, Debackere K, Marcelis L, Dierckxsens N, Demeulemeester J, Dimitriadou E, Dierickx D, Lefesvre P, Deraedt K, Graux C, Michaux L, Cools J, Tousseyn T, Vermeesch JR, Wlodarska I. Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity. Genes Chromosomes Cancer 2022; 61:603-615. [PMID: 35611992 DOI: 10.1002/gcc.23069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 11/07/2022] Open
Abstract
Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumour from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%) and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15) and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as 'second hit' in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukamia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.
Collapse
Affiliation(s)
| | - Koen Debackere
- Laboratory for Experimental Hematology, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Lukas Marcelis
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - Jonas Demeulemeester
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | | | - Daan Dierickx
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Pierre Lefesvre
- Department of Pathology, Free University Hospital, Brussels, Belgium
| | - Karen Deraedt
- Anatomo-Pathology, Hospital East Limburg, Genk, Belgium
| | - Carlos Graux
- Department of Hematology, Mont-Godinne University Hospital, Yvoir, Belgium
| | | | - Jan Cools
- Center for Human Genetics, KU Leuven, Leuven, Belgium
- Center for Cancer Biology, VIB, Leuven, Belgium
| | - Thomas Tousseyn
- Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | | |
Collapse
|
33
|
Anderson DJ, Pauler FM, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Syst 2022; 13:438-453.e5. [PMID: 35452605 DOI: 10.1016/j.cels.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/21/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans.
Collapse
Affiliation(s)
- Donovan J Anderson
- Allen Discovery Center for Lineage Tracing and Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA
| | - Florian M Pauler
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | | | - Jay Shendure
- Allen Discovery Center for Lineage Tracing, Department of Genome Sciences, and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98109, USA
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Marshall S Horwitz
- Allen Discovery Center for Lineage Tracing and Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98109, USA.
| |
Collapse
|
34
|
Al Sharhan NA, Messaoudi SA, Babu SR, Chaudhary AB, Alsharm AA, Alrefaei AF, Kadasah S, Abu-Elmagd M, Assidi M, Buhmeida A, Carracedo Á, Almawi WY. Utility of Circulating Cell-Free DNA in Assessing Microsatellite Instability and Loss of Heterozygosity in Breast Cancer Using Human Identification Approach. Genes (Basel) 2022; 13:genes13040590. [PMID: 35456396 PMCID: PMC9027523 DOI: 10.3390/genes13040590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
The diagnostic and prognostic utility of circulating cell-free DNA (cfDNA) in breast cancer (BC) patients was recently reported. Here, we investigated the use of cfDNA to examine microsatellite instability (MSI) and loss of heterozygosity (LOH) for early BC diagnosis. cfDNA and genomic DNA from 41 female BC patients and 40 healthy controls were quantified using NanoDrop spectrophotometry and real-time PCR. The stability of genomic and cfDNA was assessed using a high-resolution AmpFlSTR MiniFiler human identification kit. Significant increases in cfDNA plasma concentrations were observed in BC patients compared to controls. The genotype distribution of the eight autosomal short tandem repeat (STR) loci D7S820, D13S317, D21S11, D2S1338, D18S51, D16S539, FGA, and CSF1PO were in Hardy–Weinberg equilibrium. Significant differences in the allele frequencies of D7S820 allele-8, D21S11 allele-29, allele-30.2, allele-32.2, and CSF1PO allele-11 were seen between BC patients and controls. LOH and MSI were detected in 36.6% of the cfDNA of patients compared to genomic DNA. This study highlights the utility of plasma-derived cfDNA for earlier, less invasive, and cost-effective cancer diagnosis and molecular stratification. It also highlights the potential value of cfDNA in molecular profiling and biomarkers discovery in precision and forensic medicine.
Collapse
Affiliation(s)
- Norah A. Al Sharhan
- Department of Biopharmaceutical, Laboratories and Research Sector, Saudi Food and Drug Authority, Riyadh 3292, Saudi Arabia;
| | - Safia A. Messaoudi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 14812, Saudi Arabia; (S.A.M.); (S.R.B.); (A.B.C.)
| | - Saranya R. Babu
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 14812, Saudi Arabia; (S.A.M.); (S.R.B.); (A.B.C.)
| | - AbdulRauf B. Chaudhary
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 14812, Saudi Arabia; (S.A.M.); (S.R.B.); (A.B.C.)
- Surgery Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Abdullah A. Alsharm
- Medical Oncology Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia;
| | | | - Sultan Kadasah
- Department of Biology, Faculty of Sciences, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Muhammad Abu-Elmagd
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.-E.); (M.A.); (A.B.)
- Medical Laboratory Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.-E.); (M.A.); (A.B.)
- Medical Laboratory Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abdelbaset Buhmeida
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.-E.); (M.A.); (A.B.)
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), CIBERER, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Wassim Y. Almawi
- Faculté des Sciences de Tunis, Université de Tunis—El Manar, Tunis 1068, Tunisia
- Correspondence: ; Tel.: +216-26-784-092
| |
Collapse
|
35
|
Wang W, Wang F, Dong L, Chen N, He Y, Zhang W, He J, Zhu F. [Analysis of loss of heterozygosity at HLA loci in a patient with leukemia]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2022; 39:338-342. [PMID: 35315049 DOI: 10.3760/cma.j.cn511374-20210310-00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To detect loss of heterozygosity (LOH) at human leukocyte antigen (HLA) loci in a Chinese patient with leukemia after haploidentical hematopoietic stem cell transplantation. METHODS HLA genotyping was carried out on peripheral blood, hair follicle and buccal swab samples derived from the patient after the transplantation as well as peripheral blood samples from his parents by using PCR-sequence specific oligonucleotide probe method and PCR-sequence based typing method. Short tandem repeat (STR) loci were detected by using a 23 site STR assay kit and a self-developed 6 STR loci assay for the HLA regions. RESULTS After the transplantation, the HLA genotype of the peripheral blood sample of the patient was identical to his father. The patient was HLA-A*02:01,24:02, C*03:03,03:04, B*13:01,15:01, DRB1*08:03,12:02, DQB1*03:01,06:01 for his hair follicle specimen. However, homozygosity of the HLA loci was found in his buccal swab sample. Only the HLA-A*24:02-C*03:03-B*15:01-DRB1*08:03-DQB1*06:01 haplotype from his father's was present, while the HLA-A*02:01-C*03:04-B*13:01-DRB1*12:02-DQB1*03:01 haplotype from his mother was lost. After the transplantation, the alleles of the 23 STR sites in the patient's peripheral blood sample were consistent to his father, with no allelic loss detected in his buccal swab sample. However, at least 4 STR loci in the HLA region were lost in his buccal swab sample. CONCLUSION LOH at the HLA loci has been detected in the buccal swab sample of a patient with leukemia who received haploidentical hematopoietic stem cell transplantation.
