1
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Wang JZ, Landry AP, Raleigh DR, Sahm F, Walsh KM, Goldbrunner R, Yefet LS, Tonn JC, Gui C, Ostrom QT, Barnholtz-Sloan J, Perry A, Ellenbogen Y, Hanemann CO, Jungwirth G, Jenkinson MD, Tabatabai G, Mathiesen TI, McDermott MW, Tatagiba M, la Fougère C, Maas SLN, Galldiks N, Albert NL, Brastianos PK, Ehret F, Minniti G, Lamszus K, Ricklefs FL, Schittenhelm J, Drummond KJ, Dunn IF, Pathmanaban ON, Cohen-Gadol AA, Sulman EP, Tabouret E, Le Rhun E, Mawrin C, Moliterno J, Weller M, Bi WL, Gao A, Yip S, Niyazi M, Aldape K, Wen PY, Short S, Preusser M, Nassiri F, Zadeh G. Meningioma: International Consortium on Meningiomas consensus review on scientific advances and treatment paradigms for clinicians, researchers, and patients. Neuro Oncol 2024; 26:1742-1780. [PMID: 38695575 DOI: 10.1093/neuonc/noae082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024] Open
Abstract
Meningiomas are the most common primary intracranial tumors in adults and are increasing in incidence due to the aging population and increased access to neuroimaging. While most exhibit nonmalignant behavior, a subset of meningiomas are biologically aggressive and are associated with treatment resistance, resulting in significant neurologic morbidity and even mortality. In recent years, meaningful advances in our understanding of the biology of these tumors have led to the incorporation of molecular biomarkers into their grading and prognostication. However, unlike other central nervous system (CNS) tumors, a unified molecular taxonomy for meningiomas has not yet been established and remains an overarching goal of the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy-Not Official World Health Organization (cIMPACT-NOW) working group. Additionally, clinical equipoise still remains on how specific meningioma cases and patient populations should be optimally managed. To address these existing gaps, members of the International Consortium on Meningiomas including field-leading experts, have prepared this comprehensive consensus narrative review directed toward clinicians, researchers, and patients. Included in this manuscript are detailed overviews of proposed molecular classifications, novel biomarkers, contemporary treatment strategies, trials on systemic therapies, health-related quality-of-life studies, and management strategies for unique meningioma patient populations. In each section, we discuss the current state of knowledge as well as ongoing clinical and research challenges to road map future directions for further investigation.
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Affiliation(s)
- Justin Z Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Alexander P Landry
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - David R Raleigh
- Department of Radiation Oncology, Neurological Surgery, and Pathology, University of California San Francisco, San Francisco, California, USA
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg and German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Roland Goldbrunner
- Center of Neurosurgery, Department of General Neurosurgery, University of Cologne, Cologne, Germany
| | - Leeor S Yefet
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Jörg C Tonn
- Department of Neurosurgery, University Hospital Munich LMU, Munich, Germany
| | - Chloe Gui
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Quinn T Ostrom
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Central Brain Tumor Registry of the United States, Hinsdale, Illinois, USA
- Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Jill Barnholtz-Sloan
- Center for Biomedical Informatics & Information Technology (CBIIT), National Cancer Institute, Bethesda, Maryland, USA
- Trans Divisional Research Program (TDRP), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Bethesda, Maryland, USA
- Central Brain Tumor Registry of the United States, Hinsdale, Illinois, USA
| | - Arie Perry
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Yosef Ellenbogen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - C Oliver Hanemann
- Peninsula Schools of Medicine, University of Plymouth University, Plymouth, UK
| | - Gerhard Jungwirth
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University, Heidelberg, Germany
| | - Michael D Jenkinson
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, UK
- Institute of Translational Medicine, University of Liverpool, UK
| | - Ghazaleh Tabatabai
- Department of Neurology and Interdisciplinary Neuro-Oncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Tübingen, Germany
- Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies," Eberhard Karls University Tübingen, Tübingen, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Tübingen, Germany
| | - Tiit I Mathiesen
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Michael W McDermott
- Division of Neuroscience, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
- Miami Neuroscience Institute, Baptist Health of South Florida, Miami, Florida, USA
| | - Marcos Tatagiba
- Department of Neurosurgery, University of Tübingen, Tübingen, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Tübingen, Germany
| | - Christian la Fougère
- Nuclear Medicine and Clinical Molecular Imaging, University Hospital Tübingen, Germany
- Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies," Eberhard Karls University Tübingen, Tübingen, Germany
| | - Sybren L N Maas
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Norbert Galldiks
- Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Institute of Neuroscience and Medicine (IMN-3), Research Center Juelich, Juelich, Germany
| | - Nathalie L Albert
- Department of Nuclear Medicine, Ludwig Maximilians-University of Munich, Munich, Germany
| | - Priscilla K Brastianos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Felix Ehret
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Giuseppe Minniti
- Department of Radiological Sciences, Oncology and Anatomical Pathology, Sapienza University of Rome, Rome, Italy
| | - Katrin Lamszus
- Laboratory for Brain Tumor Biology, University Hospital Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, University Hospital Tübingen, Eberhard-Karls-University Tübingen, Tübingen, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Tübingen, Germany
| | - Katharine J Drummond
- Department of Neurosurgery, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian F Dunn
- Department of Neurosurgery, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Omar N Pathmanaban
- Division of Neuroscience and Experimental Psychology, Manchester Centre for Clinical Neurosciences, Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, UK
| | - Aaron A Cohen-Gadol
- Department of Neurological Surgery, Indiana University, Indianapolis, Indiana, USA
| | - Erik P Sulman
- Department of Radiation Oncology, NYU Grossman School of Medicine, New York, New York, USA
| | - Emeline Tabouret
- CNRS, INP, Inst Neurophysiopathol, Aix-Marseille University, Marseille, France
| | - Emelie Le Rhun
- Department of Neurology & Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Christian Mawrin
- Department of Neuropathology, University Hospital Magdeburg, Magdeburg, Germany
| | - Jennifer Moliterno
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew Gao
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Radiation Oncology, University Hospital, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
| | - Maximilian Niyazi
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Tübingen, Germany
| | - Kenneth Aldape
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Patrick Y Wen
- Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Susan Short
- Leeds Institute of Medical Research, St James's University Hospital, Leeds, UK
| | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Farshad Nassiri
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
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2
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Zhang Y, Ostrowski SM, Fisher DE. Nevi and Melanoma. Hematol Oncol Clin North Am 2024; 38:939-952. [PMID: 38880666 PMCID: PMC11368644 DOI: 10.1016/j.hoc.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Cutaneous melanoma is an aggressive form of skin cancer derived from skin melanocytes and is associated with significant morbidity and mortality. A significant fraction of melanomas are associated with precursor lesions, benign clonal proliferations of melanocytes called nevi. Nevi can be either congenital or acquired later in life. Identical oncogenic driver mutations are found in benign nevi and melanoma. While much progress has been made in our understanding of nevus formation and the molecular steps required for transformation of nevi into melanoma, the clinical diagnosis of benign versus malignant lesions remains challenging.
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Affiliation(s)
- Yifan Zhang
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA; Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stephen M Ostrowski
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA; Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David E Fisher
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA; Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02114, USA.
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3
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Ramachandran D, Mao Q, Liao D, Kamal M, Schürmann P, Eisenblätter R, Geffers R, Balint B, Lecompte L, Servant N, Chérif LL, Lamy C, Baulande S, Legoix P, Le Tourneau C, Latouche A, Hillemanns P, Scholl S, Dörk T. Methylation, Gene Expression, and Risk Genotypes at the TERT-CLPTM1L Locus in Cervical Cancer. Mol Carcinog 2024. [PMID: 39352309 DOI: 10.1002/mc.23822] [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: 05/22/2024] [Revised: 08/30/2024] [Accepted: 09/11/2024] [Indexed: 10/03/2024]
Abstract
The reverse transcriptase subunit of telomerase, TERT, is frequently activated in high-grade dysplasia and invasive cancers of the uterine cervix. Telomerase activation through hypomethylation of the TERT promoter holds promise as a biomarker for cervical cancer progression, however, specific CpG sites involved in cervical cancer risk remain to be fully defined. A recent genome-wide association study on cervical cancer identified genetic polymorphisms at 5p13.33 (close to TERT-CLPTM1L) but the underlying mechanisms are undetermined. We investigated 529 CpG sites within the TERT promoter region and 3 CpG islands nearby, and 21 CpG sites within CLPTM1L in 190 bisulfite-converted cervical tumor DNA samples from BioRAIDs (NCT02428842). We identified eight CpG sites within TERT intron 2 where methylation was significantly associated with the genotypes of cervical cancer risk variants rs27070 and rs459961 in cervical tumors after multiple testing correction (p < 9.4 × 10E-5). Hypermethylation at chr5:1289663 correlated with decreased TERT mRNA levels. In an independent series of 188 normal or dysplastic cervical tissues, rare alleles of rs27070 and rs459961 were associated with low basal CLPTM1L levels and with the absence of TERT mRNA in HPV-negative samples, consistent with their proposed role as protective variants for cervical cancer. HPV infection was associated with increased CLPTM1L and TERT levels. Collectively, our results provide a link between cervical cancer risk variants, methylation, and gene expression and implicate both TERT and CLPTM1L as genes modulated by genomic background and HPV infection during cervical cancer development.
