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Waitkus MS, Erman EN, Reitman ZJ, Ashley DM. Mechanisms of telomere maintenance and associated therapeutic vulnerabilities in malignant gliomas. Neuro Oncol 2024; 26:1012-1024. [PMID: 38285162 PMCID: PMC11145458 DOI: 10.1093/neuonc/noae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 01/30/2024] Open
Abstract
A majority of cancers (~85%) activate the enzyme telomerase to maintain telomere length over multiple rounds of cellular division. Telomerase-negative cancers activate a distinct, telomerase-independent mechanism of telomere maintenance termed alternative lengthening of telomeres (ALT). ALT uses homologous recombination to maintain telomere length and exhibits features of break-induced DNA replication. In malignant gliomas, the activation of either telomerase or ALT is nearly ubiquitous in pediatric and adult tumors, and the frequency with which these distinct telomere maintenance mechanisms (TMMs) is activated varies according to genetically defined glioma subtypes. In this review, we summarize the current state of the field of TMMs and their relevance to glioma biology and therapy. We review the genetic alterations and molecular mechanisms leading to telomerase activation or ALT induction in pediatric and adult gliomas. With this background, we review emerging evidence on strategies for targeting TMMs for glioma therapy. Finally, we comment on critical gaps and issues for moving the field forward to translate our improved understanding of glioma telomere maintenance into better therapeutic strategies for patients.
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Affiliation(s)
- Matthew S Waitkus
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Elise N Erman
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Zachary J Reitman
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
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2
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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Zhao G, Ma Q, Yang H, Jiang H, Xu Q, Luo S, Meng Z, Liu J, Zhu L, Lin Q, Li M, Fang J, Ma L, Qiu W, Mao Z, Lu Z. Base editing of the mutated TERT promoter inhibits liver tumor growth. Hepatology 2024; 79:1310-1323. [PMID: 38016019 DOI: 10.1097/hep.0000000000000700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND AND AIMS Base editing has shown great potential for treating human diseases with mutated genes. However, its potential for treating HCC has not yet been explored. APPROACH AND RESULTS We employed adenine base editors (ABEs) to correct a telomerase reverse transcriptase ( TERT ) promoter mutation, which frequently occurs in various human cancers, including HCC. The mutated TERT promoter -124 C>T is corrected to -124 C by a single guide (sg) RNA-guided and deactivated Campylobacter jejuni Cas9 (CjCas9)-fused adenine base editor (CjABE). This edit impairs the binding of the E-twenty six/ternary complex factor transcription factor family, including E-twenty six-1 and GABPA, to the TERT promoter, leading to suppressed TERT promoter and telomerase activity, decreased TERT expression and cell proliferation, and increased cell senescence. Importantly, injection of adeno-associated viruses expressing sgRNA-guided CjABE or employment of lipid nanoparticle-mediated delivery of CjABE mRNA and sgRNA inhibits the growth of liver tumors harboring TERT promoter mutations. CONCLUSIONS These findings demonstrate that a sgRNA-guided CjABE efficiently converts the mutated TERT promoter -124 C>T to -124 C in HCC cells and underscore the potential to treat HCC by the base editing-mediated correction of TERT promoter mutations.
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Affiliation(s)
- Gaoxiang Zhao
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Qingxia Ma
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Huang Yang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Hongfei Jiang
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Qianqian Xu
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Shudi Luo
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhaoyuan Meng
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Juanjuan Liu
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Lei Zhu
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Qian Lin
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Min Li
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jing Fang
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Leina Ma
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Wensheng Qiu
- Department of Oncology, Cancer Institute of The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Zhengwei Mao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, China
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4
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Dasgupta A, Prensner JR. Upstream open reading frames: new players in the landscape of cancer gene regulation. NAR Cancer 2024; 6:zcae023. [PMID: 38774471 PMCID: PMC11106035 DOI: 10.1093/narcan/zcae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
The translation of RNA by ribosomes represents a central biological process and one of the most dysregulated processes in cancer. While translation is traditionally thought to occur exclusively in the protein-coding regions of messenger RNAs (mRNAs), recent transcriptome-wide approaches have shown abundant ribosome activity across diverse stretches of RNA transcripts. The most common type of this kind of ribosome activity occurs in gene leader sequences, also known as 5' untranslated regions (UTRs) of the mRNA, that precede the main coding sequence. Translation of these upstream open reading frames (uORFs) is now known to occur in upwards of 25% of all protein-coding genes. With diverse functions from RNA regulation to microprotein generation, uORFs are rapidly igniting a new arena of cancer biology, where they are linked to cancer genetics, cancer signaling, and tumor-immune interactions. This review focuses on the contributions of uORFs and their associated 5'UTR sequences to cancer biology.
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Affiliation(s)
- Anwesha Dasgupta
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John R Prensner
- Chad Carr Pediatric Brain Tumor Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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5
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Keener R, Chhetri SB, Connelly CJ, Taub MA, Conomos MP, Weinstock J, Ni B, Strober B, Aslibekyan S, Auer PL, Barwick L, Becker LC, Blangero J, Bleecker ER, Brody JA, Cade BE, Celedon JC, Chang YC, Cupples LA, Custer B, Freedman BI, Gladwin MT, Heckbert SR, Hou L, Irvin MR, Isasi CR, Johnsen JM, Kenny EE, Kooperberg C, Minster RL, Naseri T, Viali S, Nekhai S, Pankratz N, Peyser PA, Taylor KD, Telen MJ, Wu B, Yanek LR, Yang IV, Albert C, Arnett DK, Ashley-Koch AE, Barnes KC, Bis JC, Blackwell TW, Boerwinkle E, Burchard EG, Carson AP, Chen Z, Chen YDI, Darbar D, de Andrade M, Ellinor PT, Fornage M, Gelb BD, Gilliland FD, He J, Islam T, Kaab S, Kardia SLR, Kelly S, Konkle BA, Kumar R, Loos RJF, Martinez FD, McGarvey ST, Meyers DA, Mitchell BD, Montgomery CG, North KE, Palmer ND, Peralta JM, Raby BA, Redline S, Rich SS, Roden D, Rotter JI, Ruczinski I, Schwartz D, Sciurba F, Shoemaker MB, Silverman EK, Sinner MF, Smith NL, Smith AV, Tiwari HK, Vasan RS, Weiss ST, Williams LK, Zhang Y, Ziv E, Raffield LM, Reiner AP, Arvanitis M, Greider CW, Mathias RA, Battle A. Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes. Nat Commun 2024; 15:4417. [PMID: 38789417 PMCID: PMC11126610 DOI: 10.1038/s41467-024-48394-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Genome-wide association studies (GWAS) have become well-powered to detect loci associated with telomere length. However, no prior work has validated genes nominated by GWAS to examine their role in telomere length regulation. We conducted a multi-ancestry meta-analysis of 211,369 individuals and identified five novel association signals. Enrichment analyses of chromatin state and cell-type heritability suggested that blood/immune cells are the most relevant cell type to examine telomere length association signals. We validated specific GWAS associations by overexpressing KBTBD6 or POP5 and demonstrated that both lengthened telomeres. CRISPR/Cas9 deletion of the predicted causal regions in K562 blood cells reduced expression of these genes, demonstrating that these loci are related to transcriptional regulation of KBTBD6 and POP5. Our results demonstrate the utility of telomere length GWAS in the identification of telomere length regulation mechanisms and validate KBTBD6 and POP5 as genes affecting telomere length regulation.
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Grants
- 5K12GM123914 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01AG069120 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R35GM139580 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01 DK071891 NIDDK NIH HHS
- R01HL153805 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01AG081244 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R35CA209974 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- R01HL105756 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01HL68959 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01HL079915 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01HL87681 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- R01 HL153805 NHLBI NIH HHS
- R01HL-120393 U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
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Affiliation(s)
- Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Surya B Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Carla J Connelly
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Matthew P Conomos
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Joshua Weinstock
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bohan Ni
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Benjamin Strober
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | | | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lucas Barwick
- LTRC Data Coordinating Center, The Emmes Company, LLC, Rockville, MD, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eugene R Bleecker
- Department of Medicine, Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Juan C Celedon
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yi-Cheng Chang
- Department of Internal Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- The National Heart, Lung, and Blood Institute, Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Barry I Freedman
- Internal Medicine - Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Mark T Gladwin
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama Birmingham, Birmingham, AL, USA
| | - Carmen R Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jill M Johnsen
- Department of Medicine and Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Eimear E Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Take Naseri
- Naseri & Associates Public Health Consultancy Firm and Family Health Clinic, Apia, Samoa
- International Health Institute, School of Public Health, Brown University, Providence, RI, USA
| | - Satupa'itea Viali
- Oceania University of Medicine, Apia, Samoa
- School of Medicine, National University of Samoa, Apia, Samoa
- Department of Chronic Disease Epidemiology, Yale University School of Public Health, New Haven, CT, USA
| | - Sergei Nekhai
- Center for Sickle Cell Disease and Department of Medicine, College of Medicine, Howard University, Washington DC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Baojun Wu
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ivana V Yang
- Departments of Biomedical Informatics, Medicine, and Epidemiology, University of Colorado, Boulder, CO, USA
| | - Christine Albert
- Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular, Brigham and Women's Hospital, Boston, MA, USA
| | - Donna K Arnett
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, USA
| | | | - Kathleen C Barnes
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MI, USA
| | - Zhanghua Chen
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine, New York, NY, USA
| | - Frank D Gilliland
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jiang He
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Talat Islam
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stefan Kaab
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, CA, USA
- University of California San Francisco Benioff Children's Hospital, Oakland, CA, USA
| | - Barbara A Konkle
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Rajesh Kumar
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- The Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando D Martinez
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Stephen T McGarvey
- Department of Epidemiology & International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Deborah A Meyers
- Department of Medicine, Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, AZ, USA
- Division of Pharmacogenomics, University of Arizona, Tucson, AZ, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Courtney G Montgomery
- Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Juan M Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Benjamin A Raby
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Susan Redline
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Dan Roden
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David Schwartz
- Departments of Medicine and Immunology, University of Colorado, Boulder, CO, USA
| | - Frank Sciurba
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Benjamin Shoemaker
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Moritz F Sinner
- Department of Cardiology, University Hospital, LMU Munich, Munich, Germany
| | - Nicholas L Smith
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama Birmingham, Birmingham, AL, USA
| | | | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Yingze Zhang
- Division of Pulmonary Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Marios Arvanitis
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, USA
| | - Carol W Greider
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- University Professor Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA.
- Data Science and AI Institute, Johns Hopkins University, Baltimore, MD, USA.
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6
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Karimian K, Groot A, Huso V, Kahidi R, Tan KT, Sholes S, Keener R, McDyer JF, Alder JK, Li H, Rechtsteiner A, Greider CW. Human telomere length is chromosome end-specific and conserved across individuals. Science 2024; 384:533-539. [PMID: 38603523 DOI: 10.1126/science.ado0431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/30/2024] [Indexed: 04/13/2024]
Abstract
Short telomeres cause age-related disease, and long telomeres contribute to cancer; however, the mechanisms regulating telomere length are unclear. We developed a nanopore-based method, which we call Telomere Profiling, to determine telomere length at nearly single-nucleotide resolution. Mapping telomere reads to chromosome ends showed chromosome end-specific length distributions that could differ by more than six kilobases. Examination of telomere lengths in 147 individuals revealed that certain chromosome ends were consistently longer or shorter. The same rank order was found in newborn cord blood, suggesting that telomere length is determined at birth and that chromosome end-specific telomere length differences are maintained as telomeres shorten with age. Telomere Profiling makes precision investigation of telomere length widely accessible for laboratory, clinical, and drug discovery efforts and will allow deeper insights into telomere biology.