Collapse
Affiliation(s)
- Wei Wang
- Blood Center of Zhejiang Province, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, Zhejiang 310052, China.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Tokatlian T, Asuelime GE, Mock JY, DiAndreth B, Sharma S, Toledo Warshaviak D, Daris ME, Bolanos K, Luna BL, Naradikian MS, Deshmukh K, Hamburger AE, Kamb A. Mesothelin-specific CAR-T cell therapy that incorporates an HLA-gated safety mechanism selectively kills tumor cells. J Immunother Cancer 2022; 10:jitc-2021-003826. [PMID: 35091455 PMCID: PMC8804709 DOI: 10.1136/jitc-2021-003826] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background Mesothelin (MSLN) is a classic tumor-associated antigen that is expressed in lung cancer and many other solid tumors. However, MSLN is also expressed in normal mesothelium which creates a significant risk of serious inflammation for MSLN-directed therapeutics. We have developed a dual-receptor (Tmod™) system that exploits the difference between tumor and normal tissue in a subset of patients with defined heterozygous gene loss (LOH) in their tumors. Methods T cells engineered with the MSLN CAR Tmod construct described here contain (1) a novel MSLN-activated CAR and (2) an HLA-A*02-gated inhibitory receptor (blocker). A*02 binding is intended to override T-cell cytotoxicity, even in the presence of MSLN. The Tmod system is designed to treat heterozygous HLA class I patients, selected for HLA LOH. When A*02 is absent from tumors selected for LOH, the MSLN Tmod cells are predicted to mediate potent killing of the MSLN(+)A*02(−) malignant cells. Results The sensitivity of the MSLN Tmod cells is comparable with a benchmark MSLN CAR-T that was active but toxic in the clinic. Unlike MSLN CAR-T cells, the Tmod system robustly protects surrogate “normal” cells even in mixed-cell populations in vitro and in a xenograft model. The MSLN CAR can also be paired with other HLA class I blockers, supporting extension of the approach to patients beyond A*02 heterozygotes. Conclusions The Tmod mechanism exemplified by the MSLN CAR Tmod construct provides an alternative route to leverage solid-tumor antigens such as MSLN in safer, more effective ways than previously possible.
Collapse
Affiliation(s)
| | | | | | | | - Shruti Sharma
- A2 Biotherapeutics Inc, Agoura Hills, California, USA
| | | | - Mark E Daris
- A2 Biotherapeutics Inc, Agoura Hills, California, USA
| | | | | | | | | | | | | |
Collapse
|
37
|
Kitamura S, Satoh K, Oono Y. Detection and characterization of genome-wide mutations in M1 vegetative cells of gamma-irradiated Arabidopsis. PLoS Genet 2022; 18:e1009979. [PMID: 35051177 PMCID: PMC8775353 DOI: 10.1371/journal.pgen.1009979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/04/2021] [Indexed: 11/20/2022] Open
Abstract
Radiation-induced mutations have been detected by whole-genome sequencing analyses of self-pollinated generations of mutagenized plants. However, large DNA alterations and mutations in non-germline cells were likely missed. In this study, in order to detect various types of mutations in mutagenized M1 plants, anthocyanin pigmentation was used as a visible marker of mutations. Arabidopsis seeds heterozygous for the anthocyanin biosynthetic genes were irradiated with gamma-rays. Anthocyanin-less vegetative sectors resulting from a loss of heterozygosity were isolated from the gamma-irradiated M1 plants. The whole-genome sequencing analysis of the sectors detected various mutations, including structural variations (SVs) and large deletions (≥100 bp), both of which have been less characterized in the previous researches using gamma-irradiated plant genomes of M2 or later generations. Various types of rejoined sites were found in SVs, including no-insertion/deletion (indel) sites, only-deletion sites, only-insertion sites, and indel sites, but the rejoined sites with 0–5 bp indels represented most of the SVs. Examinations of the junctions of rearrangements (SVs and large deletions), medium deletions (10–99 bp), and small deletions (2–9 bp) revealed unique features (i.e., frequency of insertions and microhomology) at the rejoined sites. These results suggest that they were formed preferentially via different processes. Additionally, mutations that occurred in putative single M1 cells were identified according to the distribution of their allele frequency. The estimated mutation frequencies and spectra of the M1 cells were similar to those of previously analyzed M2 cells, with the exception of the greater proportion of rearrangements in the M1 cells. These findings suggest there are no major differences in the small mutations (<100 bp) between vegetative and germline cells. Thus, this study generated valuable information that may help clarify the nature of gamma-irradiation-induced mutations and their occurrence in cells that develop into vegetative or reproductive tissues. Mutations that occur in plant genome are not only related to plant evolution and speciation in nature, and also useful to identify novel gene functions and to develop new cultivars. Ionizing radiations induce various types of mutations throughout genomes in individual cells of an irradiated/mutagenized plant. However, current knowledge on radiation-induced genome-wide mutations in plants relied on the analyses of self-pollinated generations (M2 or later generations) of the mutagenized plants (M1 generation). Thus, mutations that are hardly transmitted to the next generation and those occurred in non-germline cells could not be investigated. Here, using anthocyanin pigmentation as a visible marker to reduce the genomic complexity in M1 plants, we achieved reliable detection of radiation-induced genome-wide mutations. We demonstrated that rearrangements, which were hardly detected in previous analyses using M2 genomes, occurred substantially often in gamma-irradiated M1 cells. We also revealed that mutation profile of the M1 cells was comparable with that of M2 genomes reported in previous analyses, except for the higher proportion of rearrangements in the M1 genome. Together with unique features at rejoined sites of rearrangements, medium deletions, and small deletions in the M1 genome, our findings are helpful to know the nature of genome-wide mutations induced by gamma-irradiation.