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Affiliation(s)
| | - Qianqian Mao
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Dandan Liao
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - Peter Schürmann
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | | | - Robert Geffers
- Genome Analytics, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Lolita Lecompte
- Institut Curie, INSERM U900, Mines Paris Tech, Paris/Saint-Cloud, France
| | - Nicolas Servant
- Institut Curie, INSERM U900, Mines Paris Tech, Paris/Saint-Cloud, France
| | - Linda Larbi Chérif
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - Constance Lamy
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - Sylvain Baulande
- Institut Curie, ICGex Next-Generation Sequencing platform, Paris, France
| | - Patricia Legoix
- Institut Curie, ICGex Next-Generation Sequencing platform, Paris, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
- Institut Curie, INSERM U900, Mines Paris Tech, Paris/Saint-Cloud, France
| | - Aurélien Latouche
- Institut Curie, INSERM U900, Mines Paris Tech, Paris/Saint-Cloud, France
- Conservatoire National des Arts et Métiers, Paris, France
| | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Suzy Scholl
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris and Saint-Cloud, France
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
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4
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Beird HC, Cloutier JM, Gokgoz N, Eeles C, Griffin AM, Ingram DR, Wani KM, Segura RL, Cohen L, Ho C, Wunder JS, Andrulis IL, Futreal PA, Haibe-Kains B, Lazar AJ, Wang WL, Przybyl J, Demicco EG. Epigenomic and transcriptomic profiling of solitary fibrous tumors identifies site-specific patterns and candidate genes regulated by DNA methylation. J Transl Med 2024:102146. [PMID: 39357799 DOI: 10.1016/j.labinv.2024.102146] [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: 07/15/2024] [Revised: 09/11/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
Solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm which can arise at any anatomic site and is characterized by recurrent NAB2::STAT6 fusions and metastatic progression in 10-30%. The cell of origin has not been identified. Despite some progress in understanding the contribution of heterogeneous fusion types and secondary mutations to SFT biology, epigenetic alterations in extrameningeal SFT remain largely unexplored, and most sarcoma research to date has focused on the use of methylation profiling for tumor classification. We interrogated genome-wide DNA methylation in 79 SFTs to identify informative epigenetic changes. RNA-seq data from targeted panels and data from the Cancer Genome Atlas (TCGA) were used for orthogonal validation of selected findings. In unsupervised clustering analysis, the top 500 most variable CpGs segregated SFTs by primary anatomic site. Differentially methylated genes (DMGs) associated with primary SFT site included EGFR, TBX15, multiple HOX genes and their cofactors EBF1, EBF3, and PBX1, as well as RUNX1 and MEIS1. Of the 20 DMGs that were interrogated on the RNA-seq panel, twelve were significantly differentially expressed according to site. However, with the exception of TBX15, most of these also showed differential expression according to NAB2::STAT6 fusion type, suggesting that the fusion oncogene contributes to transcriptional regulation of these genes. Transcriptomic data confirmed an inverse correlation between gene methylation and the expression of TBX15 in both SFT and TCGA sarcomas. TBX15 also showed differential mRNA expression and 5' UTR methylation between tumors located in different anatomic sites in TCGA data. In all analyses, TBX15 methylation and mRNA expression retained the strongest association with tissue of origin in SFT and other sarcomas, suggesting a possible marker to distinguish metastatic tumors from new primaries without genomic profiling. Epigenetic signatures may further help to identify SFT progenitor cells at different anatomic sites.
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Affiliation(s)
- Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey M Cloutier
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital Toronto, ON, Canada
| | - Christopher Eeles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Anthony M Griffin
- University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Canada
| | - Davis R Ingram
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khalida M Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano Segura
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luca Cohen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carl Ho
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jay S Wunder
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital Toronto, ON, Canada; University of Toronto Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital Toronto, ON, Canada; Department of Molecular Genetics Canada & Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Medical Biophysics, University of Toronto, & Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joanna Przybyl
- Department of Surgery, McGill University & Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Elizabeth G Demicco
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital & Department of Laboratory Medicine and pathobiology, University of Toronto, Toronto, ON, Canada.
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5
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Woo BJ, Moussavi-Baygi R, Karner H, Karimzadeh M, Yousefi H, Lee S, Garcia K, Joshi T, Yin K, Navickas A, Gilbert LA, Wang B, Asgharian H, Feng FY, Goodarzi H. Integrative identification of non-coding regulatory regions driving metastatic prostate cancer. Cell Rep 2024; 43:114764. [PMID: 39276353 DOI: 10.1016/j.celrep.2024.114764] [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: 06/13/2023] [Revised: 07/08/2024] [Accepted: 08/29/2024] [Indexed: 09/17/2024] Open
Abstract
Large-scale sequencing efforts have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of variants occur within non-coding genomic regions. We designed an integrative computational and experimental framework to identify recurrently mutated non-coding regulatory regions that drive tumor progression. Applying this framework to sequencing data from a large prostate cancer patient cohort revealed a large set of candidate drivers. We used (1) in silico analyses, (2) massively parallel reporter assays, and (3) in vivo CRISPR interference screens to systematically validate metastatic castration-resistant prostate cancer (mCRPC) drivers. One identified enhancer region, GH22I030351, acts on a bidirectional promoter to simultaneously modulate expression of the U2-associated splicing factor SF3A1 and chromosomal protein CCDC157. SF3A1 and CCDC157 promote tumor growth in vivo. We nominated a number of transcription factors, notably SOX6, to regulate expression of SF3A1 and CCDC157. Our integrative approach enables the systematic detection of non-coding regulatory regions that drive human cancers.
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Affiliation(s)
- Brian J Woo
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Arc Institute, Palo Alto, CA 94305, USA
| | - Ruhollah Moussavi-Baygi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Heather Karner
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Arc Institute, Palo Alto, CA 94305, USA
| | - Mehran Karimzadeh
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Vector Institute, Toronto, ON, Canada; Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada; Arc Institute, Palo Alto, CA 94305, USA
| | - Hassan Yousefi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Arc Institute, Palo Alto, CA 94305, USA
| | - Sean Lee
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Arc Institute, Palo Alto, CA 94305, USA
| | - Kristle Garcia
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tanvi Joshi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Keyi Yin
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Albertas Navickas
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Arc Institute, Palo Alto, CA 94305, USA
| | - Bo Wang
- Vector Institute, Toronto, ON, Canada; Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
| | - Hosseinali Asgharian
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Felix Y Feng
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA.
| | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Arc Institute, Palo Alto, CA 94305, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
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6
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Yan L, Fu K, Li L, Li Q, Zhou X. Potential of sonobiopsy as a novel diagnosis tool for brain cancer. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200840. [PMID: 39077551 PMCID: PMC11284684 DOI: 10.1016/j.omton.2024.200840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Brain tumors have a poor prognosis. Early, accurate diagnosis and treatment are crucial. Although brain surgical biopsy can provide an accurate diagnosis, it is highly invasive and risky and is not suitable for follow-up examination. Blood-based liquid biopsies have a low detection rate of tumor biomarkers and limited evaluation ability due to the existence of the blood-brain barrier (BBB). The BBB is composed of brain capillary endothelial cells through tight junctions, which prevents the release of brain tumor markers to the human peripheral circulation, making it more difficult to diagnose, predict prognosis, and evaluate therapeutic response through brain tumor markers than other tumors. Focused ultrasound (FUS)-enabled liquid biopsy (sonobiopsy) is an emerging technique using FUS to promote the release of tumor markers into the circulatory system and cerebrospinal fluid, thus facilitating tumor detection. The feasibility and safety data from both animal models and clinical trials support sonobiopsy as a great potential in the diagnosis of brain diseases.