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Affiliation(s)
- Kayarash Karimian
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aljona Groot
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vienna Huso
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ramin Kahidi
- Health Sciences Program, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kar-Tong Tan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, The Broad Institute, Cambridge, MA, USA
| | - Samantha Sholes
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Keener
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - John F McDyer
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan K Alder
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Andreas Rechtsteiner
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Carol W Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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7
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Tang Q, Hu G, Sang Y, Chen Y, Wei G, Zhu M, Chen M, Li S, Liu R, Peng Z. Therapeutic targeting of PLK1 in TERT promoter-mutant hepatocellular carcinoma. Clin Transl Med 2024; 14:e1703. [PMID: 38769666 PMCID: PMC11106514 DOI: 10.1002/ctm2.1703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Hotspot mutations in the promoter of telomerase reverse transcriptase (TERT) gene are the most common genetic variants in hepatocellular carcinoma (HCC) and associated with poor prognosis of the disease. However, no drug was currently approved for treating TERT promoter mutation positive HCC patients. Here, we aim to explore the potential therapeutic strategy for targeting TERT promoter mutation in HCC. METHODS The Liver Cancer Model Repository database was used for screening potential drugs to selectively suppress the growth of TERT promoter mutant HCC cells. RNA-seq, CRISPR-Cas9 technology and siRNA transfection were performed for mechanistic studies. Cell counting kit-8 (CCK8) assay and the xenograft tumour models were used for cell growth detection in vitro and in vivo, respectively. Cell apoptosis and cell cycle arrest were analysed by Annexin V-FITC staining and/or propidium iodide staining. RESULTS PLK1 inhibitors were remarkably more sensitive to HCC cells harbouring TERT promoter mutation than wild-type cells in vitro and in vivo, which were diminished after TERT promoter mutation was edited to the wild-type nucleotide. Comparing the HCC cells with wild-type promoter of TERT, PLK1 inhibitors specifically downregulated Smad3 to regulate TERT for inducing apoptosis and G2/M arrest in TERT mutant HCC cells. Moreover, knockout of Smad3 counteracted the effects of PLK1 inhibitors in TERT mutant HCC cells. Finally, a cooperative effect of PLK1 and Smad3 inhibition was observed in TERT mutant cells. CONCLUSIONS PLK1 inhibition selectively suppressed the growth of TERT mutant HCC cells through Smad3, thus contributed to discover a novel therapeutic strategy to treat HCC patients harbouring TERT promoter mutations. KEY POINTS TERT promoter mutation confers sensitivity to PLK1 inhibitors in HCC. The selective growth inhibition of TERT mutant HCC cells induced by PLK1 inhibitor was mediated by Smad3. Combined inhibition of PLK1 and Smad3 showed a cooperative anti-tumor effect in TERT mutant HCC cells.
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Affiliation(s)
- Qin Tang
- Department of Radiation OncologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Guanghui Hu
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Ye Sang
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Yulu Chen
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Guangyan Wei
- Department of Radiation OncologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Meiyan Zhu
- Department of Radiation OncologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Mengke Chen
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Shiyong Li
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Rengyun Liu
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Zhenwei Peng
- Department of Radiation OncologyThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Institute of Precision MedicineThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
- Cancer CenterThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
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8
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Bennett DC. Review: Are moles senescent? Pigment Cell Melanoma Res 2024; 37:391-402. [PMID: 38361107 DOI: 10.1111/pcmr.13163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/01/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
Melanocytic nevi (skin moles) have been regarded as a valuable example of cell senescence occurring in vivo. However, a study of induced nevi in a mouse model reported that the nevi were arrested by cell interactions rather than a cell-autonomous process like senescence, and that size distributions of cell nests within nevi could not be accounted for by a stochastic model of oncogene-induced senescence. Moreover, others reported that some molecular markers used to identify cell senescence in human nevi are also found in melanoma cells-not senescent. It has thus been questioned whether nevi really are senescent, with potential implications for melanoma diagnosis and therapy. Here I review these areas, along with the genetic, biological, and molecular evidence supporting senescence in nevi. In conclusion, there is strong evidence that cells of acquired human benign (banal) nevi are very largely senescent, though some must contain a minor non-senescent cell subpopulation. There is also persuasive evidence that this senescence is primarily induced by dysfunctional telomeres rather than directly oncogene-induced.
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Affiliation(s)
- Dorothy C Bennett
- Molecular & Clinical Sciences Research Institute, St George's University of London, London, UK
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9
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Manrique-Silva E, David ME, Maider AM, García-Casado Z, Moro R, Requena C, Través V, Virós A, Kumar R, Nagore E. Clinical, histological, and molecular differences in melanoma due to different TERT promoter mutations subtypes. A retrospective cross-sectional study in 684 melanoma patients. Pigment Cell Melanoma Res 2024; 37:343-351. [PMID: 38153178 DOI: 10.1111/pcmr.13155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 10/05/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
Differences in survival according to the pTERT mutation subtypes (-124C > T, -146C > T, and tandem -138_139CC > TT) have been observed. The present study aimed to describe the clinical as the histopathological and molecular cutaneous melanoma features according to the presence of the three most prevalent pTERT mutation subtypes (-124C > T, -146C > T, and tandem -138_139CC > TT). A retrospective cross-sectional study including 684 patients was designed, and a Partial Least-Squares Discriminant Analysis (PLS-DA) was performed. After the PSL-DA, it was observed that the tandem -138_139CC > TT subtype differs from the other subtypes. The model demonstrated that the -124C > T and the -138_139 CC > TT subtypes were associated with fast-growing melanomas (OR 0.5, CI 0.29-0.86, p = .012) and with Breslow >2 mm (OR 0.6, CI 0.37-0.97, p = .037), compared to the -146C > T mutation. Finally, the -124C > T appeared to be more associated with the presence of TILs (non-brisk) than the -146C > T (OR 0.6, CI 0.40-1.01, p = .05). These findings confirmed that the -124C > T and the tandem -138_139 CC > TT subtypes are both highly associated with the presence of features of aggressiveness; however, only the -124C > T was highly associated with TILs. This difference could explain the worse survival rate associated with the tandem -138_139CC > TT mutations.
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Affiliation(s)
- Esperanza Manrique-Silva
- Escuela de Doctorado, Universidad Católica de Valencia "San Vicente Mártir", València, Spain
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Millán-Esteban David
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
- School of Medicine, Universidad Católica de Valencia "San Vicente Mártir", València, Spain
| | - Aguerralde-Martin Maider
- Máster de Ingeniería de Análisis de Datos, Toma de Decisiones y Mejora de Procesos, Universidad Politécnica de Valencia, Valencia, Spain
| | - Zaida García-Casado
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Ruggero Moro
- Instituto Dermatológico Dr. Alonso, Hospital Vithas Valencia 9 de Octubre, Spain
| | - Celia Requena
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Victor Través
- Department of Pathological Anatomy, Fundación Instituto Valenciano de Oncología, Valencia, Spain
| | - Amaya Virós
- Skin Cancer and Aging Lab, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Rajiv Kumar
- Division of Functional Genome Analysis, Deutsches Krebsforschüngzentrum, Heidelberg, Germany
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Eduardo Nagore
- Escuela de Doctorado, Universidad Católica de Valencia "San Vicente Mártir", València, Spain
- Department of Dermatology, Fundación Instituto Valenciano de Oncología, Valencia, Spain
- School of Medicine, Universidad Católica de Valencia "San Vicente Mártir", València, Spain
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10
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Chen B, Weng Y, Li M, Bian Z, Tao Y, Zhou W, Lu H, He S, Liao R, Huang J, Wang Q, Xu M, Ge Y, Cao W, Lei M, Zhang Y. LINC02454-CCT complex interaction is essential for telomerase activity and cell proliferation in head and neck squamous cell carcinoma. Cancer Lett 2024; 588:216734. [PMID: 38401886 DOI: 10.1016/j.canlet.2024.216734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/03/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
Telomerase activity is upregulated in head and neck squamous cell carcinoma (HNSCC), yet its regulatory mechanisms remain unclear. Here, we identified a cancer-specific lncRNA (LINC02454) associated with poor prognosis by using LncRNA chip of our HNSCC cohorts and external datasets. Through employing negative-stain transmission electron microscopy (NS-TEM), we discovered an interaction between LINC02454 and CCT complex which would augment telomerase activity for maintaining telomere homeostasis. Supporting this, in the telomerase repeat amplification protocol (TRAP) assay and quantitative fluorescence in situ hybridization (Q-FISH) analysis, LINC02454 depletion significantly reduced telomerase activity and shortened telomere length. Consistently, pathways related to telomerase, mitosis, and apoptosis were significantly impacted upon LINC02454 knockdown in RNAseq analysis. Functionally, LINC02454-deficient cells exhibited a more significant senescence phenotype in β-galactosidase staining, cell cycle, and apoptosis assays. We further confirmed the role of LINC02454 in HNSCC proliferation through a combination of in vitro and in vivo experiments. The therapeutic potential of targeting LINC02454 was verified by adenovirus-shRNA approach in HNSCC patient-derived xenograft (PDX) models. In summary, our findings provided valuable insights into the molecular mechanisms of HNSCC tumorigenesis and potential targets for future treatment modalities.
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Affiliation(s)
- Biying Chen
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Yue Weng
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mingyue Li
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhouliang Bian
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Ye Tao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenkai Zhou
- Department of Oral Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Hong Lu
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shufang He
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jie Huang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Wang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Ming Xu
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Yunhui Ge
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wei Cao
- Department of Oral Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China.
| | - Ming Lei
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yanjie Zhang
- Department of Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201900, China; Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
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11
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Lv JJ, Yao QL, Jiang XB, Ren M, Cai X, Dai B, Kong YY. Primary leptomeningeal melanocytic neoplasms: A clinicopathologic, immunohistochemical, and molecular study of 12 cases. Hum Pathol 2024; 148:32-40. [PMID: 38670237 DOI: 10.1016/j.humpath.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
This study investigated the clinicopathological, immunohistochemical, and molecular features of primary leptomeningeal melanocytic neoplasms (LMNs). Twelve LMN cases were retrospectively reviewed. We performed Fluorescence in-situ hybridization (including a 4-probe FISH assay with CDKN2A and MYC assay) and Next-Generation sequencing analyses on available cases. Histologically, 2 tumours were classified as melanocytomas (MC), 2 as intermediate-grade melanocytomas (IMC), and 8 as leptomeningeal melanomas (LMM). Two rare cases of LMM were associated with large plaque-like blue nevus. One MC case was associated with Ota. Ten cases (83.3%) showed melanocytic cells with benign features diffusely proliferating within the meninges. The Ki-67 in three categories differed (MC 0-1%, IMC 0-3%, LMM 3-10%). 57.1% of LMM cases (4/7) were positive for FISH. Nine of 10 tumours harboured activating hotspot mutations in GNAQ, GNA11, or PLCB4. Additional mutations of EIF1AX, SF3B1, or BAP1 were found in 40%, 30%, and 10% of tumours, respectively. During the follow-up (median = 43 months), 5 LMM patients experienced recurrence and/or metastasis, 3 of them died of the disease and the other 2 are alive with the tumour. Our study is by far the first cohort of LMN cases tested by FISH. In addition to morphological indicators including necrosis and mitotic figures, using a combination of Ki-67 and FISH helps to differentiate between IMC and LMM, especially in LMM cases with less pleomorphic features. SF3B1 mutation is first described in 2 cases of plaque-type blue nevus associated with LMM. Patients with SF3B1 mutation might be related to poor prognosis in LMN.
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Affiliation(s)
- Jiao-Jie Lv
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Qian-Lan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xue-Bing Jiang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China; Department of Pathology, Minhang Hospital, Fudan University, Shanghai, 201100, People's Republic of China
| | - Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xu Cai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Bo Dai
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China; Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China.
| | - Yun-Yi Kong
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
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12
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Maloberti T, De Leo A, Coluccelli S, Sanza V, Gruppioni E, Altimari A, Comito F, Melotti B, Marchese PV, Dika E, Venturi F, Corti B, Ciccimarra G, Ciceu CA, Tallini G, de Biase D. Molecular Characterization of Advanced-Stage Melanomas in Clinical Practice Using a Laboratory-Developed Next-Generation Sequencing Panel. Diagnostics (Basel) 2024; 14:800. [PMID: 38667446 PMCID: PMC11048853 DOI: 10.3390/diagnostics14080800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Cutaneous melanoma is one of the most lethal tumors among skin cancers, characterized by complex genetic and molecular alterations that result in uncontrolled cell proliferation and metastatic spread. Next-generation sequencing (NGS) enables the simultaneous examination of numerous genes, making this molecular technique essential for melanoma diagnosis, prognostic stratification, and therapy planning. Herein, we present the experience with our laboratory-designed NGS panel for the routine assessment of advanced-stage melanoma. A total of 260 specimens of advanced-stage melanomas were evaluated utilizing a laboratory-developed multi-gene NGS panel, which allowed the investigation of 229 amplicons in 25 oncogene/oncosuppressor genes. The NGS panel proved to be a reliable tool, failing to produce results in only 1.2% of the samples tested. BRAF and TERT were the two more commonly altered genes in 44.0% and 59.9% of samples, respectively. In 59.3% of the mutated cases, at least two concomitant variants were detected. In eight cases, both primary lesion and metastatic disease were analyzed by NGS. In all specimens (8/8, 100%), a perfect concordance in variants harbored by the primary and recurrence lesions was observed. Finally, this study described the validity of a laboratory-developed multi-gene NGS panel built specifically for advanced-stage melanomas in ordinary clinical practice.