Collapse
Affiliation(s)
- Satoshi Kitamura
- Project “Ion Beam Mutagenesis”, Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology, Takasaki, Japan
- * E-mail:
| | - Katsuya Satoh
- Project “Ion Beam Mutagenesis”, Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology, Takasaki, Japan
| | - Yutaka Oono
- Project “Ion Beam Mutagenesis”, Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute, National Institutes for Quantum Science and Technology, Takasaki, Japan
| |
Collapse
|
38
|
Wieland I, Schanze I, Felgendreher IM, Barthlen W, Vogelgesang S, Mohnike K, Zenker M. Integration of genomic analysis and transcript expression of ABCC8 and KCNJ11 in focal form of congenital hyperinsulinism. Front Endocrinol (Lausanne) 2022; 13:1015244. [PMID: 36339418 PMCID: PMC9634566 DOI: 10.3389/fendo.2022.1015244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The focal form of CHI is caused by an autosomal recessive pathogenic variant affecting the paternal homologue of genes ABCC8 or KCNJ11 and a second somatic event specifically occurring in the affected islet of Langerhans. The approach of this study was to integrate the genetic changes occurring in pancreatic focal lesions of CHI at the genomic and transcriptional level. RESEARCH DESIGN AND METHODS Patients receiving therapeutic surgery and with proven ABCC8 or KCNJ11 pathogenic variants were selected and analyzed for loss of heterozygosity (LOH), changes in copy number and uniparental disomy (UPD) on the short am of chromosome 11 by molecular microarray analysis and methylation-specific MLPA. Gene expression was analyzed by RT-PCR and Massive Analysis of cDNA Ends (MACE). RESULTS Both genes, ABCC8 and KCNJ11, are located in proximity to the Beckwith-Wiedemann (BWS) imprinting control region on chromosome 11p15. Somatic paternal uniparental isodisomy (UPD) at chromosome 11p was identified as second genetic event in focal lesions resulting in LOH and monoallelic expression of the mutated ABCC8/KCNJ11 alleles. Of five patients with samples available for microarray analysis, the breakpoints of UPD on chromosome 11p were different. Samples of two patients were analyzed further for changes in gene expression. Profound downregulation of growth suppressing genes CDKN1 and H19 was detected in focal lesions whereas growth promoting gene ASCL2 and pancreatic transcription factors of the endocrine cell lineage were upregulated. CONCLUSIONS Paternal UPD on the short arm of chromosome 11 appears to be the major second genetic event specifically within focal lesions of CHI but no common breakpoint for UDP can be delineated. We show for the first time upregulation of growth promoting ASCL2 (achaete-scute homolog 2) suggestive of a driving factor in postnatal focal expansion in addition to downregulation of growth suppressing genes CDKN1C and H19.
Collapse
Affiliation(s)
- Ilse Wieland
- Institute of Human Genetics, University Hospital Otto-von-Guericke- University Magdeburg, Magdeburg, Germany
- *Correspondence: Ilse Wieland,
| | - Ina Schanze
- Institute of Human Genetics, University Hospital Otto-von-Guericke- University Magdeburg, Magdeburg, Germany
| | - Ina Marianti Felgendreher
- Institute of Human Genetics, University Hospital Otto-von-Guericke- University Magdeburg, Magdeburg, Germany
| | - Winfried Barthlen
- Department of Pediatric Surgery, Protestant Hospital of Bethel Foundation, University Hospital OWL, University of Bielefeld, Bielefeld, Germany
| | - Silke Vogelgesang
- University Medicine, Institute of Pathology, University of Greifswald, Greifswald, Germany
| | - Klaus Mohnike
- Dept of Pediatrics, University Hospital Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Otto-von-Guericke- University Magdeburg, Magdeburg, Germany
| |
Collapse
|
39
|
Zaimoku Y, Patel BA, Adams SD, Shalhoub R, Groarke EM, Lee AAC, Kajigaya S, Feng X, Rios OJ, Eager H, Alemu L, Quinones Raffo D, Wu CO, Flegel WA, Young NS. HLA associations, somatic loss of HLA expression, and clinical outcomes in immune aplastic anemia. Blood 2021; 138:2799-2809. [PMID: 34724566 PMCID: PMC8718630 DOI: 10.1182/blood.2021012895] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Immune aplastic anemia (AA) features somatic loss of HLA class I allele expression on bone marrow cells, consistent with a mechanism of escape from T-cell-mediated destruction of hematopoietic stem and progenitor cells. The clinical significance of HLA abnormalities has not been well characterized. We examined the somatic loss of HLA class I alleles and correlated HLA loss and mutation-associated HLA genotypes with clinical presentation and outcomes after immunosuppressive therapy in 544 AA patients. HLA class I allele loss was detected in 92 (22%) of the 412 patients tested, in whom there were 393 somatic HLA gene mutations and 40 instances of loss of heterozygosity. Most frequently affected was HLA-B*14:02, followed by HLA-A*02:01, HLA-B*40:02, HLA-B*08:01, and HLA-B*07:02. HLA-B*14:02, HLA-B*40:02, and HLA-B*07:02 were also overrepresented in AA. High-risk clonal evolution was correlated with HLA loss, HLA-B*14:02 genotype, and older age, which yielded a valid prediction model. In 2 patients, we traced monosomy 7 clonal evolution from preexisting clones harboring somatic mutations in HLA-A*02:01 and HLA-B*40:02. Loss of HLA-B*40:02 correlated with higher blood counts. HLA-B*07:02 and HLA-B*40:01 genotypes and their loss correlated with late-onset of AA. Our results suggest the presence of specific immune mechanisms of molecular pathogenesis with clinical implications. HLA genotyping and screening for HLA loss may be of value in the management of immune AA. This study was registered at clinicaltrials.gov as NCT00001964, NCT00061360, NCT00195624, NCT00260689, NCT00944749, NCT01193283, and NCT01623167.