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Affiliation(s)
- Li Yan
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, China
| | - Kang Fu
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, China
| | - Le Li
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, China
| | - Qing Li
- Ultrasound Diagnosis and Treatment Center, Xi’an International Medical Center Hospital, Xi’an, China
| | - Xiaodong Zhou
- Ultrasound Diagnosis and Treatment Center, Xi’an International Medical Center Hospital, Xi’an, China
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7
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Zheng YL, Wu X, Williams M, Verhulst S, Lin J, Takahashi Y, Ma JX, Wang Y. High-throughput single telomere analysis using DNA microarray and fluorescent in situ hybridization. Nucleic Acids Res 2024:gkae812. [PMID: 39291738 DOI: 10.1093/nar/gkae812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 08/30/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024] Open
Abstract
The human telomere system is highly dynamic. Both short and long leucocyte average telomere lengths (aTL) are associated with an increased risk of cancer and early death, illustrating the complex relationship between TL and human health and the importance of assessing TL distributions with single TL analysis. A DNA microarray and telomere fluorescent in situ hybridization (DNA-array-FISH) approach was developed to measure the base-pair (bp) lengths of single telomeres. On average 32000 telomeres were measured per DNA sample with one microarray chip assaying 96 test DNA samples. Various telomere parameters, i.e. aTL and the frequency of short/long telomeres, were computed to delineate TL distribution. The intra-assay and inter-assay coefficient of variations of aTL ranged from 1.37% to 3.98%. The correlation coefficient (r) of aTL in repeated measurements ranged from 0.91 to 1.00, demonstrating high measurement precision. aTLs measured by DNA-array-FISH predicted aTLs measured by terminal restriction fragment (TRF) analysis with r ranging 0.87-0.99. A new accurate and high-throughput method has been developed to measure the bp lengths of single telomeres. The large number of single TL data provides an opportunity for an in-depth analysis of telomere dynamics and the complex relationship between telomere and age-related diseases.
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Affiliation(s)
- Yun-Ling Zheng
- Cancer Prevention and Control Program, Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Xingjia Wu
- Cancer Prevention and Control Program, Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Madeline Williams
- Cancer Prevention and Control Program, Department of Oncology, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yusuke Takahashi
- Department of Biochemistry, Wake Forest School of Medicine, NC 27157, USA
| | - Jian-Xing Ma
- Department of Biochemistry, Wake Forest School of Medicine, NC 27157, USA
| | - Ying Wang
- TelohealthDx, LLC, Clarksburg, MD 20871, USA
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8
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Sako A, Matsuse M, Saenko V, Tanaka A, Otsubo R, Morita M, Kuba S, Nishihara E, Suzuki K, Ogi T, Kawakami A, Mitsutake N. TERT Promoter Mutations Increase Tumor Aggressiveness by Altering TERT mRNA Splicing in Papillary Thyroid Carcinoma. J Clin Endocrinol Metab 2024; 109:e1827-e1838. [PMID: 38576411 DOI: 10.1210/clinem/dgae220] [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: 11/30/2023] [Revised: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
CONTEXT Telomerase reverse transcriptase promoter (TERT-p) mutations, which upregulate TERT expression, are strongly associated with tumor aggressiveness and worse prognosis in papillary thyroid carcinomas (PTCs). TERT expression is also observed in a proportion of PTCs without TERT-p mutations, but such tumors show less aggressiveness and better prognosis than TERT-p mutation-positive tumors. OBJECTIVE TERT has multiple splicing variants whose relationships with the TERT-p status and clinicopathological characteristics remain poorly understood. We examined the relationship between the TERT-p mutational status, the TERT splicing pattern, and clinicopathological features. METHODS We investigated the expression of 2 major variants, α deletion (dA) and β deletion (dB), in a series of 207 PTCs operated on between November 2001 and March 2020 in Nagasaki University Hospital and Kuma Hospital. RESULTS The TERT-p mutations were found in 33 cases, and among 174 mutation-negative cases, 24 showed TERT expression. All cases were classified into 3 groups: the TERT-p mutation-negative/expression-negative group (mut-/exp-), the TERT-p mutation-negative/expression-positive group (mut-/exp+), and the TERT-p mutation-positive group (mut+/exp+). The +A+B/dB ratio in mut+/exp+ was significantly higher than that in mut-/exp+ PTCs. Analysis with clinicopathological data revealed that +A+B expression was associated with higher PTC aggressiveness, whereas dB expression counteracted this effect. Functional in vitro study demonstrated that dB strongly inhibited cell growth, migration, and clonogenicity, suggesting its tumor-suppressive role. CONCLUSION These results provide evidence that the TERT-p mutations alter the expression of different TERT splice variants, which, in turn, associates with different tumor aggressiveness.
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Affiliation(s)
- Ayaka Sako
- Department of Radiation Medical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- Department of Endocrinology and Metabolism, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Michiko Matsuse
- Department of Radiation Medical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Vladimir Saenko
- Department of Radiation Molecular Epidemiology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki 852-8523, Japan
| | - Aya Tanaka
- Department of Surgical Oncology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Ryota Otsubo
- Department of Surgical Oncology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Michi Morita
- Department of Surgery, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Sayaka Kuba
- Department of Surgery, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Eijun Nishihara
- Department of Internal Medicine, Kuma Hospital, Kobe 650-0011, Japan
| | - Keiji Suzuki
- Department of Radiation Medical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Norisato Mitsutake
- Department of Radiation Medical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- Department of Radiation Molecular Epidemiology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki 852-8523, Japan
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9
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Abi-Raad R, Shi Q, Chen F, Antony V, Hsiao WY, Simsir A, Liu X, Brandler TC, Cai G. TERT promoter mutations and additional molecular alterations in thyroid fine-needle aspiration specimens: A multi-institutional study with histopathologic follow-up. Am J Clin Pathol 2024:aqae117. [PMID: 39250709 DOI: 10.1093/ajcp/aqae117] [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: 07/18/2024] [Accepted: 08/15/2024] [Indexed: 09/11/2024] Open
Abstract
OBJECTIVES TERT promoter mutations are not infrequently encountered in thyroid carcinomas; however, it is unclear if additional molecular alterations may play a role in determining tumor behavior. METHODS Fine-needle aspiration (FNA) specimens from 32 patients with TERT promoter mutations detected by ThyroSeq v3 from 4 institutions were included in the study. FNA diagnoses, molecular results, and surgical follow-up were retrospectively reviewed and analyzed. RESULTS There were 5 benign and 27 malignant neoplasms, including 7 high-grade thyroid carcinomas (HGCs) on histopathologic follow-up. Of 4 cases with an isolated TERT mutation, 3 (75%) cases were malignant. Of 17 cases harboring a co-occurring TERT mutation with 1 additional molecular alteration, 13 (76%) displayed malignancy on histopathologic follow-up. All 11 cases with TERT mutations plus 2 or more additional molecular alterations were malignant on follow-up. Furthermore, HGC was not seen in cases with an isolated TERT mutation, while 80% of cases harboring TERT mutations plus 3 additional molecular alterations showed HGC. CONCLUSIONS TERT promoter mutations are commonly associated with malignancy, particularly HGCs, when multiple co-occurring molecular alterations are present. However, TERT promoter mutations may occasionally be detected in benign thyroid neoplasms when encountered in isolation or with fewer than 2 additional molecular alterations.