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Affiliation(s)
- Thais Maloberti
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Antonio De Leo
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
| | - Sara Coluccelli
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Viviana Sanza
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Elisa Gruppioni
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Annalisa Altimari
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
| | - Francesca Comito
- Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy (B.M.); (P.V.M.)
| | - Barbara Melotti
- Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy (B.M.); (P.V.M.)
| | - Paola Valeria Marchese
- Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy (B.M.); (P.V.M.)
| | - Emi Dika
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Federico Venturi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
- Oncologic Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Barbara Corti
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Giulia Ciccimarra
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy; (G.C.); (C.A.C.)
| | - Crina Adriana Ciceu
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy; (G.C.); (C.A.C.)
| | - Giovanni Tallini
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (E.D.); (F.V.)
| | - Dario de Biase
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (T.M.); (A.D.L.); (S.C.); (V.S.); (E.G.); (A.A.); (G.T.)
- Department of Pharmacy and Biotechnology, University of Bologna, 40138 Bologna, Italy; (G.C.); (C.A.C.)
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13
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Raghav A, Jeong GB. Nanoquercetin and Extracellular Vesicles as Potential Anticancer Therapeutics in Hepatocellular Carcinoma. Cells 2024; 13:638. [PMID: 38607076 PMCID: PMC11011524 DOI: 10.3390/cells13070638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
Despite world-class sophisticated technologies, robotics, artificial intelligence, and machine learning approaches, cancer-associated mortalities and morbidities have shown continuous increments posing a healthcare burden. Drug-based interventions were associated with systemic toxicities and several limitations. Natural bioactive compounds derived nanoformulations, especially nanoquercetin (nQ), are alternative options to overcome drug-associated limitations. Moreover, the EVs-based cargo targeted delivery of nQ can have enormous potential in treating hepatocellular carcinoma (HCC). EVs-based nQ delivery synergistically regulates and dysregulates several pathways, including NF-κB, p53, JAK/STAT, MAPK, Wnt/β-catenin, and PI3K/AKT, along with PBX3/ERK1/2/CDK2, and miRNAs intonation. Furthermore, discoveries on possible checkpoints of anticancer signaling pathways were studied, which might lead to the development of modified EVs infused with nQ for the development of innovative treatments for HCC. In this work, we abridged the control of such signaling systems using a synergetic strategy with EVs and nQ. The governing roles of extracellular vesicles controlling the expression of miRNAs were investigated, particularly in relation to HCC.
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Affiliation(s)
| | - Goo Bo Jeong
- Department of Anatomy and Cell Biology, College of Medicine, Gachon University, 155 Getbeol-ro, Yeonsu-gu, Incheon 21999, Republic of Korea;
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Zheng L, Wang Y, Liu Z, Wang Z, Tao C, Wu A, Li H, Xiao T, Li Z, Rong W. Identification of molecular characteristics of hepatocellular carcinoma with microvascular invasion based on deep targeted sequencing. Cancer Med 2024; 13:e7043. [PMID: 38572921 PMCID: PMC10993708 DOI: 10.1002/cam4.7043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND As an indicator of tumor invasiveness, microvascular invasion (MVI) is a crucial risk factor for postoperative relapse, metastasis, and unfavorable prognosis in hepatocellular carcinoma (HCC). Nevertheless, the genetic mechanisms underlying MVI, particularly for Chinese patients, remain mostly uncharted. METHODS We applied deep targeted sequencing on 66 Chinese HCC samples. Focusing on the telomerase reverse transcriptase (TERT) promoter (TERTp) and TP53 co-mutation (TERTp+/TP53+) group, gene set enrichment analysis (GSEA) was used to explore the potential molecular mechanisms of the TERTp+/TP53+ group on tumor progression and metastasis. Additionally, we evaluated the tumor immune microenvironment of the TERTp+/TP53+ group in HCC using multiplex immunofluorescence (mIF) staining. RESULTS Among the 66 HCC samples, the mutated genes that mostly appeared were TERT, TP53, and CTNNB1. Of note, we found 10 cases with TERTp+/TP53+, of which nine were MVI-positive and one was MVI-negative, and there was a co-occurrence of TERTp and TP53 (p < 0.05). Survival analysis demonstrated that patients with the TERTp+/TP53+ group had lower the disease-free survival (DFS) (p = 0.028). GSEA results indicated that telomere organization, telomere maintenance, DNA replication, positive regulation of cell cycle, and negative regulation of immune response were significantly enriched in the TERTp+/TP53+ group (all adjusted p-values (p.adj) < 0.05). mIF revealed that the TERTp+/TP53+ group decreased CD8+ T cells infiltration (p = 0.25) and enhanced PDL1 expression (p = 0.55). CONCLUSIONS TERTp+/TP53+ was significantly enriched in MVI-positive patients, leading to poor prognosis for HCC patients by promoting proliferation of HCC cell and inhibiting infiltration of immune cell surrounding HCC. TERTp+/TP53+ can be utilized as a potential indicator for predicting MVI-positive patients and poor prognosis, laying a preliminary foundation for further exploration of co-mutation in HCC with MVI and clinical treatment.
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Affiliation(s)
- Linlin Zheng
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yaru Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhenrong Liu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhihao Wang
- Department of Hepatobiliary Hernia SurgeryLiaocheng Dongcangfu People's HospitalLiaochengChina
| | - Changcheng Tao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Anke Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Haiyang Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Zhuo Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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15
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Kordowitzki P, Graczyk S, Mechsner S, Sehouli J. Shedding Light on the Interaction Between Rif1 and Telomeres in Ovarian Cancer. Aging Dis 2024; 15:535-545. [PMID: 37548940 PMCID: PMC10917528 DOI: 10.14336/ad.2023.0716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/16/2023] [Indexed: 08/08/2023] Open
Abstract
Ovarian cancer, more precisely high-grade serous ovarian cancer, is one of the most lethal age-independent gynecologic malignancies in women worldwide, regardless of age. There is mounting evidence that there is a link between telomeres and the RIF1 protein and the proliferation of cancer cells. Telomeres are hexameric (TTAGGG) tandem repeats at the tip of chromosomes that shorten as somatic cells divide, limiting cell proliferation and serving as an important barrier in preventing cancer. RIF1 (Replication Time Regulation Factor 1) plays, among other factors, an important role in the regulation of telomere length. Interestingly, RIF1 appears to influence the DNA double-strand break (DSB) repair pathway. However, detailed knowledge regarding the interplay between RIF1 and telomeres and their degree of engagement in epithelial ovarian cancer (EOC) is still elusive, despite the fact that such knowledge could be of relevance in clinical practice to find novel biomarkers. In this review, we provide an update of recent literature to elucidate the relation between telomere biology and the RIF1 protein during the development of ovarian cancer in women.
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Affiliation(s)
- Paweł Kordowitzki
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.
- Department of Gynecology including Center of oncological surgery (CVK) and Department of Gynaecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany.
| | - Szymon Graczyk
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.
| | - Sylvia Mechsner
- Department of Gynecology including Center of oncological surgery (CVK) and Department of Gynaecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany.
| | - Jalid Sehouli
- Department of Gynecology including Center of oncological surgery (CVK) and Department of Gynaecology (CBF), European Competence Center for Ovarian Cancer, Charite, Berlin, Germany.
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Pérez González S, Heredia-Soto V, Girón de Francisco M, Pérez-Fernández E, Casans-Francés R, Mendiola Sabio M, González-Peramato P. Telomerase Reverse Transcriptase-Promoter Mutation in Young Patients with Bladder Tumors. Curr Issues Mol Biol 2024; 46:2845-2855. [PMID: 38666908 PMCID: PMC11049539 DOI: 10.3390/cimb46040178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The TERT (Telomerase Reverse Transcriptase) gene promoter mutation is one of the most prevalent mutations in urothelial bladder tumors and this mutation is related to bladder tumor progression. Our purpose was to evaluate the presence of this mutation in a population of patients who were first diagnosed at age ≤ 40 years and to examine its relationship with tumor characteristics and progression. A molecular study was performed to detect the two most prevalent mutations in the TERT promoter (C228T and C250T). The study included 29 patients, with a mean follow-up of 152 months. There were no statistically significant differences in the clinical or tumor characteristics according to the presence or absence of the mutation. Although the mutation group showed poorer recurrence-free survival (RFS), there was no statistically significant difference and there was no difference in progression-free survival by group (p > 0.05). The pTERT mutations in bladder tumor cells occurred less frequently in younger patients than in older patients, a finding that could indicate different mechanisms of carcinogenesis. The trend towards lower RFS in patients with mutated pTERT needs to be confirmed by further studies, given the small number of patients included in these studies due to the low incidence of bladder tumors in this age group.
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Affiliation(s)
| | - Victoria Heredia-Soto
- Translational Oncology Research Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ), 28046 Madrid, Spain
- Center for Biomedical Research in the Cancer Network (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | | | - Rubén Casans-Francés
- Department of Anesthesia and Pain Medicine, Infanta Elena University Hospital, 28342 Madrid, Spain
| | - Marta Mendiola Sabio
- Center for Biomedical Research in the Cancer Network (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Molecular Pathology and Therapeutic Targets Group, Hospital La Paz Institute for Health Research (IdiPAZ), 28046 Madrid, Spain
| | - Pilar González-Peramato
- Department of Pathology, La Paz University Hospital, 28046 Madrid, Spain
- Faculty of Medicine, Universidad Autónoma de Madrid, 28029 Madrid, Spain
- Cellular Engineering Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ), 28046 Madrid, Spain
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Hu Y, Xu S, Dong L, Pan Z, Zhang L, Zhan W. Clinical features combined with ultrasound characteristics to predict TERT promoter mutations in papillary thyroid carcinoma: a single-center study over the past 5 years. Front Endocrinol (Lausanne) 2024; 15:1322731. [PMID: 38562417 PMCID: PMC10982409 DOI: 10.3389/fendo.2024.1322731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Purpose Telomerase reverse transcriptase (TERT) has been reported in papillary thyroid carcinoma (PTC). This study aimed to investigate the correlation of TERT promoter mutations with clinical and ultrasound (US) features in PTC and to develop a model to predict TERT promoter mutations. Methods Preoperative US images, postoperative pathological features, and TERT promoter mutation information were evaluated in 365 PTC patients confirmed by surgery. Univariate and multivariate factor analyses were performed to identify risk factors for TERT promoter mutations. A predictive model was established to assess the clinical predictive value. Results Of the 365 patients with PTC (498 nodules), the number of those with TERT promoter mutations was 67 cases (75 nodules), and the number of those without mutations was 298 cases (423 nodules). The median age was 40 years in the wild-type group and 60 years in the mutant group. Male patients made up 35.82% of the mutant group and 22.82% of the wild-type group. Multivariate analysis revealed that the independent risk factors associated with the occurrence of TERT promoter mutation in PTC were as follows: older age (odds ratio (OR) = 1.07; p = 0.002), maximum diameter of ≥ 10 mm (OR = 3.94; p < 0.0001), unilateral (OR = 4.15; p < 0.0001), multifocal (OR = 7.69; p < 0.0001), adjacent to the thyroid capsule (OR = 1.94; p = 0.044), and accompanied by other benign nodules (OR = 1.94, p = 0.039). A predictive model was established, and the area under the curve (AUC) of the receiver operating characteristic was 0.839. TERT promoter mutations were associated with high-risk US and clinical features compared with the wild-type group. Conclusion TERT promoter mutations were associated with older ages. They were also found to be multifocal, with a maximum diameter of ≥ 10 mm, unilateral, adjacent to the thyroid capsule, and accompanied by other benign nodules. The predictive model was of high diagnostic value.