Collapse
Affiliation(s)
- Yoshitaka Zaimoku
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sharon D Adams
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Audrey Ai Chin Lee
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Olga Julia Rios
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Holly Eager
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Lemlem Alemu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Colin O Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
40
|
Eksi SE, Chitsazan A, Sayar Z, Thomas GV, Fields AJ, Kopp RP, Spellman PT, Adey AC. Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Nat Commun 2021; 12:7292. [PMID: 34911933 PMCID: PMC8674326 DOI: 10.1038/s41467-021-27615-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying precise molecular subtypes attributable to specific stages of localized prostate cancer has proven difficult due to high levels of heterogeneity. Bulk assays represent a population-average, which mask the heterogeneity that exists at the single-cell level. In this work, we sequence the accessible chromatin regions of 14,424 single-cells from 18 flash-frozen prostate tumours. We observe shared chromatin features among low-grade prostate cancer cells are lost in high-grade tumours. Despite this loss, high-grade tumours exhibit an enrichment for FOXA1, HOXB13 and CDX2 transcription factor binding sites, indicating a shared trans-regulatory programme. We identify two unique genes encoding neuronal adhesion molecules that are highly accessible in high-grade prostate tumours. We show NRXN1 and NLGN1 expression in epithelial, endothelial, immune and neuronal cells in prostate cancer using cyclic immunofluorescence. Our results provide a deeper understanding of the active gene regulatory networks in primary prostate tumours, critical for molecular stratification of the disease.
Collapse
Affiliation(s)
- Sebnem Ece Eksi
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA.
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR, 97209, USA.
| | - Alex Chitsazan
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
| | - Zeynep Sayar
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR, 97209, USA
| | - George V Thomas
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Pathology & Laboratory Medicine, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Andrew J Fields
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Ryan P Kopp
- Department of Urology, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Paul T Spellman
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Andrew C Adey
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA.
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA.
| |
Collapse
|
41
|
Janko K, Bartoš O, Kočí J, Roslein J, Drdová EJ, Kotusz J, Eisner J, Mokrejš M, Štefková-Kašparová E. Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. Mol Biol Evol 2021; 38:5255-5274. [PMID: 34410426 PMCID: PMC8662595 DOI: 10.1093/molbev/msab249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.
Collapse
Affiliation(s)
- Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Roslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Eisner
- Department of Mathematics, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Martin Mokrejš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- IT4Innovations, VŠB—Technical University of Ostrava, Ostrava-Poruba, Czech Republic
| | - Eva Štefková-Kašparová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Czech Republic
| |
Collapse
|
42
|
Yan H, Yu CC, Fine SA, Youssof AL, Yang YR, Yan J, Karg DC, Cheung EC, Friedman RA, Ying H, Chen EI, Luo J, Miao Y, Qiu W, Su GH. Loss of the wild-type KRAS allele promotes pancreatic cancer progression through functional activation of YAP1. Oncogene 2021; 40:6759-6771. [PMID: 34663879 PMCID: PMC8688281 DOI: 10.1038/s41388-021-02040-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 01/02/2023]
Abstract
Human pancreatic ductal adenocarcinoma (PDAC) harboring one KRAS mutant allele often displays increasing genomic loss of the remaining wild-type (WT) allele (known as LOH at KRAS) as tumors progress to metastasis, yet the molecular ramification of this WT allelic loss is unknown. In this study, we showed that the restoration of WT KRAS expression in human PDAC cell lines with LOH at KRAS significantly attenuated the malignancy of PDAC cells both in vitro and in vivo, demonstrating a tumor-suppressive role of the WT KRAS allele. Through RNA-Seq, we identified the HIPPO signaling pathway to be positively regulated by WT KRAS in PDAC cells. In accordance with this observation, PDAC cells with LOH at KRAS exhibited increased nuclear localization and activation of transcriptional co-activator YAP1. Mechanistically, we discovered that WT KRAS expression sequestered YAP1 from the nucleus, through enhanced 14-3-3zeta interaction with phosphorylated YAP1 at S127. Consistently, expression of a constitutively-active YAP1 mutant in PDAC cells bypassed the growth inhibitory effects of WT KRAS. In patient samples, we found that the YAP1-activation genes were significantly upregulated in tumors with LOH at KRAS, and YAP1 nuclear localization predicted poor survival for PDAC patients. Collectively, our results reveal that the WT allelic loss leads to functional activation of YAP1 and enhanced tumor malignancy, which explains the selection advantage of the tumor cells with LOH at KRAS during pancreatic cancer clonal evolution and progression to metastasis, and should be taken into consideration in future therapeutic strategies targeting KRAS.
Collapse
Affiliation(s)
- Han Yan
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Pancreas Center & Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chih-Chieh Yu
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Stuart A Fine
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ayman Lee Youssof
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ye-Ran Yang
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jun Yan
- Department of Pathology, Tianjin First Center Hospital, Tianjin, TJ, China
| | - Dillon C Karg
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Edwin C Cheung
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard A Friedman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, and Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Haoqiang Ying
- Molecular and Cellular Oncology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily I Chen
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pharmacology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Yi Miao
- Pancreas Center & Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wanglong Qiu
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Gloria H Su
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Otolaryngology and Head & Neck Surgery, Columbia University Irving Medical Center, New York, NY, USA.
- Pancreas Center, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
43
|
Mandl A, Welch JM, Kapoor G, Parekh VI, Schrump DS, Ripley RT, Walter MF, Del Rivero J, Jha S, Simonds WF, Jensen RT, Weinstein LS, Blau JE, Agarwal SK. Two distinct classes of thymic tumors in patients with MEN1 show LOH at the MEN1 locus. Endocr Relat Cancer 2021; 28:L15-L19. [PMID: 34515662 PMCID: PMC8558845 DOI: 10.1530/erc-21-0226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 11/08/2022]
Abstract
Patients with the multiple endocrine neoplasia type 1 (MEN1) syndrome carry germline heterozygous loss-of-function mutations in the MEN1 gene which predisposes them to develop various endocrine and non-endocrine tumors. Over 90% of the tumors show loss of heterozygosity (LOH) at chromosome 11q13, the MEN1 locus, due to somatic loss of the wild-type MEN1 allele. Thymic neuroendocrine tumors (NETs) or thymic carcinoids are uncommon in MEN1 patients but are a major cause of mortality. LOH at the MEN1 locus has not been demonstrated in thymic tumors. The goal of this study was to investigate the molecular aspects of MEN1-associated thymic tumors including LOH at the MEN1 locus and RNA-sequencing (RNA-Seq) to identify genes associated with tumor development and potential targeted therapy. A retrospective chart review of 294 patients with MEN1 germline mutations identified 14 patients (4.8%) with thymic tumors (12 thymic NETs and 2 thymomas). LOH at the MEN1 locus was identified in 10 tumors including the 2 thymomas, demonstrating that somatic LOH at the MEN1 locus is also the mechanism for thymic tumor development. Unsupervised principal component analysis and hierarchical clustering of RNA-Seq data showed that thymic NETs formed a homogenous transcriptomic group separate from thymoma and normal thymus. KSR2 (kinase suppressor of Ras 2), that promotes Ras-mediated signaling, was abundantly expressed in thymic NETs, a potential therapeutic target. The molecular insights gained from our study about thymic tumors combined with similar data from other MEN1-associated tumors may lead to better surveillance and treatment of these rare tumors.