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Affiliation(s)
- Rita Abi-Raad
- Department of Pathology, Yale University School of Medicine, New Haven, CT, US
| | - Qiuying Shi
- Department of Pathology, Emory University Hospital, Atlanta, GA, US
| | - Fei Chen
- Department of Pathology, New York University Langone Health, New York, NY, US
| | - Vijay Antony
- Department of Pathology, Yale Cancer Center, Yale University School of Medicine, New Haven, CT, US
| | - Wen-Yu Hsiao
- Department of Pathology, Emory University Hospital, Atlanta, GA, US
| | - Aylin Simsir
- Department of Pathology, New York University Langone Health, New York, NY, US
| | - Xiaoying Liu
- Department of Pathology and Laboratory Medicine, Dartmouth Health and Geisel School of Medicine at Dartmouth, Lebanon, NH, US
| | - Tamar C Brandler
- Department of Pathology, New York University Langone Health, New York, NY, US
| | - Guoping Cai
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT, US
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10
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Coltoff A, Kuykendall A. Emerging drug profile: JAK inhibitors. Leuk Lymphoma 2024; 65:1258-1269. [PMID: 38739701 DOI: 10.1080/10428194.2024.2353434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024]
Abstract
Dysregulated JAK/STAT hyperactivity is essential to the pathogenesis of myelofibrosis, and JAK inhibitors are the first-line treatment option for many patients. There are four FDA-approved JAK inhibitors for patients with myelofibrosis. Single-agent JAK inhibition can improve splenomegaly, symptom burden, cytopenias, and possibly survival in patients with myelofibrosis. Despite their efficacy, JAK inhibitors produce variable or short-lived responses, in part due to the large network of cooperating signaling pathways and downstream targets of JAK/STAT, which mediates upfront or acquired resistance to JAK inhibitors. Synergistic inhibition of JAK/STAT accessory pathways can increase the rates and duration of response for patients with myelofibrosis. Two recently reported, placebo-controlled phase III trials of novel agents added to JAK inhibition met their primary endpoint, and additional late-stage studies are ongoing. This paper will review role of dysregulated JAK/STAT signaling, biological plausible additional therapeutic targets and the recent advancements in combination strategies with JAK inhibitors for myelofibrosis.
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Affiliation(s)
- Alexander Coltoff
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Andrew Kuykendall
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL, USA
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11
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Jansen P, Galetzka W, Lodde GC, Standl F, Zaremba A, Herbst R, Terheyden P, Utikal J, Pföhler C, Ulrich J, Kreuter A, Mohr P, Gutzmer R, Meier F, Dippel E, Weichenthal M, Placke JM, Landsberg J, Möller I, Sucker A, Paschen A, Hadaschik E, Zimmer L, Livingstone E, Schadendorf D, Ugurel S, Stang A, Griewank KG. Shortened progression free and overall survival to immune-checkpoint inhibitors in BRAF-, RAS- and NF1- ("Triple") wild type melanomas. Eur J Cancer 2024; 208:114208. [PMID: 39018633 DOI: 10.1016/j.ejca.2024.114208] [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: 05/10/2024] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND Melanomas lacking mutations in BRAF, NRAS and NF1 are frequently referred to as "triple wild-type" (tWT) melanomas. They constitute 5-10 % of all melanomas and remain poorly characterized regarding clinical characteristics and response to therapy. This study investigates the largest multicenter collection of tWT-melanomas to date. METHODS Targeted next-generation sequencing of the TERT promoter and 29 melanoma-associated genes were performed on 3109 melanoma tissue samples of the prospective multicenter study ADOREG/TRIM of the DeCOG revealing 292 patients suffering from tWT-melanomas. Clinical characteristics and mutational patterns were analyzed. As subgroup analysis, we analyzed 141 tWT-melanoma patients receiving either anti-CTLA4 plus anti-PD1 or anti PD1 monotherapy as first line therapy in AJCC stage IV. RESULTS 184 patients with cutaneous melanomas, 56 patients with mucosal melanomas, 34 patients with acral melanomas and 18 patients with melanomas of unknown origin (MUP) were included. A TERT promoter mutation could be identified in 33.2 % of all melanomas and 70.5 % of all tWT-melanomas harbored less than three mutations per sample. For the 141 patients with stage IV disease, mPFS independent of melanoma type was 6.2 months (95 % CI: 4-9) and mOS was 24.8 months (95 % CI: 14.2-53.4) after first line anti-CTLA4 plus anti-PD1 therapy. After first-line anti-PD1 monotherapy, mPFS was 4 months (95 %CI: 2.9-8.5) and mOS was 29.18 months (95 % CI: 17.5-46.2). CONCLUSIONS While known prognostic factors such as TERT promoter mutations and TMB were equally distributed among patients who received either anti-CTLA4 plus anti-PD1 combination therapy or anti-PD1 monotherapy as first line therapy, we did not find a prolonged mPFS or mOS in either of those. For both therapy concepts, mPFS and mOS were considerably shorter than reported for melanomas with known oncogene mutations.
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Affiliation(s)
- Philipp Jansen
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany; Department of Dermatology, University Hospital Bonn, Bonn.
| | - Wolfgang Galetzka
- Institute for medical informatics, biometry and epidemiology, University Hospital Essen, Essen, Germany
| | - Georg C Lodde
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Fabian Standl
- Institute for medical informatics, biometry and epidemiology, University Hospital Essen, Essen, Germany
| | - Anne Zaremba
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Rudolf Herbst
- Hauttumorzentrum, Helios Klinikum Erfurt, Erfurt, Germany
| | | | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Heidelberg, Germany
| | - Claudia Pföhler
- Department of Dermatology, Saarland University Medical School, Homburg, Saar, Germany
| | - Jens Ulrich
- Department of Dermatology and Venereology, Harzklinikum Dorothea Christiane Erxleben, Quedlinburg, Germany
| | - Alexander Kreuter
- Department of Dermatology, Venereology and Allergology, HELIOS St. Elisabeth Klinik Oberhausen, University Witten/Herdecke, Oberhausen, Germany
| | - Peter Mohr
- Dermatological Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany
| | - Ralf Gutzmer
- Skin Cancer Unit, Hannover Medical School, Hannover, Germany & Department of Dermatology, Johannes Wesling Medical Center, Ruhr University Bochum, Minden, Germany
| | - Friedegund Meier
- Department of Dermatology, Dermatooncology, University Hospital Carl Gustav Carus, TU Dresden, Dresden Germany
| | - Edgar Dippel
- Department of Dermatology Ludwigshafen, Klinikum der Stadt Ludwigshafen am Rhein gGmbH, Ludwigshafen, Germany
| | | | - Jan-Malte Placke
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | | | - Inga Möller
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Annette Paschen
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Eva Hadaschik
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Lisa Zimmer
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Elisabeth Livingstone
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
| | - Andreas Stang
- Institute for medical informatics, biometry and epidemiology, University Hospital Essen, Essen, Germany
| | - Klaus G Griewank
- Department of Dermatology, University Hospital Essen, Essen, Germany & German Cancer Consortium (DKTK), partner site Essen, Düsseldorf, Germany
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12
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Huang B, Fan C, Chen K, Rao J, Ou P, Tian C, Yang Y, Cooper DN, Zhao H. VCAT: an integrated variant function annotation tools. Hum Genet 2024:10.1007/s00439-024-02699-6. [PMID: 39192052 DOI: 10.1007/s00439-024-02699-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
The development of sequencing technology has promoted discovery of variants in the human genome. Identifying functions of these variants is important for us to link genotype to phenotype, and to diagnose diseases. However, it usually requires researchers to visit multiple databases. Here, we presented a one-stop webserver for variant function annotation tools (VCAT, https://biomed.nscc-gz.cn/zhaolab/VCAT/ ) that is the first one connecting variant to functions via the epigenome, protein, drug and RNA. VCAT is also the first one to make all annotations visualized in interactive charts or molecular structures. VCAT allows users to upload data in VCF format, and download results via a URL. Moreover, VCAT has annotated a huge number (1,262,041,068) of variants collected from dbSNP, 1000 Genomes projects, gnomAD, ICGC, TCGA, and HPRC Pangenome project. For these variants, users are able to searcher their functions, related diseases and drugs from VCAT. In summary, VCAT provides a one-stop webserver to explore the potential functions of human genomic variants including their relationship with diseases and drugs.
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Affiliation(s)
- Bi Huang
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, People's Republic of China
| | - Cong Fan
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, People's Republic of China
| | - Ken Chen
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jiahua Rao
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Peihua Ou
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chong Tian
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - David N Cooper
- School of Medicine, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan Jiang West Road, Guangzhou, 500001, People's Republic of China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, People's Republic of China.