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Affiliation(s)
- Yan Hu
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shangyan Xu
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lei Dong
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zuxian Pan
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lu Zhang
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Weiwei Zhan
- Department of Ultrasound, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Koca DS, Kolpakov V, Ihlow J, von Laffert M, Erb-Eigner K, Herbst H, Kriese K, Schweizer L, Bertelmann E. Prevalence of TERT Promoter Mutations in Orbital Solitary Fibrous Tumors. Curr Issues Mol Biol 2024; 46:1467-1484. [PMID: 38392213 PMCID: PMC10887834 DOI: 10.3390/cimb46020095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
The orbital manifestation of a solitary fibrous tumor (SFT) is exceptionally rare and poses specific challenges in diagnosis and treatment. Its rather exceptional behavior among all SFTs comprises a high tendency towards local recurrence, but it rarely culminates in metastatic disease. This raises the question of prognostic factors in orbital SFTs (oSFTs). Telomerase reverse transcriptase (TERT)-promoter mutations have previously been linked to an unfavorable prognosis in SFTs of other locations. We analyzed the prevalence of TERT promoter mutations of SFTs in the orbital compartment. We performed a retrospective, descriptive clinico-histopathological analysis of nine cases of oSFTs between the years of 2017 and 2021. A TERT promoter mutation was present in one case, which was classified with intermediate metastatic risk. Local recurrence or progress occurred in six cases after primary resection; no distant metastases were reported. Multimodal imaging repeatedly showed particular morphologic patterns, including tubular vascular structures and ADC reduction. The prevalence of the TERT promoter mutation in oSFT was 11%, which is similar to the prevalence of extra-meningeal SFTs of the head and neck and lower than that in other extra-meningeal compartments. In the present study, the TERT promoter mutation in oSFT manifested in a case with an unfavorable prognosis, comprising aggressive local tumor growth, local recurrence, and eye loss.
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Affiliation(s)
- David Sinan Koca
- Department of Ophthalmology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Vladimir Kolpakov
- Department of Ophthalmology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Jana Ihlow
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Berlin Institute of Health Charité Clinician Scientist Program, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin Institute of Health Biomedical Innovation Academy, Anna-Louisa-Karsch-Str., 210178 Berlin, Germany
| | - Maximilian von Laffert
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Department of Diagnostics, Institute of Pathology, Universitätsklinikum Leipzig AöR, Liebigstraße 26, 04103 Leipzig, Germany
| | - Katharina Erb-Eigner
- Department of Radiology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Hermann Herbst
- Department of Pathology, Vivantes Hospital Neukölln, Vivantes Netzwerk für Gesundheit GmbH Berlin, Rudower Straße 48, 12351 Berlin, Germany
| | - Karen Kriese
- Department of Pathology, Vivantes Hospital Neukölln, Vivantes Netzwerk für Gesundheit GmbH Berlin, Rudower Straße 48, 12351 Berlin, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Edinger Institute, Institute of Neurology, University of Frankfurt am Main, 60528 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt-Mainz, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), 60596 Frankfurt am Main, Germany
| | - Eckart Bertelmann
- Department of Ophthalmology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
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Gorria T, Crous C, Pineda E, Hernandez A, Domenech M, Sanz C, Jares P, Muñoz-Mármol AM, Arpí-Llucía O, Melendez B, Gut M, Esteve A, Esteve-Codina A, Parra G, Alameda F, Carrato C, Aldecoa I, Mallo M, de la Iglesia N, Balana C. The C250T Mutation of TERTp Might Grant a Better Prognosis to Glioblastoma by Exerting Less Biological Effect on Telomeres and Chromosomes Than the C228T Mutation. Cancers (Basel) 2024; 16:735. [PMID: 38398126 PMCID: PMC10886885 DOI: 10.3390/cancers16040735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The aim of this study was to determine how TERTp mutations impact glioblastoma prognosis. MATERIALS AND METHODS TERTp mutations were assessed in a retrospective cohort of 258 uniformly treated glioblastoma patients. RNA-sequencing and whole exome sequencing results were available in a subset of patients. RESULTS Overall, there were no differences in outcomes between patients with mutated TERTp-wt or TERTp. However, we found significant differences according to the type of TERTp mutation. Progression-free survival (mPFS) was 9.1 months for those with the C250T mutation and 7 months for those with either the C228T mutation or TERTp-wt (p = 0.016). Overall survival (mOS) was 21.9 and 15 months, respectively (p = 0.026). This differential effect was more pronounced in patients with MGMTp methylation (mPFS: p = 0.008; mOS: p = 0.021). Multivariate analysis identified the C250T mutation as an independent prognostic factor for longer mOS (HR 0.69; p = 0.044). We found no differences according to TERTp mutation status in molecular alterations common in glioblastoma, nor in copy number variants in genes related to alternative lengthening of telomeres. Nevertheless, in the gene enrichment analysis adjusted for MGMTp methylation status, some Reactome gene sets were differentially enriched, suggesting that the C250T mutation may exert a lesser effect on telomeres or chromosomes. CONCLUSIONS In our series, patients exhibiting the C250T mutation had a more favorable prognosis compared to those with either TERPp-wt or TERTp C228T mutations. Additionally, our findings suggest a reduced involvement of the C250T mutation in the underlying biological mechanisms related to telomeres.
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Affiliation(s)
- Teresa Gorria
- Medical Oncology, Hospital Clínic, Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; (T.G.); (C.C.); (E.P.)
| | - Carme Crous
- Medical Oncology, Hospital Clínic, Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; (T.G.); (C.C.); (E.P.)
| | - Estela Pineda
- Medical Oncology, Hospital Clínic, Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; (T.G.); (C.C.); (E.P.)
| | - Ainhoa Hernandez
- Medical Oncology, Institut Catala d’Oncologia (ICO) Badalona, Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (A.H.); (M.D.); (A.E.)
| | - Marta Domenech
- Medical Oncology, Institut Catala d’Oncologia (ICO) Badalona, Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (A.H.); (M.D.); (A.E.)
| | - Carolina Sanz
- Pathology Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (C.S.); (A.M.M.-M.); (C.C.)
| | - Pedro Jares
- Department of Pathology, Biomedical Diagnostic Centre (CDB) and Neurological Tissue Bank of the Biobank-IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (P.J.); (I.A.)
| | - Ana María Muñoz-Mármol
- Pathology Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (C.S.); (A.M.M.-M.); (C.C.)
| | - Oriol Arpí-Llucía
- Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain;
| | - Bárbara Melendez
- Molecular Pathology Research Unit, Hospital Universitario de Toledo, 45007 Toledo, Spain;
| | - Marta Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; (M.G.); (A.E.-C.); (G.P.)
| | - Anna Esteve
- Medical Oncology, Institut Catala d’Oncologia (ICO) Badalona, Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (A.H.); (M.D.); (A.E.)
- Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), 08916 Badalona, Spain
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; (M.G.); (A.E.-C.); (G.P.)
| | - Genis Parra
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain; (M.G.); (A.E.-C.); (G.P.)
| | - Francesc Alameda
- Pathology Department, Neuropathology Unit, Hospital del Mar, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain;
| | - Cristina Carrato
- Pathology Department, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (C.S.); (A.M.M.-M.); (C.C.)
| | - Iban Aldecoa
- Department of Pathology, Biomedical Diagnostic Centre (CDB) and Neurological Tissue Bank of the Biobank-IDIBAPS, Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain; (P.J.); (I.A.)
| | - Mar Mallo
- Unidad de Microarrays, Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain;
| | - Nuria de la Iglesia
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain;
| | - Carmen Balana
- Pathology Department, Neuropathology Unit, Hospital del Mar, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain;
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Huber R, Lee J, Borretta L, Tessier-Cloutier B, Lum A, Yip S, Horst BA. TERT promoter mutations in atypical melanocytic lesions: A series of seven cases with adverse melanoma-specific outcome. Hum Pathol 2024; 144:34-39. [PMID: 38224873 DOI: 10.1016/j.humpath.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
The majority of melanocytic proliferations can be readily categorized as benign or malignant based on histologic assessment under the microscope by a trained dermatopathologist. However, a subset of lesions, termed Atypical Melanocytic Proliferations (AMPs), are histologically ambiguous, leading to possible diagnostic error and suboptimal treatment. Mutations in the promoter region of the catalytic subunit of telomerase, telomerase reverse transcriptase (TERT), are commonly found in melanomas but are rare in melanocytic nevi. In this study, we aimed to determine the prevalence of hot spot TERT promoter (TERT-p) mutations in AMPs with adverse melanoma-specific outcome. Studies were approved by respective institutional review boards. Using a multi-center database, we identified seven cases of melanocytic proliferations with a clinical follow-up period of at least 4 years, which were initially diagnosed as AMPs, and which recurred either as melanoma at site of prior biopsy or as metastatic melanoma. Sequencing of the TERT-p region showed hotspot mutations in three cases (43 %), suggesting that TERT-p mutations are enriched and could aid in the identification of AMPs with adverse outcome. In comparison with existing ancillary techniques for prognostication of AMPs, TERT-p mutation analysis may have advantages in terms of cost effectiveness and turnaround time, and is a promising diagnostic parameter with potential widespread utility.
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Affiliation(s)
- Reed Huber
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Jonathan Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Lisa Borretta
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | | | - Amy Lum
- Molecular Oncology, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada
| | - Basil A Horst
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, V5Z 1M9, Canada.
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Hipólito A, Xavier R, Brito C, Tomás A, Lemos I, Cabaço LC, Silva F, Oliva A, Barral DC, Vicente JB, Gonçalves LG, Pojo M, Serpa J. BRD9 status is a major contributor for cysteine metabolic remodeling through MST and EAAT3 modulation in malignant melanoma. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166983. [PMID: 38070581 DOI: 10.1016/j.bbadis.2023.166983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/31/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Cutaneous melanoma (CM) is the most aggressive skin cancer, showing globally increasing incidence. Hereditary CM accounts for a significant percentage (5-15 %) of all CM cases. However, most familial cases remain without a known genetic cause. Even though, BRD9 has been associated to CM as a susceptibility gene. The molecular events following BRD9 mutagenesis are still not completely understood. In this study, we disclosed BRD9 as a key regulator in cysteine metabolism and associated altered BRD9 to increased cell proliferation, migration and invasiveness, as well as to altered melanin levels, inducing higher susceptibility to melanomagenesis. It is evident that BRD9 WT and mutated BRD9 (c.183G>C) have a different impact on cysteine metabolism, respectively by inhibiting and activating MPST expression in the metastatic A375 cell line. The effect of the mutated BRD9 variant was more evident in A375 cells than in the less invasive WM115 line. Our data point out novel molecular and metabolic mechanisms dependent on BRD9 status that potentially account for the increased risk of developing CM and enhancing CM aggressiveness. Moreover, our findings emphasize the role of cysteine metabolism remodeling in melanoma progression and open new queues to follow to explore the role of BRD9 as a melanoma susceptibility or cancer-related gene.
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Affiliation(s)
- Ana Hipólito
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Renato Xavier
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Cheila Brito
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Ana Tomás
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Isabel Lemos
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal; Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Luís C Cabaço
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - Fernanda Silva
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Abel Oliva
- Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Duarte C Barral
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - João B Vicente
- Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Luís G Gonçalves
- Instituto de Tecnologia Química e Tecnológica (ITQB) António Xavier da Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marta Pojo
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal
| | - Jacinta Serpa
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG), Rua Prof Lima Basto, 1099-023 Lisboa, Portugal.
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Zhang J, Zhang F, Porter KI, Dakup PP, Wang S, Robertson GP, Gaddameedhi S, Zhu J. Telomere dysfunction in Tert knockout mice delays Braf V600E -induced melanoma development. Int J Cancer 2024; 154:548-560. [PMID: 37727982 PMCID: PMC10840707 DOI: 10.1002/ijc.34713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023]
Abstract
Telomerase activation is a crucial step in melanomagenesis, often occurring because of ultraviolet radiation (UVR)-induced mutations at the telomerase gene (TERT) promoter and rendering TERT transcription in response to the activated Raf-MAP kinase pathway by BRAFV600E mutation. Due to the excessively long telomeres in mice, this process does not occur during melanomagenesis in mouse models. To investigate the impact of telomere dysfunction on melanomagenesis, BrafV600E was induced in generations 1 and 4 (G1 and G4) of Tert-/- mice. Our findings revealed that, regardless of UVR exposure, melanoma development was delayed in G4 mice, which had shorter telomeres compared to G1 and wild-type C57BL/6J (G0) mice. Moreover, many G4 tumors displayed an accumulation of excessive DNA damage, as evidenced by increased γH2A.X staining. Tumors from UVR-exposed mice exhibited elevated p53 protein expression. Cultured tumor cells isolated from G4 mice displayed abundant chromosomal fusions and rearrangements, indicative of telomere dysfunction in these cells. Additionally, tumor cells derived from UVB-exposed mice exhibited constitutively elevated expression of mutant p53 proteins, suggesting that p53 was a target of UVB-induced mutagenesis. Taken together, our findings suggest that telomere dysfunction hampers melanomagenesis, and targeting telomere crisis-mediated genomic instability may hold promise for the prevention and treatment of melanoma.