Collapse
Affiliation(s)
- Adel Mandl
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - James M Welch
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Gayathri Kapoor
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Vaishali I Parekh
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - David S Schrump
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - R Taylor Ripley
- Division of General Thoracic Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Mary F Walter
- NIDDK Clinical Core, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Jaydira Del Rivero
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Smita Jha
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - William F Simonds
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Robert T Jensen
- Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Lee S Weinstein
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Jenny E Blau
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
| | - Sunita K Agarwal
- Metabolic Diseases Branch, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland, USA
- Correspondence should be addressed to S K Agarwal:
| |
Collapse
|
44
|
Martínez de LaPiscina I, Portillo Najera N, Rica I, Gaztambide S, Webb SM, Santos A, Moure MD, Paja Fano M, Hernandez MI, Chueca-Guindelain MJ, Hernández-Ramírez LC, Soto A, Valdés N, Castaño L. Clinical and genetic characteristics in patients under 30 years with sporadic pituitary adenomas. Eur J Endocrinol 2021; 185:485-496. [PMID: 34313605 DOI: 10.1530/eje-21-0075] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/27/2021] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Pituitary adenomas (PA) are rare in young patients, and additional studies are needed to fully understand their pathogenesis in this population. We describe the clinical and genetic characteristics of apparently sporadic PA in a cohort of young patients. DESIGN Clinical and molecular analysis of 235 patients (age ≤ 30 years) with PA. Clinicians from several Spanish and Chilean hospitals provided data. METHODS Genetic screening was performed via next-generation sequencing and comparative genomic hybridization array. Clinical variables were compared among paediatric, adolescent (<19 years) and young adults' (≥19-30 years) cohorts and types of adenomas. Phenotype-genotype associations were examined. RESULTS Among the total cohort, mean age was 17.3 years. Local mass effect symptoms were present in 22.0%, and prolactinomas were the most frequent (44.7%). Disease-causing germline variants were identified in 22 individuals (9.3%), more exactly in 13.1 and 4.7% of the populations aged between 0-19 and 19-30 years, respectively; genetically positive patients were younger at diagnosis and had larger tumour size. Healthy family carriers were also identified. CONCLUSIONS Variants in genes associated with syndromic forms of PAs were detected in a large cohort of apparently sporadic pituitary tumours. We have identified novel variants in well-known genes and set the possibility of incomplete disease penetrance in carriers of MEN1 alterations or a limited clinical expression of the syndrome. Despite the low penetrance observed, screening of AIP and MEN1 variants in young patients and relatives is of clinical value.
Collapse
Affiliation(s)
- Idoia Martínez de LaPiscina
- Biocruces Bizkaia Health Research Institute, University of the Basque Country (UPV-EHU), Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), European Reference Network on Rare Endocrine Conditions (Endo-ERN), Barakaldo, Spain
| | - Nancy Portillo Najera
- Pediatric Department, Biocruces Bizkaia Health Research Institute, Alto Deba Hospital, UPV-EHU, Barakaldo, Spain
| | - Itxaso Rica
- Pediatric Endocrinology Department, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, CIBERER, CIBERDEM, Endo-ERN, Barakaldo, Spain
| | - Sonia Gaztambide
- Endocrinology Department, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV-EHU, CIBERER, CIBERDEM, Endo-ERN, Barakaldo, Spain
| | - Susan M Webb
- Department of Endocrinology/Medicine, CIBERER U747, ISCIII, Research Center for Pituitary Diseases, Sant Pau Hospital, IIB-SPau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alicia Santos
- Department of Endocrinology/Medicine, CIBERER U747, ISCIII, Research Center for Pituitary Diseases, Sant Pau Hospital, IIB-SPau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Dolores Moure
- Endocrinology Department, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Endo-ERN, Barakaldo, Spain
| | - Miguel Paja Fano
- Endocrinology Service, Basurto University Hospital, Bilbo, Spain
| | - Maria Isabel Hernandez
- Institute of Maternal and Child Research (IDIMI), Faculty of Medicine, University of Chile, Santa Rosa 1234, IDIMI, Casilla, Santiago, Chile
| | - Maria Jesús Chueca-Guindelain
- Pediatric Endocrinology Unit, Navarra Complex Hospital, Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Laura Cristina Hernández-Ramírez
- Laboratory of Genomics, Research Support Network, National Autonomous University of Mexico, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Tlalpan, Mexico City, Mexico
| | - Alfonso Soto
- Endocrinology and Nutrition Department, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Sevilla, Spain
| | - Nuria Valdés
- Endocrinology and Nutrition Department, Cabueñes University Hospital, Gijón, Spain
| | - Luis Castaño
- Pediatric Endocrinology Department, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, UPV-EHU, CIBERER, CIBERDEM, Endo-ERN, Barakaldo, Spain
| |
Collapse
|
45
|
Okasho K, Mizuno K, Fukui T, Lin Y, Kamiyama Y, Sunada T, Li X, Kimura H, Sumiyoshi T, Goto T, Kobayashi T, Lin D, Wang Y, Collins CC, Inoue T, Ogawa O, Akamatsu S. Establishment and characterization of a novel treatment-related neuroendocrine prostate cancer cell line KUCaP13. Cancer Sci 2021; 112:2781-2791. [PMID: 33960594 PMCID: PMC8253279 DOI: 10.1111/cas.14935] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
The prevalence of neuroendocrine prostate cancer (NEPC) arising from adenocarcinoma (AC) upon potent androgen receptor (AR) pathway inhibition is increasing. Deeper understanding of NEPC biology and development of novel therapeutic agents are needed. However, research is hindered by the paucity of research models, especially cell lines developed from NEPC patients. We established a novel NEPC cell line, KUCaP13, from tissue of a patient initially diagnosed with AC which later recurred as NEPC. The cell line has been maintained permanently in vitro under regular cell culture conditions and is amenable to gene engineering with lentivirus. KUCaP13 cells lack the expression of AR and overexpress NEPC-associated genes, including SOX2, EZH2, AURKA, PEG10, POU3F2, ENO2, and FOXA2. Importantly, the cell line maintains the homozygous deletion of CHD1, which was confirmed in the primary AC of the index patient. Loss of heterozygosity of TP53 and PTEN, and an allelic loss of RB1 with a transcriptomic signature compatible with Rb pathway aberration were revealed. Knockdown of PEG10 using shRNA significantly suppressed growth in vivo. Introduction of luciferase allowed serial monitoring of cells implanted orthotopically or in the renal subcapsule. Although H3K27me was reduced by EZH2 inhibition, reversion to AC was not observed. KUCaP13 is the first patient-derived, treatment-related NEPC cell line with triple loss of tumor suppressors critical for NEPC development through lineage plasticity. It could be valuable in research to deepen the understanding of NEPC.