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13
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Zhang J, Xu S. High aggressiveness of papillary thyroid cancer: from clinical evidence to regulatory cellular networks. Cell Death Discov 2024; 10:378. [PMID: 39187514 PMCID: PMC11347646 DOI: 10.1038/s41420-024-02157-2] [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: 04/22/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 08/28/2024] Open
Abstract
The global incidence of thyroid cancer has increased over recent decades. Papillary thyroid cancer (PTC) is the most common type of thyroid cancer and accounts for nearly 90% of all cases. Typically, PTC has a good prognosis. However, some PTC variants exhibit more aggressive behaviour, which significantly increases the risk of postoperative recurrence. Over the past decade, the high metastatic potential of PTC has drawn the attention of many researchers and these studies have provided useful molecular markers for improved diagnosis, risk stratification and clinical approaches. The aim of this review is to discuss the progress in epidemiology, metastatic features, risk factors and molecular mechanisms associated with PTC aggressiveness. We present a detailed picture showing that epithelial-to-mesenchymal transition, cancer metabolic reprogramming, alterations in important signalling pathways, epigenetic aberrations and the tumour microenvironment are crucial drivers of PTC metastasis. Further research is needed to more fully elucidate the pathogenesis and biological behaviour underlying the aggressiveness of PTC.
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Affiliation(s)
- Junsi Zhang
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Sunwang Xu
- Department of Thyroid and Breast Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
- Department of Thyroid and Breast Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
- Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Fuzhou, China.
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14
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Casalini R, Romei C, Ciampi R, Ramone T, Prete A, Gambale C, Matrone A, Torregrossa L, Ugolini C, Elisei R. Minor role of TP53 and TERT promoter mutations in medullary thyroid carcinoma: report of new cases and revision of the literature. Endocrine 2024:10.1007/s12020-024-03990-2. [PMID: 39179735 DOI: 10.1007/s12020-024-03990-2] [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: 07/03/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
Abstract
PURPOSE Aims of this study were to investigate the prevalence of TP53 and TERT mutations in Medullary Thyroid carcinoma (MTC) and their role in inducing aggressiveness in positive cases. METHODS We performed a literature search in PubMed to identify studies investigating the prevalence of TERT and TP53 mutations in MTC. We also included data on MTC cases (n = 193) obtained at our center and unpublished. The in-silico pathogenicity of the TP53 mutations has been evaluated by predictor tools. RESULTS We identified a total of 25 and 11 published papers: all together 1280 cases have been investigated for the presence of TP53 mutations and 974 for TERT promoter mutation. Twenty-five out of 1280 (2%) cases had a TP53 mutation while only 3/974 MTC cases (0.3%) have been found to be positive for TERT promoter mutations. Among all, we identified 19 different TP53 mutations that in 12 cases were demonstrated to have an in silico predicted high pathogenic role and a high impact on protein function. Three non-sense and 4 probably not damaging mutations were also reported. The pathogenic role of the TERT promoter mutations has been previously in vitro determined. No correlation between TP53 and/or TERT mutations and aggressiveness of MTC has been demonstrated. CONCLUSION The prevalence of TP53 and TERT promoter mutations is very low in MTC. The reported mutations are pathogenic in the majority of cases. Because of their rarity it is not possible to clarify if they play or not a role in the pathogenesis and/or aggressiveness of this specific thyroid tumor.
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Affiliation(s)
- Roberta Casalini
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - Cristina Romei
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - Raffaele Ciampi
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - Teresa Ramone
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - Alessandro Prete
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - Carla Gambale
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - Antonio Matrone
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - Liborio Torregrossa
- Department of Surgical, Medical, Molecular Pathology and Critical Area, Unit of Pathology, University Hospital of Pisa, Pisa, Italy
| | - Clara Ugolini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, Unit of Pathology, University Hospital of Pisa, Pisa, Italy
| | - Rossella Elisei
- Department of Clinical and Experimental Medicine, Unit of Endocrinology, University Hospital of Pisa, Pisa, Italy.
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15
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Zhou J, Su X, Hu D, Zhang L, Chen C, Sun K, Zhang H, Liu Z. Molecular confirmation that fibrocartilaginous dysplasia is a variant of fibrous dysplasia. J Clin Pathol 2024:jcp-2024-209626. [PMID: 39153849 DOI: 10.1136/jcp-2024-209626] [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: 05/01/2024] [Accepted: 07/29/2024] [Indexed: 08/19/2024]
Abstract
AIMS Fibrocartilaginous dysplasia (FCD) is a subvariant of fibrous dysplasia (FD). This study aims to retrospectively elucidate the clinicopathological and separate genetic features of the cartilaginous and fibro-osseous components of FCD. METHODS In total, 24 patients (14 men and 10 women) with FCD were included in our cohort. The diagnosis was confirmed morphologically and immunohistochemically, and genetic features were determined via Sanger sequencing. RESULTS Five patients were polyostotic, and 19 were monostotic, predominantly concerning the femur. Radiography revealed a well-demarcated ground glass appearance with ring-like or scattered calcification. Histologically, the lesions were characterised by proliferative fibroblasts, immature woven bone and highly differentiated hyaline cartilage. The fibro-osseous components exhibited positive immunoreaction with SATB2 and a low Ki-67 proliferation index. The fibro-osseous and cartilaginous components shared mutations at codon 201 in exon 8 of the guanine nucleotide-binding protein/a-subunit (GNAS) gene, specifically CGT>CAT (p.R201H) in four patients and the wild-type isocitrate dehydrogenase (IDH)1/IDH2 gene. Telomerase reverse transcriptase (TERT) promoter mutations (C288T and C229G) occurred in both fibro-osseous and cartilaginous components in two patients. CONCLUSIONS FCD encompasses areas of conventional FD with additional cartilage. Importantly, the presence or absence of mutations in the GNAS gene and/or the TERT promoter is common between the fibro-osseous and cartilaginous components of the disease. These results further confirmed FCD as a variant of FD.
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Affiliation(s)
- Juan Zhou
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Comprehensive Oncology Center of Bone and Soft Tissue, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
| | - Xuling Su
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Comprehensive Oncology Center of Bone and Soft Tissue, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
| | - Dingjun Hu
- Department of Radiology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Zhang
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Comprehensive Oncology Center of Bone and Soft Tissue, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
| | - Chunyan Chen
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Comprehensive Oncology Center of Bone and Soft Tissue, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
| | - Keyang Sun
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Comprehensive Oncology Center of Bone and Soft Tissue, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
| | - Huizhen Zhang
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Comprehensive Oncology Center of Bone and Soft Tissue, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
| | - Zhiyan Liu
- Department of Pathology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Comprehensive Oncology Center of Bone and Soft Tissue, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
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16
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Pennisi G, Bruzzaniti P, Burattini B, Piaser Guerrato G, Della Pepa GM, Sturiale CL, Lapolla P, Familiari P, La Pira B, D’Andrea G, Olivi A, D’Alessandris QG, Montano N. Advancements in Telomerase-Targeted Therapies for Glioblastoma: A Systematic Review. Int J Mol Sci 2024; 25:8700. [PMID: 39201386 PMCID: PMC11354571 DOI: 10.3390/ijms25168700] [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: 06/25/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Glioblastoma (GBM) is a primary CNS tumor that is highly lethal in adults and has limited treatment options. Despite advancements in understanding the GBM biology, the standard treatment for GBM has remained unchanged for more than a decade. Only 6.8% of patients survive beyond five years. Telomerase, particularly the hTERT promoter mutations present in up to 80% of GBM cases, represents a promising therapeutic target due to its role in sustaining telomere length and cancer cell proliferation. This review examines the biology of telomerase in GBM and explores potential telomerase-targeted therapies. We conducted a systematic review following the PRISMA-P guidelines in the MEDLINE/PubMed and Scopus databases, from January 1995 to April 2024. We searched for suitable articles by utilizing the terms "GBM", "high-grade gliomas", "hTERT" and "telomerase". We incorporated studies addressing telomerase-targeted therapies into GBM studies, excluding non-English articles, reviews, and meta-analyses. We evaluated a total of 777 records and 46 full texts, including 36 studies in the final review. Several compounds aimed at inhibiting hTERT transcription demonstrated promising preclinical outcomes; however, they were unsuccessful in clinical trials owing to intricate regulatory pathways and inadequate pharmacokinetics. Direct hTERT inhibitors encountered numerous obstacles, including a prolonged latency for telomere shortening and the activation of the alternative lengthening of telomeres (ALT). The G-quadruplex DNA stabilizers appeared to be potential indirect inhibitors, but further clinical studies are required. Imetelstat, the only telomerase inhibitor that has undergone clinical trials, has demonstrated efficacy in various cancers, but its efficacy in GBM has been limited. Telomerase-targeted therapies in GBM is challenging due to complex hTERT regulation and inadequate inhibitor pharmacokinetics. Our study demonstrates that, despite promising preclinical results, no Telomerase inhibitors have been approved for GBM, and clinical trials have been largely unsuccessful. Future strategies may include Telomerase-based vaccines and multi-target inhibitors, which may provide more effective treatments when combined with a better understanding of telomere dynamics and tumor biology. These treatments have the potential to be integrated with existing ones and to improve the outcomes for patients with GBM.