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Affiliation(s)
- Jinglong Zhang
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210, USA
| | - Fan Zhang
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210, USA
| | - Kenneth I. Porter
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210, USA
| | - Panshak P. Dakup
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210, USA
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
| | - Shuwen Wang
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210, USA
| | - Gavin P. Robertson
- Department of Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Shobhan Gaddameedhi
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
| | - Jiyue Zhu
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA 99210, USA
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23
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Ahmadi S, Landa I. The prognostic power of gene mutations in thyroid cancer. Endocr Connect 2024; 13:e230297. [PMID: 38078934 PMCID: PMC10831542 DOI: 10.1530/ec-23-0297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
The introduction and generalization of next-generation sequencing techniques have significantly increased the identification of mutations in thyroid tumors from multiple patient cohorts. The understanding of the association between specific mutations and clinical outcomes is gradually leading to individualizing the care of patients with thyroid cancer. BRAFV600 is the most common mutation seen in thyroid cancer patients and unequivocally predicts malignancy, but when considered in isolation, it is not recommended to be used as an independent prognostic factor. Mutations in RAS are the second most common alterations in thyroid cancer but can be found in benign and malignant lesions. Rearrangements involving receptor tyrosine kinases, primarily RET, are found in a subset of thyroid tumors without mutations in either BRAF or RAS. The assessment of additional mutations is increasingly employed in thyroid cancer prognostication. The coexistence of BRAF with alterations in genes such as PIK3CA, TERT promoter, or TP53 is associated with less favorable outcomes. Similar studies have also shown that additional oncogenic mutations in RAS-mutant thyroid carcinoma, such as those affecting the EIF1AX gene, likely predict a more aggressive clinicopathologic behavior. Overall, emerging evidence suggests that the co-occurrence of specific alterations in defined genes with BRAF or RAS mutations can become prognostic tools and useful predictors of thyroid tumor aggressiveness.
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Affiliation(s)
- Sara Ahmadi
- Division of Endocrinology, Thyroid Section, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Iñigo Landa
- Division of Endocrinology, Thyroid Section, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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24
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Landa I, Cabanillas ME. Genomic alterations in thyroid cancer: biological and clinical insights. Nat Rev Endocrinol 2024; 20:93-110. [PMID: 38049644 DOI: 10.1038/s41574-023-00920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
Tumours can arise from thyroid follicular cells if they acquire driver mutations that constitutively activate the MAPK signalling pathway. In addition, a limited set of additional mutations in key genes drive tumour progression towards more aggressive and less differentiated disease. Unprecedented insights into thyroid tumour biology have come from the breadth of thyroid tumour sequencing data from patients and the wide range of mutation-specific mechanisms identified in experimental models, in combination with the genomic simplicity of thyroid cancers. This knowledge is gradually being translated into refined strategies to stratify, manage and treat patients with thyroid cancer. This Review summarizes the biological underpinnings of the genetic alterations involved in thyroid cancer initiation and progression. We also provide a rationale for and discuss specific examples of how to implement genomic information to inform both recommended and investigational approaches to improve thyroid cancer prognosis, redifferentiation strategies and targeted therapies.
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Affiliation(s)
- Iñigo Landa
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Maria E Cabanillas
- Department of Endocrine Neoplasia & Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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25
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Duan M, Song S, Wasserman H, Lee PH, Liu KJ, Gordân R, He Y, Mao P. High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma. Proc Natl Acad Sci U S A 2024; 121:e2310854121. [PMID: 38241433 PMCID: PMC10823218 DOI: 10.1073/pnas.2310854121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/20/2023] [Indexed: 01/21/2024] Open
Abstract
Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5' side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
| | - Shenghan Song
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM87131
| | - Hana Wasserman
- Program in Computational Biology and Bioinformatics, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC27708
| | - Po-Hsuen Lee
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
| | - Ke Jian Liu
- Department of Pathology, Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY11794-7263
| | - Raluca Gordân
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC27708
- Department of Computer Science, Duke University, Durham, NC27708
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC27708
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM87131
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM87131
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM87131
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Karimian K, Groot A, Huso V, Kahidi R, Tan KT, Sholes S, Keener R, McDyer JF, Alder JK, Li H, Rechtsteiner A, Greider CW. Human telomere length is chromosome specific and conserved across individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572870. [PMID: 38187739 PMCID: PMC10769321 DOI: 10.1101/2023.12.21.572870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Short telomeres cause age-related disease and long telomeres predispose to cancer; however, the mechanisms regulating telomere length are unclear. To probe these mechanisms, we developed a nanopore sequencing method, Telomere Profiling, that is easy to implement, precise, and cost effective with broad applications in research and the clinic. We sequenced telomeres from individuals with short telomere syndromes and found similar telomere lengths to the clinical FlowFISH assay. We mapped telomere reads to specific chromosome end and identified both chromosome end-specific and haplotype-specific telomere length distributions. In the T2T HG002 genome, where the average telomere length is 5kb, we found a remarkable 6kb difference in lengths between some telomeres. Further, we found that specific chromosome ends were consistently shorter or longer than the average length across 147 individuals. The presence of conserved chromosome end-specific telomere lengths suggests there are new paradigms in telomere biology that are yet to be explored. Understanding the mechanisms regulating length will allow deeper insights into telomere biology that can lead to new approaches to disease.
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Affiliation(s)
- Kayarash Karimian
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Aljona Groot
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
| | - Vienna Huso
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | | | - Kar-Tong Tan
- Harvard Medical School, Department of Genetics, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute, Cancer Program, Cambridge, MA
| | - Samantha Sholes
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Present address Merck & Co., 770 Sumneytown Pike, West Point, PA 19486
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University
| | - John F. McDyer
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh
| | - Jonathan K. Alder
- Pulmonary, Allergy, Critical Care, and Sleep Medicine Division, Department of Medicine, University of Pittsburgh
| | - Heng Li
- Dana-Farber Cancer Institute, Department of Data Sciences, Boston, MA
- Harvard Medical School, Department of Biomedical Informatics, Boston, MA
| | - Andreas Rechtsteiner
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
| | - Carol W. Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz
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27
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Xiao H, Shiu J, Chen CF, Wu J, Zhou P, Telang SS, Ruiz-Vega R, Nie Q, Lander AD, Ganesan AK. Uncovering Minimal Pathways in Melanoma Initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.08.570336. [PMID: 38106189 PMCID: PMC10723457 DOI: 10.1101/2023.12.08.570336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cutaneous melanomas are clinically and histologically heterogeneous. Most display activating mutations in Braf or Nras and complete loss of function of one or more tumor suppressor genes. Mouse models that replicate such mutations produce fast-growing, pigmented tumors. However, mice that combine Braf activation with only heterozygous loss of Pten also produce tumors and, as we show here, in an Albino background this occurs even with Braf activation alone. Such tumors arise rarely, grow slowly, and express low levels of pigmentation genes. The timing of their appearance was consistent with a single step stochastic event, but no evidence could be found that it required de novo mutation, suggesting instead the involvement of an epigenetic transition. Single-cell transcriptomic analysis revealed such tumors to be heterogeneous, including a minor cell type we term LNM ( L ow-pigment, N eural- and extracellular M atrix-signature) that displays gene expression resembling "neural crest"-like cell subsets detected in the fast-growing tumors of more heavily-mutated mice, as well as in human biopsy and xenograft samples. We provide evidence that LNM cells pre-exist in normal skin, are expanded by Braf activation, can transition into malignant cells, and persist with malignant cells through multiple rounds of transplantation. We discuss the possibility that LNM cells not only serve as a pre-malignant state in the production of some melanomas, but also as an important intermediate in the development of drug resistance.
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El Zarif T, Machaalani M, Nawfal R, Nassar AH, Xie W, Choueiri TK, Pomerantz M. TERT Promoter Mutations Frequency Across Race, Sex, and Cancer Type. Oncologist 2024; 29:8-14. [PMID: 37462445 PMCID: PMC10769781 DOI: 10.1093/oncolo/oyad208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/23/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Telomerase reverse transcriptase (TERT) gene promoter mutations have been explored, as biomarkers of improved survival for patients with cancer receiving immune checkpoint inhibitors. We sought to investigate their prevalence by race and sex across different cancer types to inform patient selection in clinical trials. RESULTS In this observational study, 31 925 patients with cancer underwent next-generation sequencing of their tumors with 88% (27 970) patients self-reported being Whites, 7.1% (2273) Asians, and 5.3% (1682) Blacks. Examining the distribution of TERT promoter mutations by race, White patients with melanoma harbored more TERT promoter mutations than Asian and Black patients (OR = 25.83; 95%CI, 6.84-217.42; P < .001). In contrast, Asian patients with head and neck cancer (HNC) harbored more TERT promoter mutations compared to White patients (OR = 2.47; 95%CI, 1.39-4.37; P = .004). In addition, the distribution of TERT promoter mutations differed by sex. Males were enriched for TERT gene promoter mutations compared to females with melanoma (OR = 1.82; 95%CI, 1.53-2.16; P < .001), cancer of unknown primary (OR = 1.96; 95%CI, 1.43-2.69; P < .001), hepatobiliary (OR = 3.89; 95%CI, 2.65-5.69; P < .001), and thyroid cancers (OR = 1.42; 95%CI, 1.10-1.84; P = .0087), while females were more enriched for TERT promoter mutations compared to males for HNC (OR = 0.56; 95%CI, 0.39-0.81; P = .0021). CONCLUSIONS The prevalence of TERT gene promoter mutations varies among patients with cancer based on race and sex. These findings inform our understanding of cancer biology and can assist in the design of future clinical trials that leverage drugs targeting TERT promoter dependencies.
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Affiliation(s)
- Talal El Zarif
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Internal Medicine, Yale New Haven Hospital, New Haven, CT, USA
| | - Marc Machaalani
- Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | - Rashad Nawfal
- Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon
| | - Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, USA
| | - Wanling Xie
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Toni K Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark Pomerantz
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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29
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Muyas F, Rodriguez MJG, Cascão R, Afonso A, Sauer CM, Faria CC, Cortés-Ciriano I, Flores I. The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients. Nat Commun 2024; 15:82. [PMID: 38167290 PMCID: PMC10762111 DOI: 10.1038/s41467-023-44287-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.
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Affiliation(s)
- Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Rita Cascão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Angela Afonso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carolin M Sauer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Claudia C Faria
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisboa, Portugal
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
| | - Ignacio Flores
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, 28029, Spain.
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, 28049, Spain.