Collapse
MESH Headings
- Adenocarcinoma/pathology
- Animals
- Apoptosis Regulatory Proteins/genetics
- Carcinoma, Neuroendocrine/genetics
- Carcinoma, Neuroendocrine/pathology
- Carcinoma, Neuroendocrine/secondary
- Cell Line, Tumor/metabolism
- Cell Line, Tumor/pathology
- DNA Helicases/genetics
- DNA-Binding Proteins/genetics
- Drug Screening Assays, Antitumor
- Enhancer of Zeste Homolog 2 Protein/antagonists & inhibitors
- Gene Deletion
- Gene Expression
- Genes, Neoplasm
- Genes, Retinoblastoma
- Genes, Tumor Suppressor
- Genes, p53
- Genetic Engineering
- Heterografts
- Homozygote
- Humans
- Karyotyping
- Loss of Heterozygosity
- Male
- Mice, SCID
- Middle Aged
- Neoplasm Recurrence, Local/pathology
- Neoplasm Transplantation
- PTEN Phosphohydrolase/genetics
- Penile Neoplasms/genetics
- Penile Neoplasms/secondary
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/pathology
- RNA-Binding Proteins/genetics
- Receptors, Androgen
- Mice
Collapse
Affiliation(s)
- Kosuke Okasho
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Kei Mizuno
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Tomohiro Fukui
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Yen‐Yi Lin
- Vancouver Prostate CentreUniversity of British ColumbiaVancouverBCCanada
| | - Yuki Kamiyama
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Takuro Sunada
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Xin Li
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Hiroko Kimura
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Takayuki Sumiyoshi
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Takayuki Goto
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Takashi Kobayashi
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Dong Lin
- Department of Experimental TherapeuticsBC Cancer AgencyVancouverBCCanada
| | - Yuzhuo Wang
- Department of Experimental TherapeuticsBC Cancer AgencyVancouverBCCanada
| | - Colin C. Collins
- Vancouver Prostate CentreUniversity of British ColumbiaVancouverBCCanada
| | - Takahiro Inoue
- Department of Nephro‐Urologic SurgeryMie University Graduate School of MedicineTsuJapan
| | - Osamu Ogawa
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| | - Shusuke Akamatsu
- Department of UrologyKyoto University Graduate School of MedicineKyotoJapan
| |
Collapse
|
46
|
Hirose T, Kobayashi A, Nobusawa S, Jimbo N. Hybrid Schwannoma/Perineurioma: Morphologic Variations and Genetic Profiles. Appl Immunohistochem Mol Morphol 2021; 29:433-439. [PMID: 33337633 DOI: 10.1097/pai.0000000000000896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022]
Abstract
To clarify the morphologic spectrum and molecular profiles of hybrid schwannoma/perineurioma (HSP), we investigated 15 tumors clinicopathologically and cytogenetically. HSP was classified into 2 morphologic types: mixed cellular and combined tumor types. The former comprising of 14 tumors mostly arose in the subcutaneous tissue of the extremities and the trunk of middle-aged adults. They were well-circumscribed and composed of elongated spindle-shaped tumor cells arranged in storiform and whorl patterns. Immunostaining revealed a mixed cellular proliferation of S-100 protein-positive and SOX10-positive Schwann cells and epithelial membrane antigen-positive, claudin 1-positive, and GLUT1-positive perineurial cells. During follow-up, no tumors were found to have recurred in any cases. In contrast, in the combined tumor type arising in the mediastinum of a young male with neurofibromatosis type 2, the intraneural perineurioma-like areas, characterized by small whorl-like structures, were present in plexiform schwannoma-like areas. No recurrence was noted in the case. Molecular analyses (array comparative genomic hybridization and fluorescence in situ hybridization) revealed LOH 22q in 2 tumors of 5 studied: one each of the mixed cellular and combined tumor types. Although the same diagnostic term, HSP, has been applied to both mixed and combined types, they should be separated from each other.
Collapse
Affiliation(s)
- Takanori Hirose
- Departments of Pathology for Regional Communication
- Department of Diagnostic Pathology, Hyogo Cancer Center, Akashi
- Department of Diagnostic Pathology, Tokushima Prefectural Central Hospital, Tokushima
| | - Anna Kobayashi
- Department of Diagnostic Pathology, Hyogo Cancer Center, Akashi
| | - Sumihito Nobusawa
- Department of Human Pathology, Gunma University School of Medicine, Maebashi, Japan
| | - Naoe Jimbo
- Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe
| |
Collapse
|
47
|
Ripamonti CB, Bossi P, Manoukian S, Locati L, Colombo M, Carcangiu ML, Vingiani A, Licitra L, Radice P. Malignant salivary gland tumours in families with breast cancer susceptibility. Virchows Arch 2021; 479:221-226. [PMID: 34100114 DOI: 10.1007/s00428-021-03105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 11/26/2022]
Abstract
Salivary gland cancers (SGCs) are rare malignancies with highly heterogeneous histological features. Patients affected with SGCs are at increased risk of secondary malignancies, including breast cancer (BC). Previous studies enlightened a possible link between SGCs and hereditary predisposition to BC. Here, we searched for SGC-affected patients in 1796 high-risk BC families recruited at the Genetic Unit of the Istituto Nazionale dei Tumori of Milan, 516 of which carried pathogenic variants in BRCA1 and/or BRCA2, the main genetic risk factors for BC. We detected five families with an individual affected with SGC, including two male patients, one carrying a constitutional mutation in BRCA1 and the other in BRCA2. Loss of heterozygosity of BRCA wild-type alleles was assessed in the patients' tumour DNA. We conclude that our observations support the hypothesis that genetic factors associated with BC susceptibility might play a role also in at least a subset of SGCs.