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Affiliation(s)
- Giovanni Pennisi
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
- Department of Neurosurgery, F. Spaziani Hospital, 03100 Frosinone, Italy; (B.L.P.); (G.D.)
| | - Placido Bruzzaniti
- Department of Neurosurgery, F. Spaziani Hospital, 03100 Frosinone, Italy; (B.L.P.); (G.D.)
- Department of Human Neurosciences, Division of Neurosurgery, Policlinico Umberto I University Hospital, Sapienza, University of Rome, 00157 Rome, Italy;
| | - Benedetta Burattini
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
| | - Giacomo Piaser Guerrato
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
| | - Giuseppe Maria Della Pepa
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
| | - Carmelo Lucio Sturiale
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
| | | | - Pietro Familiari
- Department of Human Neurosciences, Division of Neurosurgery, Policlinico Umberto I University Hospital, Sapienza, University of Rome, 00157 Rome, Italy;
| | - Biagia La Pira
- Department of Neurosurgery, F. Spaziani Hospital, 03100 Frosinone, Italy; (B.L.P.); (G.D.)
| | - Giancarlo D’Andrea
- Department of Neurosurgery, F. Spaziani Hospital, 03100 Frosinone, Italy; (B.L.P.); (G.D.)
| | - Alessandro Olivi
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
| | - Quintino Giorgio D’Alessandris
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
| | - Nicola Montano
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (B.B.); (G.P.G.); (G.M.D.P.); (C.L.S.); (A.O.); (Q.G.D.); (N.M.)
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17
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Zheng C, Sarin KY. Unveiling the genetic landscape of hereditary melanoma: From susceptibility to surveillance. Cancer Treat Res Commun 2024; 40:100837. [PMID: 39137473 DOI: 10.1016/j.ctarc.2024.100837] [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: 11/23/2023] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
The multifactorial etiology underlying melanoma development involves an array of genetic, phenotypic, and environmental factors. Genetic predisposition for melanoma is further influenced by the complex interplay between high-, medium-, and low-penetrance genes, each contributing to varying degrees of susceptibility. Within this network, high-penetrance genes, including CDKN2A, CDK4, BAP1, and POT1, are linked to a pronounced risk for disease, whereas medium- and low-penetrance genes, such as MC1R, MITF, and others, contribute only moderately to melanoma risk. Notably, these genetic factors not only heighten the risk of melanoma but may also increase susceptibility towards internal malignancies, such as pancreatic cancer, renal cell cancer, or neural tumors. Genetic testing and counseling hold paramount importance in the clinical context of suspected hereditary melanoma, facilitating risk assessment, personalized surveillance strategies, and informed decision-making. As our understanding of the genomic landscape deepens, this review paper aims to comprehensively summarize the genetic underpinnings of hereditary melanoma, as well as current screening and management strategies for the disease.
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Affiliation(s)
- Chenming Zheng
- Stanford University Department of Dermatology, Redwood City, CA, USA
| | - Kavita Y Sarin
- Stanford University Department of Dermatology, Redwood City, CA, USA.
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18
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Hasegawa K, Zhao Y, Garbuzov A, Corces MR, Neuhöfer P, Gillespie VM, Cheung P, Belk JA, Huang YH, Wei Y, Chen L, Chang HY, Artandi SE. Clonal inactivation of TERT impairs stem cell competition. Nature 2024; 632:201-208. [PMID: 39020172 PMCID: PMC11291281 DOI: 10.1038/s41586-024-07700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/11/2024] [Indexed: 07/19/2024]
Abstract
Telomerase is intimately associated with stem cells and cancer, because it catalytically elongates telomeres-nucleoprotein caps that protect chromosome ends1. Overexpression of telomerase reverse transcriptase (TERT) enhances the proliferation of cells in a telomere-independent manner2-8, but so far, loss-of-function studies have provided no evidence that TERT has a direct role in stem cell function. In many tissues, homeostasis is shaped by stem cell competition, a process in which stem cells compete on the basis of inherent fitness. Here we show that conditional deletion of Tert in the spermatogonial stem cell (SSC)-containing population in mice markedly impairs competitive clone formation. Using lineage tracing from the Tert locus, we find that TERT-expressing SSCs yield long-lived clones, but that clonal inactivation of TERT promotes stem cell differentiation and a genome-wide reduction in open chromatin. This role for TERT in competitive clone formation occurs independently of both its reverse transcriptase activity and the canonical telomerase complex. Inactivation of TERT causes reduced activity of the MYC oncogene, and transgenic expression of MYC in the TERT-deleted pool of SSCs efficiently rescues clone formation. Together, these data reveal a catalytic-activity-independent requirement for TERT in enhancing stem cell competition, uncover a genetic connection between TERT and MYC and suggest that a selective advantage for stem cells with high levels of TERT contributes to telomere elongation in the male germline during homeostasis and ageing.
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Affiliation(s)
- Kazuteru Hasegawa
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Stanford, CA, USA
| | - Alina Garbuzov
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford, CA, USA
| | - Patrick Neuhöfer
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Victoria M Gillespie
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peggie Cheung
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford, CA, USA
| | - Lu Chen
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Nuclear Dynamics and Cancer Program, Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Steven E Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
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19
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Li J, Han Z, Ma C, Chi H, Jia D, Zhang K, Feng Z, Han B, Qi M, Li G, Li X, Xue H. Intraoperative rapid molecular diagnosis aids glioma subtyping and guides precise surgical resection. Ann Clin Transl Neurol 2024; 11:2176-2187. [PMID: 38924338 PMCID: PMC11330232 DOI: 10.1002/acn3.52138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
OBJECTIVE The molecular era of glioma diagnosis and treatment has arrived, and a single rapid histopathology is no longer sufficient for surgery. This study sought to present an automatic integrated gene detection system (AIGS), which enables rapid intraoperative detection of IDH/TERTp mutations. METHODS A total of 78 patients with gliomas were included in this study. IDH/TERTp mutations were detected intraoperatively using AIGS in 41 of these patients, and they were guided to surgical resection (AIGS detection group). The remaining 37 underwent histopathology-guided conventional surgical resection (non-AIGS detection group). The clinical utility of this technique was evaluated by comparing the accuracy of glioma subtype diagnosis before and after TERTp mutation results were obtained by pathologists and the extent of resection (EOR) and patient prognosis for molecular pathology-guided glioma surgery. RESULTS With NGS/Sanger sequencing and chromosome detection as the gold standard, the accuracy of AIGS results was 100%. And the timing was well matched to the intraoperative rapid pathology report. After obtaining the TERTp mutation detection results, the accuracy of the glioma subtype diagnosis made by the pathologists increased by 19.51%. Molecular pathology-guided surgical resection of gliomas significantly increased EOR (99.06% vs. 93.73%, p < 0.0001) and also improved median OS (26.77 vs. 13.47 months, p = 0.0289) and median PFS (15.90 vs. 10.57 months, p = 0.0181) in patients with glioblastoma. INTERPRETATION Using AIGS intraoperatively to detect IDH/TERTp mutations to accurately diagnose glioma subtypes can help achieve maximum safe resection of gliomas, which in turn improves the survival prognosis of patients.