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30
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Kim MK, Park H, Oh YL, Shin JH, Kim TH, Hahn SY. Association of Ultrasonography Features of Follicular Thyroid Carcinoma With Tumor Invasiveness and Prognosis Based on WHO Classification and TERT Promoter Mutation. Korean J Radiol 2024; 25:103-112. [PMID: 38184773 PMCID: PMC10788599 DOI: 10.3348/kjr.2023.0461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/20/2023] [Accepted: 11/02/2023] [Indexed: 01/08/2024] Open
Abstract
OBJECTIVE To investigate the association of ultrasound (US) features of follicular thyroid carcinoma (FTC) with tumor invasiveness and prognosis based on the World Health Organization (WHO) classification and telomerase reverse transcriptase (TERT) promoter mutations. MATERIALS AND METHODS This retrospective study included 54 surgically confirmed FTC patients with US images and TERT promoter mutations (41 females and 13 males; median age [interquartile range], 40 years [30-51 years]). The WHO classification consisted of minimally invasive (MI), encapsulated angioinvasive (EA), and widely invasive (WI) FTCs. Alternative classifications included Group 1 (MI-FTC and EA-FTC with wild type TERT), Group 2 (WI-FTC with wild type TERT), and Group 3 (EA-FTC and WI-FTC with mutant TERT). Each nodule was categorized according to the US patterns of the Korean Thyroid Imaging Reporting and Data System (K-TIRADS) and American College of Radiology-TIRADS (ACR-TIRADS). The Jonckheere-Terpstra and Cochran-Armitage tests were used for statistical analysis. RESULTS Among 54 patients, 29 (53.7%) had MI-FTC, 16 (29.6%) had EA-FTC, and nine (16.7%) had WI-FTC. In both the classifications, lobulation, irregular margins, and final assessment categories showed significant differences (all Ps ≤ 0.04). Furthermore, the incidences of lobulation, irregular margin, and high suspicion category tended to increase with increasing tumor invasiveness and worse prognosis (all Ps for trend ≤ 0.006). In the WHO groups, hypoechogenicity differed significantly among the groups (P = 0.01) and tended to increase in proportion as tumor invasiveness increased (P for trend = 0.02). In the alternative group, punctate echogenic foci were associated with prognosis (P = 0.03, P for trend = 0.03). CONCLUSION Increasing tumor invasiveness and worsening prognosis in FTC based on the WHO classification and TERT promoter mutation results were positively correlated with US features that indicate malignant probability according to both K-TIRADS and ACR-TIRADS.
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Affiliation(s)
- Myoung Kyoung Kim
- Department of Radiology and Center for Imaging Science, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyunju Park
- Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young Lyun Oh
- Department of Pathology, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jung Hee Shin
- Department of Radiology and Center for Imaging Science, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Tae Hyuk Kim
- Department of Medicine, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Soo Yeon Hahn
- Department of Radiology and Center for Imaging Science, Thyroid Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Di Nunno V, Aprile M, Bartolini S, Gatto L, Tosoni A, Ranieri L, De Biase D, Asioli S, Franceschi E. The Biological and Clinical Role of the Telomerase Reverse Transcriptase Gene in Glioblastoma: A Potential Therapeutic Target? Cells 2023; 13:44. [PMID: 38201248 PMCID: PMC10778438 DOI: 10.3390/cells13010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Glioblastoma IDH-wildtype represents the most lethal and frequent primary tumor of the central nervous system. Thanks to important scientific efforts, we can now investigate its deep genomic assessment, elucidating mutated genes and altered biological mechanisms in addition to its clinical aggressiveness. The telomerase reverse transcriptase gene (TERT) is the most frequently altered gene in solid tumors, including brain tumors and GBM IDH-wildtype. In particular, it can be observed in approximately 80-90% of GBM IDH-wildtype cases. Its clonal distribution on almost all cancer cells makes this gene an optimal target. However, the research of effective TERT inhibitors is complicated by several biological and clinical obstacles which can be only partially surmounted. Very recently, novel immunological approaches leading to TERT inhibition have been investigated, offering the potential to develop an effective target for this altered protein. Here, we perform a narrative review investigating the biological role of TERT alterations on glioblastoma and the principal obstacles associated with TERT inhibitions in this population. Moreover, we discuss possible combination treatment strategies to overcome these limitations.
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Affiliation(s)
- Vincenzo Di Nunno
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Marta Aprile
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Stefania Bartolini
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Lidia Gatto
- Department of Oncology, Azienda Unità Sanitaria Locale (AUSL) Bologna, 40139 Bologna, Italy
| | - Alicia Tosoni
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Lucia Ranieri
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Dario De Biase
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, 40126 Bologna, Italy
| | - Sofia Asioli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Surgical Pathology Section, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Enrico Franceschi
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
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Lin S, Shen R, Huang J, Liu Y, Li H, Xu Q. Identification of genomic-wide genetic links between cutaneous melanoma and obesity-related physical traits via cFDR. Genes Genomics 2023; 45:1549-1562. [PMID: 37768517 DOI: 10.1007/s13258-023-01446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Both epidemiological and clinical studies have suggested the comorbidity between cutaneous melanoma (CM) and obesity-related physical traits. However, it remains unclear about their shared genetic architecture. OBJECTIVE To determine the shared genetic architecture between CM and obesity-related physical traits through conditional false discovery rate (cFDR) analysis. METHOD Quantile-quantile plots were firstly built to assess the pleiotropic enrichment of shared single nucleotide polymorphisms between CM and each trait. Then, cFDR and conjunctional cFDR (ccFDR) were used to identify the shared risk loci between CM and each trait. Moreover, the functional evaluation of shared risk genes was carried out through analyses of expression quantitative trait loci (eQTL), Kyoto Encyclopedia of Genes and Genomes and gene ontology, respectively. Finally, single-cell sequence analysis was performed to locate the expression of eQTL-mapped genes in tissues. RESULTS Successive pleiotropic enrichment was found between CM and 5 obesity-related traits or height. 24 shared risk loci were identified between CM and 13 traits except appendicular lean mass using ccFDR analysis, with 17 novel and 4 validated loci. The functions of ccFDR-identified and eQTL-mapped genes were revealed to be mainly involved in cellular senescence, proliferation, meiotic nuclear division, cell cycle, and the metabolism of lipid, cholesterol and glucose. Single-cell sequence analysis showed that keratinocytes contribute to the occurrence and aggressiveness of CM through secreting paracrine cytokines. CONCLUSION Our findings demonstrate the significant genetic correlation between CM and obesity-related physical traits, which may provide a novel genetical basis for the pathogenesis and treatment of CM.
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Affiliation(s)
- Shen Lin
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Runnan Shen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jingqian Huang
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yanhan Liu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Hongpeng Li
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qingfang Xu
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
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Webersinke G, Burghofer J, Malli T, Rammer M, Jahn SW, Niendorf A, Tavassoli FA, Moinfar F. TERT Promoter Mutation c.-124C>T Commonly Occurs in Low-Grade Fibromatosis-like Metaplastic Breast Carcinoma. Arch Pathol Lab Med 2023; 147:1451-1457. [PMID: 36897999 DOI: 10.5858/arpa.2022-0159-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 03/12/2023]
Abstract
CONTEXT.— Low-grade fibromatosis-like metaplastic carcinoma (FLMC) is a very rare subtype of triple-negative metaplastic (spindle cell) breast carcinoma. It is characterized by the proliferation of spindle cells closely resembling fibromatosis, which represents a benign fibroblastic/myofibroblastic breast proliferation. Unlike most triple-negative and basal-like breast cancers, FLMC has a very low potential for metastases, but demonstrates frequent local recurrences. OBJECTIVE.— To genetically characterize FLMC. DESIGN.— To this end, we analyzed 7 cases by targeted next-generation sequencing for 315 cancer-related genes and performed comparative microarray copy number analysis in 5 of these cases. RESULTS.— All cases shared TERT alterations (6 patients with recurrent c.-124C>T TERT promoter mutation and 1 patient with copy number gain encompassing the TERT locus), had oncogenic PIK3CA/PIK3R1 mutations (activation of the PI3K/AKT/mTOR pathway), and lacked mutations in TP53. TERT was overexpressed in all FLMCs. CDKN2A/B loss or mutation was observed in 4 of 7 cases (57%). Furthermore, tumors displayed chromosomal stability, with only few copy number variations and a low tumor mutational burden. CONCLUSIONS— We conclude that FLMCs typically show the recurrent TERT promoter mutation c.-124C>T, activation of the PI3K/AKT/mTOR pathway, low genomic instability, and wild-type TP53. In conjunction with previous data of metaplastic (spindle cell) carcinoma with and without fibromatosis-like morphology, FLMC is most likely distinguished by TERT promoter mutation. Thus, our data support the notion of a distinct subgroup within low-grade metaplastic breast cancer with spindle cell morphology and associated TERT mutations.
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Affiliation(s)
- Gerald Webersinke
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Jonathan Burghofer
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Theodora Malli
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Melanie Rammer
- From the Laboratory for Molecular Genetic Diagnostics, Ordensklinikum Linz/Hospital of the Sisters of Charity, Linz, Austria (Webersinke, Burghofer, Malli, Rammer)
| | - Stephan Wenzel Jahn
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria (Jahn, Moinfar)
| | - Axel Niendorf
- Department of Pathology and Molecular Diagnostic, Hamburg-West, Hamburg, Germany (Niendorf)
| | - Fattaneh A Tavassoli
- Department of Pathology, Yale University School of Medicine, New Haven Connecticut (Tavassoli)
| | - Farid Moinfar
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria (Jahn, Moinfar)
- Department of Pathology and Molecular Pathology, Vinzenz Pathologieverbund Linz, Austria (Moinfar)
- The Vincent Academy of Pathology, Linz, Austria (Moinfar)
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Krueger KE. Neo-Darwinian Principles Exemplified in Cancer Genomics. Mol Cancer Res 2023; 21:1251-1260. [PMID: 37721477 DOI: 10.1158/1541-7786.mcr-23-0247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/13/2023] [Accepted: 09/14/2023] [Indexed: 09/19/2023]
Abstract
Within the last two decades, the advent of next-generation sequencing accompanied by single-cell technologies has enabled cancer researchers to study in detail mutations and other genetic aberrations that transpire during transformation of cells to a neoplastic state. This article covers the insights gained through these extensive studies where neo-Darwinian principles can be inferred to play roles throughout neoplastic transformation. The cells promoted during cancer development exhibit cancer hallmarks combined with the related enabling characteristics as outlined by Hanahan and Weinberg, analogous to natural selection and survival of the fittest. Selection of driver mutations that inactivate proteins encoded by tumor suppressor genes differs in profound ways from mutations that activate tumor promoter proteins. In most cases, the later stages of cancer development are characterized by sudden, extensive damage to chromosomes in a process that is not Darwinian in nature. Nevertheless, cells that survive these cataclysmic events remain subject to Darwinian selection promoting clones exhibiting the greatest rates of progression. Duplications of chromosomal segments containing oncogenes, deletions of segments harboring tumor suppressor genes, or distinctive chromosomal rearrangements are often found in cells progressing into later stages of cancer. In summary, the technological developments in genome sequencing since the start of the century have given us clear insights into genomic alterations promoting tumor progression where neo-Darwinian mechanisms of clonal selection can be inferred to play a primary role.
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Tan KT, Slevin MK, Leibowitz ML, Garrity-Janger M, Li H, Meyerson M. Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569101. [PMID: 38077026 PMCID: PMC10705422 DOI: 10.1101/2023.11.30.569101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Alterations in the structure and location of telomeres are key events in cancer genome evolution. However, previous genomic approaches, unable to span long telomeric repeat arrays, could not characterize the nature of these alterations. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeat arrays, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. Analysis of lung adenocarcinoma genome sequences identified somatic neotelomere and telomere-spanning fusion alterations. These results provide a framework for systematic study of telomeric repeat arrays in cancer genomes, that could serve as a model for understanding the somatic evolution of other repetitive genomic elements.
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Affiliation(s)
- Kar-Tong Tan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Michael K. Slevin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mitchell L. Leibowitz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Max Garrity-Janger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Lead contact
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Godoy PM, Oyedeji A, Mudd JL, Morikis VA, Zarov AP, Longmore GD, Fields RC, Kaufman CK. Functional analysis of recurrent CDC20 promoter variants in human melanoma. Commun Biol 2023; 6:1216. [PMID: 38030698 PMCID: PMC10686982 DOI: 10.1038/s42003-023-05526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Small nucleotide variants in non-coding regions of the genome can alter transcriptional regulation, leading to changes in gene expression which can activate oncogenic gene regulatory networks. Melanoma is heavily burdened by non-coding variants, representing over 99% of total genetic variation, including the well-characterized TERT promoter mutation. However, the compendium of regulatory non-coding variants is likely still functionally under-characterized. We developed a pipeline to identify hotspots, i.e. recurrently mutated regions, in melanoma containing putatively functional non-coding somatic variants that are located within predicted melanoma-specific regulatory regions. We identified hundreds of statistically significant hotspots, including the hotspot containing the TERT promoter variants, and focused on a hotspot in the promoter of CDC20. We found that variants in the promoter of CDC20, which putatively disrupt an ETS motif, lead to lower transcriptional activity in reporter assays. Using CRISPR/Cas9, we generated an indel in the CDC20 promoter in human A375 melanoma cell lines and observed decreased expression of CDC20, changes in migration capabilities, increased growth of xenografts, and an altered transcriptional state previously associated with a more proliferative and less migratory state. Overall, our analysis prioritized several recurrent functional non-coding variants that, through downregulation of CDC20, led to perturbation of key melanoma phenotypes.