Collapse
Affiliation(s)
- Carla B Ripamonti
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Research Department, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20133, Milan, Italy.
| | - Paolo Bossi
- Unit of Head and Neck Cancers, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology Fondazione, IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Laura Locati
- Unit of Head and Neck Cancers, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Research Department, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20133, Milan, Italy
| | - Maria L Carcangiu
- Unit of Anatomic Pathology 1, Department of Pathology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Andrea Vingiani
- Unit of Anatomic Pathology 2, Department of Pathology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
| | - Lisa Licitra
- Unit of Head and Neck Cancers, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Research Department, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Amadeo 42, 20133, Milan, Italy
| |
Collapse
|
48
|
Ziegler A, Duclaux-Loras R, Revenu C, Charbit-Henrion F, Begue B, Duroure K, Grimaud L, Guihot AL, Desquiret-Dumas V, Zarhrate M, Cagnard N, Mas E, Breton A, Edouard T, Billon C, Frank M, Colin E, Lenaers G, Henrion D, Lyonnet S, Faivre L, Alembik Y, Philippe A, Moulin B, Reinstein E, Tzur S, Attali R, McGillivray G, White SM, Gallacher L, Kutsche K, Schneeberger P, Girisha KM, Nayak SS, Pais L, Maroofian R, Rad A, Vona B, Karimiani EG, Lekszas C, Haaf T, Martin L, Ruemmele F, Bonneau D, Cerf-Bensussan N, Del Bene F, Parlato M. Bi-allelic variants in IPO8 cause a connective tissue disorder associated with cardiovascular defects, skeletal abnormalities, and immune dysregulation. Am J Hum Genet 2021; 108:1126-1137. [PMID: 34010604 PMCID: PMC8206386 DOI: 10.1016/j.ajhg.2021.04.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/23/2021] [Indexed: 12/17/2022] Open
Abstract
Dysregulated transforming growth factor TGF-β signaling underlies the pathogenesis of genetic disorders affecting the connective tissue such as Loeys-Dietz syndrome. Here, we report 12 individuals with bi-allelic loss-of-function variants in IPO8 who presented with a syndromic association characterized by cardio-vascular anomalies, joint hyperlaxity, and various degree of dysmorphic features and developmental delay as well as immune dysregulation; the individuals were from nine unrelated families. Importin 8 belongs to the karyopherin family of nuclear transport receptors and was previously shown to mediate TGF-β-dependent SMADs trafficking to the nucleus in vitro. The important in vivo role of IPO8 in pSMAD nuclear translocation was demonstrated by CRISPR/Cas9-mediated inactivation in zebrafish. Consistent with IPO8’s role in BMP/TGF-β signaling, ipo8−/− zebrafish presented mild to severe dorso-ventral patterning defects during early embryonic development. Moreover, ipo8−/− zebrafish displayed severe cardiovascular and skeletal defects that mirrored the human phenotype. Our work thus provides evidence that IPO8 plays a critical and non-redundant role in TGF-β signaling during development and reinforces the existing link between TGF-β signaling and connective tissue defects.
Collapse
Affiliation(s)
- Alban Ziegler
- Department of Biochemistry and Molecular Biology, CHU d'Angers, 49000 Angers, France; University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France
| | - Rémi Duclaux-Loras
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM, UMR1163, 75015 Paris, France
| | - Céline Revenu
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, 75012 Paris, France; Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75005 Paris, France
| | - Fabienne Charbit-Henrion
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM, UMR1163, 75015 Paris, France; Department of Pediatric Gastroenterology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, 75015 Paris, France; Department of Molecular Genetics, Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Bernadette Begue
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM, UMR1163, 75015 Paris, France
| | - Karine Duroure
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, 75012 Paris, France; Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75005 Paris, France
| | - Linda Grimaud
- University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France
| | - Anne Laure Guihot
- University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France
| | - Valérie Desquiret-Dumas
- Department of Biochemistry and Molecular Biology, CHU d'Angers, 49000 Angers, France; University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France
| | - Mohammed Zarhrate
- Genomics Core Facility, Institut Imagine-Structure Fédérative de Recherche Necker, INSERM U1163 et INSERM US24/CNRS UMS3633, Paris Descartes Sorbonne Paris Cité University, 75015 Paris, France
| | - Nicolas Cagnard
- Bioinformatics Core Facility, INSERM-UMR 1163, Imagine Institute, 75015 Paris, France
| | - Emmanuel Mas
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse 31300, France; Centre de Référence des Maladies Rares Digestives, and Pediatric Clinical Research Unit, Toulouse Clinical Investigation Center INSERM U1436, Hôpital des Enfants, CHU de Toulouse, Toulouse 31300, France
| | - Anne Breton
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse 31300, France; Centre de Référence des Maladies Rares Digestives, and Pediatric Clinical Research Unit, Toulouse Clinical Investigation Center INSERM U1436, Hôpital des Enfants, CHU de Toulouse, Toulouse 31300, France
| | - Thomas Edouard
- Reference Centre for Marfan Syndrome and Reference Centre on Rare Bone Diseases, Pediatric Clinical Research Unit, Children's Hospital, Toulouse University Hospital, RESTORE, INSERM UMR1301, 31300 Toulouse, France
| | - Clarisse Billon
- Centre de Génétique, Centre de Référence des Maladies Vasculaires Rares, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Michael Frank
- Centre de Génétique, Centre de Référence des Maladies Vasculaires Rares, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, 75015 Paris, France
| | - Estelle Colin
- Department of Biochemistry and Molecular Biology, CHU d'Angers, 49000 Angers, France
| | - Guy Lenaers
- University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France
| | - Daniel Henrion
- University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France
| | - Stanislas Lyonnet
- Université de Paris, Imagine Institute, Laboratory of Embryology and Genetics of Malformations, INSERM UMR 1163, 75015 Paris, France; Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 75015 Paris, France
| | - Laurence Faivre
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, 21000 Dijon, France
| | - Yves Alembik
- Département de Génétique Médicale, CHU de Hautepierre, 67200 Strasbourg, France
| | - Anaïs Philippe