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Affiliation(s)
- Jia Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
- Institute of Brain and Brain‐Inspired ScienceShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Brain Function RemodelingJinanShandongChina
| | - Zhe Han
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
- Institute of Brain and Brain‐Inspired ScienceShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Brain Function RemodelingJinanShandongChina
| | - Caizhi Ma
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
- Institute of Brain and Brain‐Inspired ScienceShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Brain Function RemodelingJinanShandongChina
| | - Huizhong Chi
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
- Institute of Brain and Brain‐Inspired ScienceShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Brain Function RemodelingJinanShandongChina
| | - Deze Jia
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Kailiang Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Zichao Feng
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Bo Han
- Department of PathologyShandong University Qilu HospitalJinanShandongChina
- Department of PathologyShandong University School of Basic Medical SciencesJinanShandongChina
| | - Mei Qi
- Department of PathologyShandong University Qilu HospitalJinanShandongChina
- Department of PathologyShandong University School of Basic Medical SciencesJinanShandongChina
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
- Institute of Brain and Brain‐Inspired ScienceShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Brain Function RemodelingJinanShandongChina
| | - Xueen Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of MedicineShandong UniversityJinanShandongChina
- Institute of Brain and Brain‐Inspired ScienceShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Brain Function RemodelingJinanShandongChina
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20
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Gnanapragasam A, Kirbizakis E, Li A, White KH, Mortenson KL, Cavalcante de Moura J, Jawhar W, Yan Y, Falter R, Russett C, Giannias B, Camilleri-Broët S, Bertos N, Cools-Lartigue J, Garzia L, Sangwan V, Ferri L, Zhang X, Bailey SD. HiChIP-Based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 That Confers Genetic Susceptibility to Gastroesophageal Cancer. Cancer Res 2024; 84:2377-2389. [PMID: 38748784 PMCID: PMC11247317 DOI: 10.1158/0008-5472.can-23-2397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/01/2024] [Accepted: 05/08/2024] [Indexed: 07/16/2024]
Abstract
Genome-wide association studies (GWAS) have identified more than a hundred single nucleotide variants (SNV) associated with the risk of gastroesophageal cancer (GEC). The majority of the identified SNVs map to noncoding regions of the genome. Uncovering the causal SNVs and genes they modulate could help improve GEC prevention and treatment. Herein, we used HiChIP against histone 3 lysine 27 acetylation (H3K27ac) to simultaneously annotate active promoters and enhancers, identify the interactions between them, and detect nucleosome-free regions (NFR) harboring potential causal SNVs in a single assay. The application of H3K27ac HiChIP in GEC relevant models identified 61 potential functional SNVs that reside in NFRs and interact with 49 genes at 17 loci. The approach led to a 67% reduction in the number of SNVs in linkage disequilibrium at these 17 loci, and at 7 loci, a single putative causal SNV was identified. One SNV, rs147518036, located within the promoter of the UDP-glucuronate decarboxylase 1 (UXS1) gene, seemed to underlie the GEC risk association captured by the rs75460256 index SNV. The rs147518036 SNV creates a GABPA DNA recognition motif, resulting in increased promoter activity, and CRISPR-mediated inhibition of the UXS1 promoter reduced the viability of the GEC cells. These findings provide a framework that simplifies the identification of potentially functional regulatory SNVs and target genes underlying risk-associated loci. In addition, the study implicates increased expression of the enzyme UXS1 and activation of its metabolic pathway as a predisposition to gastric cancer, which highlights potential therapeutic avenues to treat this disease. Significance: Epigenomic footprinting using a histone posttranslational modification targeted 3D genomics methodology elucidates functional noncoding sequence variants and their target genes at cancer risk loci.
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Affiliation(s)
- Ansley Gnanapragasam
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Eftyhios Kirbizakis
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Anna Li
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Kyle H White
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | | | - Juliana Cavalcante de Moura
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Wajih Jawhar
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Surgery, McGill University, Montreal, Canada
| | - Yifei Yan
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Reilly Falter
- Department of Experimental Medicine, McGill University, Montreal, Canada
| | - Colleen Russett
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Betty Giannias
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Sophie Camilleri-Broët
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Nicholas Bertos
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
| | - Jonathan Cools-Lartigue
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Livia Garzia
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
- Department of Surgery, McGill University, Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Veena Sangwan
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Lorenzo Ferri
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
| | - Xiaoyang Zhang
- Department of Experimental Medicine, McGill University, Montreal, Canada
| | - Swneke D Bailey
- The Cancer Research Program, Research Institute of the McGill University Health Centre (RI-MUHC), Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
- Department of Surgery, McGill University, Montreal, Canada
- Department of Pathology, McGill University, Montreal, Canada
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Tan KT, Slevin MK, Leibowitz ML, Garrity-Janger M, Shan J, Li H, Meyerson M. Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. CELL GENOMICS 2024; 4:100588. [PMID: 38917803 PMCID: PMC11293586 DOI: 10.1016/j.xgen.2024.100588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 11/09/2023] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Alterations in the structure and location of telomeres are pivotal in cancer genome evolution. 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 repeats, 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. These results provide a framework for the systematic study of telomeric repeats in cancer genomes, which could serve as a model for understanding the somatic evolution of other repetitive genomic elements.
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Affiliation(s)
- Kar-Tong Tan
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | | | - Mitchell L Leibowitz
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Max Garrity-Janger
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Jidong Shan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Heng Li
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA.
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA.
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Nevarez AJ, Mudla A, Diaz SA, Hao N. Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome. PLoS Comput Biol 2024; 20:e1012271. [PMID: 39078811 PMCID: PMC11288469 DOI: 10.1371/journal.pcbi.1012271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/22/2024] [Indexed: 08/02/2024] Open
Abstract
Melanoma showcases a complex interplay of genetic alterations and intra- and inter-cellular morphological changes during metastatic transformation. While pivotal, the role of specific mutations in dictating these changes still needs to be fully elucidated. Telomerase promoter mutations (TERTp mutations) significantly influence melanoma's progression, invasiveness, and resistance to various emerging treatments, including chemical inhibitors, telomerase inhibitors, targeted therapy, and immunotherapies. We aim to understand the morphological and phenotypic implications of the two dominant monoallelic TERTp mutations, C228T and C250T, enriched in melanoma metastasis. We developed isogenic clonal cell lines containing the TERTp mutations and utilized dual-color expression reporters steered by the endogenous Telomerase promoter, giving us allelic resolution. This approach allowed us to monitor morpholomic variations induced by these mutations. TERTp mutation-bearing cells exhibited significant morpholome differences from their wild-type counterparts, with increased allele expression patterns, augmented wound-healing rates, and unique spatiotemporal dynamics. Notably, the C250T mutation exerted more pronounced changes in the morpholome than C228T, suggesting a differential role in metastatic potential. Our findings underscore the distinct influence of TERTp mutations on melanoma's cellular architecture and behavior. The C250T mutation may offer a unique morpholomic and systems-driven advantage for metastasis. These insights provide a foundational understanding of how a non-coding mutation in melanoma metastasis affects the system, manifesting in cellular morpholome.
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Affiliation(s)
- Andres J. Nevarez
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Anusorn Mudla
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Sabrina A. Diaz
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
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23
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Regner MJ, Garcia-Recio S, Thennavan A, Wisniewska K, Mendez-Giraldez R, Felsheim B, Spanheimer PM, Parker JS, Perou CM, Franco HL. Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598858. [PMID: 38948758 PMCID: PMC11212881 DOI: 10.1101/2024.06.13.598858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Annotation of the cis-regulatory elements that drive transcriptional dysregulation in cancer cells is critical to improving our understanding of tumor biology. Herein, we present a compendium of matched chromatin accessibility (scATAC-seq) and transcriptome (scRNA-seq) profiles at single-cell resolution from human breast tumors and healthy mammary tissues processed immediately following surgical resection. We identify the most likely cell-of-origin for luminal breast tumors and basal breast tumors and then introduce a novel methodology that implements linear mixed-effects models to systematically quantify associations between regions of chromatin accessibility (i.e. regulatory elements) and gene expression in malignant cells versus normal mammary epithelial cells. These data unveil regulatory elements with that switch from silencers of gene expression in normal cells to enhancers of gene expression in cancer cells, leading to the upregulation of clinically relevant oncogenes. To translate the utility of this dataset into tractable models, we generated matched scATAC-seq and scRNA-seq profiles for breast cancer cell lines, revealing, for each subtype, a conserved oncogenic gene expression program between in vitro and in vivo cells. Together, this work highlights the importance of non-coding regulatory mechanisms that underlie oncogenic processes and the ability of single-cell multi-omics to define the regulatory logic of BC cells at single-cell resolution.