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Affiliation(s)
- Paula M Godoy
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Abimbola Oyedeji
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Jacqueline L Mudd
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Vasilios A Morikis
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anna P Zarov
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gregory D Longmore
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
- Departments of Medicine (Oncology) and Cell Biology and Physiology and the ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ryan C Fields
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University in Saint Louis, St. Louis, MO, USA.
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Tan IL, Perez AR, Lew RJ, Sun X, Baldwin A, Zhu YK, Shah MM, Berger MS, Doudna JA, Fellmann C. Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis. Cell Rep 2023; 42:113339. [PMID: 37917583 PMCID: PMC10725516 DOI: 10.1016/j.celrep.2023.113339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 07/25/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Glioblastoma (GBM) is the most common lethal primary brain cancer in adults. Despite treatment regimens including surgical resection, radiotherapy, and temozolomide (TMZ) chemotherapy, growth of residual tumor leads to therapy resistance and death. At recurrence, a quarter to a third of all gliomas have hypermutated genomes, with mutational burdens orders of magnitude greater than in normal tissue. Here, we quantified the mutational landscape progression in a patient's primary and recurrent GBM, and we uncovered Cas9-targetable repeat elements. We show that CRISPR-mediated targeting of highly repetitive loci enables rapid elimination of GBM cells, an approach we term "genome shredding." Importantly, in the patient's recurrent GBM, we identified unique repeat sequences with TMZ mutational signature and demonstrated that their CRISPR targeting enables cancer-specific cell ablation. "Cancer shredding" leverages the non-coding genome and therapy-induced mutational signatures for targeted GBM cell depletion and provides an innovative paradigm to develop treatments for hypermutated glioma.
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Affiliation(s)
- I-Li Tan
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexendar R Perez
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94131, USA; Silico Therapeutics, San Francisco, CA 94131, USA
| | - Rachel J Lew
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Xiaoyu Sun
- Silico Therapeutics, San Francisco, CA 94131, USA
| | - Alisha Baldwin
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yong K Zhu
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mihir M Shah
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94131, USA
| | - Jennifer A Doudna
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christof Fellmann
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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Kouroukli AG, Rajaram N, Bashtrykov P, Kretzmer H, Siebert R, Jeltsch A, Bens S. Targeting oncogenic TERT promoter variants by allele-specific epigenome editing. Clin Epigenetics 2023; 15:183. [PMID: 37993930 PMCID: PMC10666398 DOI: 10.1186/s13148-023-01599-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Activation of dominant oncogenes by small or structural genomic alterations is a common driver mechanism in many cancers. Silencing of such dominantly activated oncogenic alleles, thus, is a promising strategy to treat cancer. Recently, allele-specific epigenome editing (ASEE) has been described as a means to reduce transcription of genes in an allele-specific manner. In cancer, specificity to an oncogenic allele can be reached by either targeting directly a pathogenic single-nucleotide variant or a polymorphic single-nucleotide variant linked to the oncogenic allele. To investigate the potential of ASEE in cancer, we here explored this approach by targeting variants at the TERT promoter region. The TERT promoter region has been described as one of the most frequently mutated non-coding cancer drivers. RESULTS Sequencing of the TERT promoter in cancer cell lines showed 53% (41/77) to contain at least one heterozygous sequence variant allowing allele distinction. We chose the hepatoblastoma cell line Hep-G2 and the lung cancer cell line A-549 for this proof-of-principle study, as they contained two different kinds of variants, namely the activating mutation C228T in the TERT core promoter and the common SNP rs2853669 in the THOR region, respectively. These variants were targeted in an allele-specific manner using sgRNA-guided dCas9-DNMT3A-3L complexes. In both cell lines, we successfully introduced DNA methylation specifically to the on-target allele of the TERT promoter with limited background methylation on the off-target allele or an off-target locus (VEGFA), respectively. We observed a maximum CpG methylation gain of 39% and 76% on the target allele when targeting the activating mutation and the common SNP, respectively. The epigenome editing translated into reduced TERT RNA expression in Hep-G2. CONCLUSIONS We applied an ASEE-mediated approach to silence TERT allele specifically. Our results show that the concept of dominant oncogene inactivation by allele-specific epigenome editing can be successfully translated into cancer models. This new strategy may have important advantages in comparison with existing therapeutic approaches, e.g., targeting telomerase, especially with regard to reducing adverse side effects.
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Affiliation(s)
- Alexandra G Kouroukli
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Nivethika Rajaram
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Helene Kretzmer
- Computational Genomics, Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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Koleilat A, Kumar V, Al Hmada Y, Milosevic D, Zheng G, Lopes MB, Ida CM. Concurrent TERT promoter C228T and C250T mutations in diffuse gliomas: Rare occurrence of intratumoral heterogeneity. J Neuropathol Exp Neurol 2023; 82:1044-1047. [PMID: 37812785 DOI: 10.1093/jnen/nlad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
Affiliation(s)
- Alaa Koleilat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Vijay Kumar
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Youssef Al Hmada
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Dragana Milosevic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Gang Zheng
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Maria Beatriz Lopes
- Department of Pathology, University of Virginia Health, Charlottesville, VA, USA
| | - Cristiane M Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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Wang Y, Armendariz D, Wang L, Zhao H, Xie S, Hon GC. Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567880. [PMID: 38045327 PMCID: PMC10690208 DOI: 10.1101/2023.11.20.567880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic studies have associated thousands of enhancers with breast cancer. However, the vast majority have not been functionally characterized. Thus, it remains unclear how variant-associated enhancers contribute to cancer. Here, we perform single-cell CRISPRi screens of 3,512 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of >500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of variant-associated enhancers disrupts breast cancer gene programs. We observe variant-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple variant-associated enhancers indirectly regulate TP53. Comparative studies illustrate sub-type specific functions between enhancers in ER+ and ER- cells. Finally, we developed the pySpade package to facilitate analysis of single-cell enhancer screens. Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.
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Affiliation(s)
- Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | | | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Huan Zhao
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Current address: Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Tora R, Welch J, Sun J, Agarwal SK, Bell DA, Merino M, Weinstein LS, Simonds WF, Jha S. Phenotypic Profiling and Molecular Mechanisms in Hyperparathyroidism-jaw Tumor Syndrome. J Clin Endocrinol Metab 2023; 108:3165-3177. [PMID: 37339334 PMCID: PMC10655532 DOI: 10.1210/clinem/dgad368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 06/22/2023]
Abstract
CONTEXT Hyperparathyroidism-jaw tumor (HPT-JT) syndrome is a heritable form of primary hyperparathyroidism caused by germline inactivating mutations in CDC73 encoding parafibromin and is associated with an increased risk of parathyroid cancer. There is little evidence to guide the management of patients with the disease. OBJECTIVE (1) Characterize the natural history of HPT-JT, (2) correlate genotype and histology of parathyroid tumors with parafibromin immunostaining, (3) understand molecular changes downstream to CDC73 loss. DESIGN Retrospective study of patients with HPT-JT syndrome (genetically confirmed or affected first-degree relatives). Independent review of uterine tumor from 2 patients and staining for parafibromin on parathyroid tumors from 19 patients (13 adenomas, 6 carcinomas) was performed. RNA-sequencing was performed in 21 parathyroid samples (8 HPT-JT-related adenomas, 6 HPT-JT-related carcinomas, and 7 sporadic carcinomas with wild-type CDC73). RESULTS We identified 68 patients from 29 kindreds with HPT-JT with median age at last follow-up of 39 [interquartile range, 29-53] years. A total of 55/68 (81%) developed primary hyperparathyroidism; 17/55 (31%) had parathyroid carcinoma. Twelve of 32 (38%) females developed uterine tumors. Of the 11 patients who had surgical resection for uterine tumors, 12/24 (50%) tumors were rare mixed epithelial mesenchymal polypoid lesions. Four of 68 patients (6%) developed solid kidney tumors; 3/4 had a CDC73 variant at p.M1 residue. Parafibromin staining of parathyroid tumors did not correlate with tumor histology or genotype. RNA-sequencing showed a significant association of HPT-JT-related parathyroid tumors with transmembrane receptor protein tyrosine kinase signaling pathway, mesodermal commitment pathway, and cell-cell adhesion. CONCLUSIONS Multiple, recurrent atypical adenomyomatous uterine polyps appear to be enriched in women with HPT-JT and appear characteristic of the disease. Patients with CDC73 variants at p.M1 residue appear predisposed to kidney tumors. CLINICAL TRIAL NUMBER NCT04969926.
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Affiliation(s)
- Rana Tora
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Welch
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jian Sun
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sunita K Agarwal
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debra A Bell
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Maria Merino
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lee S Weinstein
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - William F Simonds
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Smita Jha
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Tornesello ML, Cerasuolo A, Starita N, Amiranda S, Bonelli P, Tuccillo FM, Buonaguro FM, Buonaguro L, Tornesello AL. Reactivation of telomerase reverse transcriptase expression in cancer: the role of TERT promoter mutations. Front Cell Dev Biol 2023; 11:1286683. [PMID: 38033865 PMCID: PMC10684755 DOI: 10.3389/fcell.2023.1286683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Telomerase activity and telomere elongation are essential conditions for the unlimited proliferation of neoplastic cells. Point mutations in the core promoter region of the telomerase reverse transcriptase (TERT) gene have been found to occur at high frequencies in several tumour types and considered a primary cause of telomerase reactivation in cancer cells. These mutations promote TERT gene expression by multiple mechanisms, including the generation of novel binding sites for nuclear transcription factors, displacement of negative regulators from DNA G-quadruplexes, recruitment of epigenetic activators and disruption of long-range interactions between TERT locus and telomeres. Furthermore, TERT promoter mutations cooperate with TPP1 promoter nucleotide changes to lengthen telomeres and with mutated BRAF and FGFR3 oncoproteins to enhance oncogenic signalling in cancer cells. TERT promoter mutations have been recognized as an early marker of tumour development or a major indicator of poor outcome and reduced patients survival in several cancer types. In this review, we summarize recent findings on the role of TERT promoter mutations, telomerase expression and telomeres elongation in cancer development, their clinical significance and therapeutic opportunities.
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Affiliation(s)
- Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Andrea Cerasuolo
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Noemy Starita
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Sara Amiranda
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Patrizia Bonelli
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Franca Maria Tuccillo
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Franco M. Buonaguro
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Luigi Buonaguro
- Innovative Immunological Models Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
| | - Anna Lucia Tornesello
- Innovative Immunological Models Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy
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43
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Heo J, Lee S, Park J, Yang H, Park H, Ki CS, Oh YL, Kim HI, Kim SW, Chung JH, Kim K, Kim TH. Age-associated mortality is partially mediated by TERT promoter mutation status in differentiated thyroid carcinoma. PLoS One 2023; 18:e0294145. [PMID: 37948420 PMCID: PMC10637683 DOI: 10.1371/journal.pone.0294145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Age at diagnosis (AAD) and telomerase reverse transcriptase (TERT) promoter mutations are prognostic factors in differentiated thyroid carcinoma (DTC), and the prevalence of the mutations increases with AAD. Considering this correlation, we investigated whether an interaction between AAD and the mutations is present and whether the mutation mediates the effect of AAD on the mortality rate in DTC. METHODS The study included 393 patients with DTC who were followed-up after thyroidectomy at a single medical center in Korea from 1994 to 2004. Multivariable Cox regression was used to investigate the interaction of AAD and TERT promoter mutation. Mediation analysis was conducted using a regression-based causal mediation model. RESULTS The age-associated mortality rate increased progressively in all DTC patients and wild-type TERT group (WT-TERT) with a linear trend (p < 0.001) contrary to mutant TERT group (M-TERT) (p = 0.301). Kaplan-Meier curves declined progressively with increasing AAD in the entire group, but the change was without significance in M-TERT. The effect of AAD on mortality was not significant (adjusted HR: 1.07, 95% CI 0.38-3.05) in M-TERT. An interaction between AAD and TERT promoter mutation (p = 0.005) was found in a multivariable Cox regression. TERT promoter mutations mediated the effect of AAD on the mortality rate by 36% in DTC in a mediation analysis. CONCLUSIONS Considering the mediation of TERT promoter mutation on the effect of AAD on mortality, inclusion of TERT promoter mutation in a stage classification to achieve further individualized prediction in DTC is necessary.