- Département de Génétique Médicale, CHU de Hautepierre, 67200 Strasbourg, France
| | - Bruno Moulin
- Nephrology and Transplantation Department, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 67200 Strasbourg, France
| | - Eyal Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba 4428164, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shay Tzur
- Genomic Research Department, Emedgene Technologies, 67443 Tel Aviv, Israel
| | - Ruben Attali
- Genomic Research Department, Emedgene Technologies, 67443 Tel Aviv, Israel
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville 3052, Melbourne, VIC, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville 3052, Melbourne, VIC, Australia
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville 3052, Melbourne, VIC, Australia; Department of Paediatrics, The University of Melbourne, 3010 Parkville, Melbourne, VIC, Australia
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Pauline Schneeberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576104, India
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Aboulfazl Rad
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Barbara Vona
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany; Institute of Human Genetics, Julius Maximilians University Würzburg, 97074 Würzburg, Germany
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace London, SW17 ORE London, UK; Innovative Medical Research Center, Mashhad Branch, Islamic Azdad University, Mashhad 9133736351, Iran
| | - Caroline Lekszas
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074 Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074 Würzburg, Germany
| | - Ludovic Martin
- University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France; Department of Dermatology, CHU d'Angers, 49000 Angers, France
| | - Frank Ruemmele
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM, UMR1163, 75015 Paris, France; Department of Pediatric Gastroenterology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Dominique Bonneau
- Department of Biochemistry and Molecular Biology, CHU d'Angers, 49000 Angers, France; University of Angers, MitoVasc, UMR CNRS 6015, INSERM 1083, 49933 Angers, France
| | - Nadine Cerf-Bensussan
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM, UMR1163, 75015 Paris, France
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, 75012 Paris, France; Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75005 Paris, France.
| | - Marianna Parlato
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM, UMR1163, 75015 Paris, France.
| |
Collapse
|
49
|
Mikawa T, Shibata E, Shimada M, Ito K, Ito T, Kanda H, Takubo K, Shimada A, Lleonart ME, Inagaki N, Yokode M, Kondoh H. Characterization of genetically modified mice for phosphoglycerate mutase, a vitally-essential enzyme in glycolysis. PLoS One 2021; 16:e0250856. [PMID: 33914812 PMCID: PMC8084212 DOI: 10.1371/journal.pone.0250856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/15/2021] [Indexed: 01/14/2023] Open
Abstract
Glycolytic metabolism is closely involved in physiological homeostasis and pathophysiological states. Among glycolytic enzymes, phosphoglycerate mutase (PGAM) has been reported to exert certain physiological role in vitro, whereas its impact on glucose metabolism in vivo remains unclear. Here, we report the characterization of Pgam1 knockout mice. We observed that homozygous knockout mice of Pgam1 were embryonic lethal. Although we previously reported that both PGAM-1 and -2 affect global glycolytic profile of cancers in vitro, in vivo glucose parameters were less affected both in the heterozygous knockout of Pgam1 and in Pgam2 transgenic mice. Thus, the impact of PGAM on in vivo glucose metabolism is rather complex than expected before.
Collapse
Affiliation(s)
- Takumi Mikawa
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eri Shibata
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Midori Shimada
- Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Ken Ito
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomiko Ito
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroaki Kanda
- Department of Pathology, Saitama Cancer Center, Saitama, Japan
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | | | | | - Nobuya Inagaki
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Yokode
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Kondoh
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- * E-mail:
| |
Collapse
|
50
|
Choufani S, Ko JM, Lou Y, Shuman C, Fishman L, Weksberg R. Paternal Uniparental Disomy of the Entire Chromosome 20 in a Child with Beckwith-Wiedemann Syndrome. Genes (Basel) 2021; 12:genes12020172. [PMID: 33513760 PMCID: PMC7911624 DOI: 10.3390/genes12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic alterations at imprinted genes on different chromosomes have been linked to several imprinting disorders (IDs) such as Beckwith-Wiedemann syndrome (BWS) and pseudohypoparathyroidism type 1b (PHP1b). Here, we present a male patient with these two distinct IDs caused by two independent mechanisms-loss of methylation (LOM) at chromosome 11p15.5 associated with multi-locus imprinting disturbances (MLID and paternal uniparental disomy of chromosome 20 (patUPD20). A clinical diagnosis of BWS was made based on the clinical features of macrosomia, macroglossia, and umbilical hernia. The diagnosis of PHP1b was supported by the presence of reduced growth velocity and mild learning disability as well as hypocalcemia and hyperphosphatemia at 14 years of age. Molecular analyses, including genome-wide DNA methylation (Illumina 450k array), bisulfite pyrosequencing, single nucleotide polymorphism (SNP) array and microsatellite analysis, demonstrated loss of methylation (LOM) at IC2 on chromosome 11p15.5, and paternal isodisomy of the entire chromosome 20. In addition, imprinting disturbances were noted at the differentially methylated regions (DMRs) associated with DIRAS3 on chromosome 1 and PLAGL1 on chromosome 6. This is the first case report of PHP1b due to patUPD20 diagnosed in a BWS patient with LOM at IC2 demonstrating etiologic heterogeneity for multiple imprinting disorders in a single individual.
Collapse
Affiliation(s)
- Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
| | - Jung Min Ko
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Youliang Lou
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
| | - Cheryl Shuman
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada;
| | - Leona Fishman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Pediatrics, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; (S.C.); (J.M.K.); (Y.L.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, Canada;
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Pediatrics, University of Toronto, Toronto, ON M5S 1A1, Canada
- Correspondence:
| |
Collapse
|