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Affiliation(s)
- Jung Heo
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang-si, Gyeonggi-do, Korea
| | - Sungjoo Lee
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Jun Park
- Division of Endocrinology, Department of Medicine, Sahmyook Medical Center, Seoul, Korea
| | - Heera Yang
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyunju Park
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam-si, Gyeonggi-do, Korea
| | | | - Young Lyun Oh
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye In Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon-si, Gyeongsangnam-do, Korea
| | - Sun Wook Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hoon Chung
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyunga Kim
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
- Biomedical Statistics Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
- Department of Data Convergence and Future Medicine, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae Hyuk Kim
- Division of Endocrinology and Metabolism, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Chua BH, Zaal Anuar N, Ferry L, Domrane C, Wittek A, Mukundan VT, Jha S, Butter F, Tenen DG, Defossez PA, Kappei D. E4F1 and ZNF148 are transcriptional activators of the -57A > C and wild-type TERT promoter. Genome Res 2023; 33:gr.277724.123. [PMID: 37918959 PMCID: PMC10760450 DOI: 10.1101/gr.277724.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Point mutations within the TERT promoter are the most recurrent somatic noncoding mutations identified across different cancer types, including glioblastoma, melanoma, hepatocellular carcinoma, and bladder cancer. They are most abundant at -146C > T and -124C > T, and rarer at -57A > C, with the latter originally described as a familial case, but subsequently shown also to occur somatically. All three mutations create de novo E26-specific (ETS) binding sites and result in activation of the TERT gene, allowing cancer cells to achieve replicative immortality. Here, we used a systematic proteomics screen to identify transcription factors preferentially binding to the -146C > T, -124C > T, and -57A > C mutations. Although we confirmed binding of multiple ETS factors to the mutant -146C > T and -124C > T sequences, we identified E4F1 as a -57A > C-specific binder and ZNF148 as a TERT wild-type (WT) promoter binder that showed reduced interaction with the -124C > T allele. Both proteins are activating transcription factors that bind specifically to the -57A > C and WT (at position 124) TERT promoter sequence in corresponding cell lines, and up-regulate TERT transcription and telomerase activity. Our work describes new regulators of TERT gene expression with possible roles in cancer.
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Affiliation(s)
- Boon Haow Chua
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore
| | - Nurkaiyisah Zaal Anuar
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Laure Ferry
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Cecilia Domrane
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Anna Wittek
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Vineeth T Mukundan
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
- Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institute, 17493 Greifswald, Germany
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 117599 Singapore;
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596 Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 117599 Singapore
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45
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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46
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Abstract
Background: Very little was known about the molecular pathogenesis of thyroid cancer until the late 1980s. As part of the Centennial celebration of the American Thyroid Association, we review the historical discoveries that contributed to our current understanding of the genetic underpinnings of thyroid cancer. Summary: The pace of discovery was heavily dependent on scientific breakthroughs in nucleic acid sequencing technology, cancer biology, thyroid development, thyroid cell signaling, and growth regulation. Accordingly, we attempt to link the primary observations on thyroid cancer molecular genetics with the methodological and scientific advances that made them possible. Conclusions: The major genetic drivers of the common forms of thyroid cancer are now quite well established and contribute to a significant extent to how we diagnose and treat the disease. However, many challenges remain. Future work will need to unravel the complexity of thyroid cancer ecosystems, which is likely to be a major determinant of their biological behavior and on how they respond to therapy.
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Affiliation(s)
- James A. Fagin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yuri E. Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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47
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Todeschi J, Dannhoff G, Chibbaro S, Segbedji F, Spatola G, Mallereau CH, Noel G, Schott R, Lhermitte B, Cebula H, Ganau M. Second Cancer Affecting the Central Nervous System: Systematic Literature Review Exploring the Link Between Malignant Melanoma and Glioblastoma. World Neurosurg 2023; 179:178-184. [PMID: 37625631 DOI: 10.1016/j.wneu.2023.08.073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is a malignant primary brain cancer, among the most devastating and lethal diseases of the central nervous system. Similarly, malignant melanoma (MM) is responsible for most skin cancer-related deaths. A link between those 2 aggressive cancers has not yet been established. We present here a systematic review of the literature and an exemplificative case. METHODS A systematic review of the literature was conducted to assess possible commonalities between MM and GBM. An exemplificative surgical vignette of a 73-year-old patient with the occurrence of a frontobasal GBM after surgical removal of a metastasis of MM in the same location was then detailed. RESULTS Fifteen studies published in the English international literature support a link between MM and GBM, both based on epidemiologic and pathophysiologic/genetic aspects. This theory is reinforced by our surgical vignette of a collision tumor with the occurrence of both tumors in the same location several years apart. CONCLUSIONS The evidence reported in the literature, as well as our surgical vignette, support a likely link between the pathogenesis of GBM and MM.
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Affiliation(s)
- Julien Todeschi
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Guillaume Dannhoff
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France.
| | - Salvatore Chibbaro
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Felix Segbedji
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Giorgio Spatola
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | | | - Georges Noel
- Department of Radiotherapy, Strasbourg University Hospital, Strasbourg, France
| | - Roland Schott
- Department of Neuro-oncology, Strasbourg University Hospital, Strasbourg, France
| | - Benoit Lhermitte
- Histopathology Unit, Strasbourg University Hospital, Strasbourg, France
| | - Hélène Cebula
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
| | - Mario Ganau
- Department of Neurosurgery, Strasbourg University Hospital, Strasbourg, France
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Landa I, Thornton CEM, Xu B, Haase J, Krishnamoorthy GP, Hao J, Knauf JA, Herbert ZT, Martínez P, Blasco MA, Ghossein R, Fagin JA. Telomerase Upregulation Induces Progression of Mouse BrafV600E-Driven Thyroid Cancers and Triggers Nontelomeric Effects. Mol Cancer Res 2023; 21:1163-1175. [PMID: 37478162 DOI: 10.1158/1541-7786.mcr-23-0144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Mutations in the promoter of the telomerase reverse transcriptase (TERT) gene are the paradigm of a cross-cancer alteration in a noncoding region. TERT promoter mutations (TPM) are biomarkers of poor prognosis in cancer, including thyroid tumors. TPMs enhance TERT transcription, which is otherwise silenced in adult tissues, thus reactivating a bona fide oncoprotein. To study TERT deregulation and its downstream consequences, we generated a Tert mutant promoter mouse model via CRISPR/Cas9 engineering of the murine equivalent locus (Tert-123C>T) and crossed it with thyroid-specific BrafV600E-mutant mice. We also employed an alternative model of Tert overexpression (K5-Tert). Whereas all BrafV600E animals developed well-differentiated papillary thyroid tumors, 29% and 36% of BrafV600E+Tert-123C>T and BrafV600E+K5-Tert mice progressed to poorly differentiated cancers at week 20, respectively. Tert-upregulated tumors showed increased mitosis and necrosis in areas of solid growth, and older animals displayed anaplastic-like features, that is, spindle cells and macrophage infiltration. Murine TPM increased Tert transcription in vitro and in vivo, but temporal and intratumoral heterogeneity was observed. RNA-sequencing of thyroid tumor cells showed that processes other than the canonical Tert-mediated telomere maintenance role operate in these specimens. Pathway analysis showed that MAPK and PI3K/AKT signaling, as well as processes not previously associated with this tumor etiology, involving cytokine, and chemokine signaling, were overactivated. These models constitute useful preclinical tools to understand the cell-autonomous and microenvironment-related consequences of Tert-mediated progression in advanced thyroid cancers and other aggressive tumors carrying TPMs. IMPLICATIONS Telomerase-driven cancer progression activates pathways that can be dissected and perhaps therapeutically exploited.
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Affiliation(s)
- Iñigo Landa
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Caitlin E M Thornton
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob Haase
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Gnana P Krishnamoorthy
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jingzhu Hao
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Jeffrey A Knauf
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paula Martínez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - María A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Wang Z, Luo M, Liang Q, Zhao K, Hu Y, Wang W, Feng X, Hu B, Teng J, You T, Li R, Bao Z, Pan W, Yang T, Zhang C, Li T, Dong X, Yi X, Liu B, Zhao L, Li M, Chen K, Song W, Yang J, Li MJ. Landscape of enhancer disruption and functional screen in melanoma cells. Genome Biol 2023; 24:248. [PMID: 37904237 PMCID: PMC10614365 DOI: 10.1186/s13059-023-03087-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/12/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those in enhancers, can shape tumor evolution, thereby emphasizing the importance in systematically deciphering enhancer disruptions in melanoma. RESULTS Here, we leveraged 297 melanoma whole-genome sequencing samples to prioritize highly recurrent regions. By performing a genome-scale CRISPR interference (CRISPRi) screen on highly recurrent region-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers reveal many known and hidden mechanisms underlying melanoma growth. Utilizing extensive functional validation experiments, we demonstrate that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A, and another distal enhancer is able to sustain PTEN tumor-suppressive potential via long-range interactions. CONCLUSIONS Our study establishes a catalogue of crucial enhancers and their target genes in melanoma growth and progression, and illuminates the identification of novel mechanisms of dysregulation for melanoma driver genes and new therapeutic targeting strategies.
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Affiliation(s)
- Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Menghan Luo
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Scientific Research Center, Wenzhou Medical University, Wenzhou, China
| | - Ke Zhao
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuelin Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bolang Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianjin Teng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianyi You
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ran Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhengkai Bao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wenhao Pan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Tielong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chao Zhang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ting Li
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Li Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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Di Biasi L, De Marco F, Auriemma Citarella A, Castrillón-Santana M, Barra P, Tortora G. Refactoring and performance analysis of the main CNN architectures: using false negative rate minimization to solve the clinical images melanoma detection problem. BMC Bioinformatics 2023; 24:386. [PMID: 37821815 PMCID: PMC10568761 DOI: 10.1186/s12859-023-05516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Melanoma is one of the deadliest tumors in the world. Early detection is critical for first-line therapy in this tumor pathology and it remains challenging due to the need for histological analysis to ensure correctness in diagnosis. Therefore, multiple computer-aided diagnosis (CAD) systems working on melanoma images were proposed to mitigate the need of a biopsy. However, although the high global accuracy is declared in literature results, the CAD systems for the health fields must focus on the lowest false negative rate (FNR) possible to qualify as a diagnosis support system. The final goal must be to avoid classification type 2 errors to prevent life-threatening situations. Another goal could be to create an easy-to-use system for both physicians and patients. RESULTS To achieve the minimization of type 2 error, we performed a wide exploratory analysis of the principal convolutional neural network (CNN) architectures published for the multiple image classification problem; we adapted these networks to the melanoma clinical image binary classification problem (MCIBCP). We collected and analyzed performance data to identify the best CNN architecture, in terms of FNR, usable for solving the MCIBCP problem. Then, to provide a starting point for an easy-to-use CAD system, we used a clinical image dataset (MED-NODE) because clinical images are easier to access: they can be taken by a smartphone or other hand-size devices. Despite the lower resolution than dermoscopic images, the results in the literature would suggest that it would be possible to achieve high classification performance by using clinical images. In this work, we used MED-NODE, which consists of 170 clinical images (70 images of melanoma and 100 images of naevi). We optimized the following CNNs for the MCIBCP problem: Alexnet, DenseNet, GoogleNet Inception V3, GoogleNet, MobileNet, ShuffleNet, SqueezeNet, and VGG16. CONCLUSIONS The results suggest that a CNN built on the VGG or AlexNet structure can ensure the lowest FNR (0.07) and (0.13), respectively. In both cases, discrete global performance is ensured: 73% (accuracy), 82% (sensitivity) and 59% (specificity) for VGG; 89% (accuracy), 87% (sensitivity) and 90% (specificity) for AlexNet.
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Affiliation(s)
- Luigi Di Biasi
- Department of Computer Science, University of Salerno, Fisciano, Italy.
| | - Fabiola De Marco
- Department of Computer Science, University of Salerno, Fisciano, Italy
| | | | | | - Paola Barra
- Department of Science and Technology, Parthenope University of Naples, Naples, Italy
| | - Genoveffa Tortora
- Department of Computer Science, University of Salerno, Fisciano, Italy
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