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Affiliation(s)
- Matthew J. Regner
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Susana Garcia-Recio
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA, 77030
| | - Kamila Wisniewska
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Raul Mendez-Giraldez
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brooke Felsheim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Philip M. Spanheimer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S. Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hector L. Franco
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Clinical and Translational Cancer Research, University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00935
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24
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Ralli S, Vira T, Robles-Espinoza CD, Adams DJ, Brooks-Wilson AR. Variant ranking pipeline for complex familial disorders. Sci Rep 2024; 14:13599. [PMID: 38866901 PMCID: PMC11169219 DOI: 10.1038/s41598-024-64169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Identifying genetic susceptibility factors for complex disorders remains a challenging task. To analyze collections of small and large pedigrees where genetic heterogeneity is likely, but biological commonalities are plausible, we have developed a weights-based pipeline to prioritize variants and genes. The Weights-based vAriant Ranking in Pedigrees (WARP) pipeline prioritizes variants using 5 weights: disease incidence rate, number of cases in a family, genome fraction shared amongst cases in a family, allele frequency and variant deleteriousness. Weights, except for the population allele frequency weight, are normalized between 0 and 1. Weights are combined multiplicatively to produce family-specific-variant weights that are then averaged across all families in which the variant is observed to generate a multifamily weight. Sorting multifamily weights in descending order creates a ranked list of variants and genes for further investigation. WARP was validated using familial melanoma sequence data from the European Genome-phenome Archive. The pipeline identified variation in known germline melanoma genes POT1, MITF and BAP1 in 4 out of 13 families (31%). Analysis of the other 9 families identified several interesting genes, some of which might have a role in melanoma. WARP provides an approach to identify disease predisposing genes in studies with small and large pedigrees.
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Affiliation(s)
- Sneha Ralli
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Tariq Vira
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | | | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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25
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Ng YB, Akincilar SC. Shaping DNA damage responses: Therapeutic potential of targeting telomeric proteins and DNA repair factors in cancer. Curr Opin Pharmacol 2024; 76:102460. [PMID: 38776747 DOI: 10.1016/j.coph.2024.102460] [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: 12/10/2022] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 05/25/2024]
Abstract
Shelterin proteins regulate genomic stability by preventing inappropriate DNA damage responses (DDRs) at telomeres. Unprotected telomeres lead to persistent DDR causing cell cycle inhibition, growth arrest, and apoptosis. Cancer cells rely on DDR to protect themselves from DNA lesions and exogenous DNA-damaging agents such as chemotherapy and radiotherapy. Therefore, targeting DDR machinery is a promising strategy to increase the sensitivity of cancer cells to existing cancer therapies. However, the success of these DDR inhibitors depends on other mutations, and over time, patients develop resistance to these therapies. This suggests the need for alternative approaches. One promising strategy is co-inhibiting shelterin proteins with DDR molecules, which would offset cellular fitness in DNA repair in a mutation-independent manner. This review highlights the associations and dependencies of the shelterin complex with the DDR proteins and discusses potential co-inhibition strategies that might improve the therapeutic potential of current inhibitors.
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Affiliation(s)
- Yu Bin Ng
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Semih Can Akincilar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore.
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26
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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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27
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Deb S, Berei J, Miliavski E, Khan MJ, Broder TJ, Akurugo TA, Lund C, Fleming SE, Hillwig R, Ross J, Puri N. The Effects of Smoking on Telomere Length, Induction of Oncogenic Stress, and Chronic Inflammatory Responses Leading to Aging. Cells 2024; 13:884. [PMID: 38891017 PMCID: PMC11172003 DOI: 10.3390/cells13110884] [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: 02/29/2024] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024] Open
Abstract
Telomeres, potential biomarkers of aging, are known to shorten with continued cigarette smoke exposure. In order to further investigate this process and its impact on cellular stress and inflammation, we used an in vitro model with cigarette smoke extract (CSE) and observed the downregulation of telomere stabilizing TRF2 and POT1 genes after CSE treatment. hTERT is a subunit of telomerase and a well-known oncogenic marker, which is overexpressed in over 85% of cancers and may contribute to lung cancer development in smokers. We also observed an increase in hTERT and ISG15 expression levels after CSE treatment, as well as increased protein levels revealed by immunohistochemical staining in smokers' lung tissue samples compared to non-smokers. The effects of ISG15 overexpression were further studied by quantifying IFN-γ, an inflammatory protein induced by ISG15, which showed greater upregulation in smokers compared to non-smokers. Similar changes in gene expression patterns for TRF2, POT1, hTERT, and ISG15 were observed in blood and buccal swab samples from smokers compared to non-smokers. The results from this study provide insight into the mechanisms behind smoking causing telomere shortening and how this may contribute to the induction of inflammation and/or tumorigenesis, which may lead to comorbidities in smokers.
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Affiliation(s)
- Shreya Deb
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Joseph Berei
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Edward Miliavski
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Muhammad J. Khan
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Taylor J. Broder
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Thomas A. Akurugo
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Cody Lund
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Sara E. Fleming
- Department of Pathology, UW Health SwedishAmerican Hospital, Rockford, IL 61107, USA;
| | - Robert Hillwig
- Department of Health Sciences Education, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA;
| | - Joseph Ross
- Department of Family and Community Medicine, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA;
| | - Neelu Puri
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
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28
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Ibrahim MB, Flanagan J, Ibrahim T, Rouleau E. Unraveling noncoding DNA variants and epimutations: a paradigm shift in hereditary cancer research. Future Oncol 2024; 20:1289-1298. [PMID: 38722139 PMCID: PMC11318707 DOI: 10.2217/fon-2023-0665] [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: 11/16/2023] [Accepted: 03/11/2024] [Indexed: 06/12/2024] Open
Abstract
Exhaustive efforts have been dedicated to uncovering genomic aberrations linked to cancer susceptibility. Noncoding sequence variants and epigenetic alterations significantly influence gene regulation and could contribute to cancer development. However, exploring noncoding regions in hereditary cancer susceptibility demands cutting-edge methodologies for functionally characterizing genomic discoveries. Additionally, comprehending the impact on cancer development of variants in noncoding DNA and the epigenome necessitates integrating diverse data through bioinformatic analyses. As novel technologies and analytical methods continue to advance, this realm of research is rapidly gaining traction. Within this mini-review, we delve into future research domains concerning aberrations in noncoding DNA regions, such as pseudoexons, promoter variants and cis-epimutations.
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Affiliation(s)
- Maria Baz Ibrahim
- Department of Oncogenetics & Tumor Biology, Paul Brousse Hospital, Villejuif, France
| | - James Flanagan
- Department of Surgery & Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Tony Ibrahim
- International Department of Medical Oncology, Gustave Roussy, 94805, Villejuif, France
| | - Etienne Rouleau
- Department of Biology & Pathology-Cancer Genetics Laboratory, Gustave Roussy, 94805, Villejuif, France
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29
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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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30
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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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31
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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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32
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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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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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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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36
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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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37
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Bertrand A, Ba I, Kermasson L, Pirabakaran V, Chable N, Lainey E, Ménard C, Kallel F, Picard C, Hadiji S, Coolen-Allou N, Blanchard E, de Villartay JP, Moshous D, Roelens M, Callebaut I, Kannengiesser C, Revy P. Characterization of novel mutations in the TEL-patch domain of the telomeric factor TPP1 associated with telomere biology disorders. Hum Mol Genet 2024; 33:612-623. [PMID: 38176734 DOI: 10.1093/hmg/ddad210] [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: 07/11/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Telomeres are nucleoprotein structures that protect the chromosome ends from degradation and fusion. Telomerase is a ribonucleoprotein complex essential to maintain the length of telomeres. Germline defects that lead to short and/or dysfunctional telomeres cause telomere biology disorders (TBDs), a group of rare and heterogeneous Mendelian diseases including pulmonary fibrosis, dyskeratosis congenita, and Høyeraal-Hreidarsson syndrome. TPP1, a telomeric factor encoded by the gene ACD, recruits telomerase at telomere and stimulates its activity via its TEL-patch domain that directly interacts with TERT, the catalytic subunit of telomerase. TBDs due to TPP1 deficiency have been reported only in 11 individuals. We here report four unrelated individuals with a wide spectrum of TBD manifestations carrying either heterozygous or homozygous ACD variants consisting in the recurrent and previously described in-frame deletion of K170 (K170∆) and three novel missense mutations G179D, L184R, and E215V. Structural and functional analyses demonstrated that the four variants affect the TEL-patch domain of TPP1 and impair telomerase activity. In addition, we identified in the ACD gene several motifs associated with small deletion hotspots that could explain the recurrence of the K170∆ mutation. Finally, we detected in a subset of blood cells from one patient, a somatic TERT promoter-activating mutation that likely provides a selective advantage over non-modified cells, a phenomenon known as indirect somatic genetic rescue. Together, our results broaden the genetic and clinical spectrum of TPP1 deficiency and specify new residues in the TEL-patch domain that are crucial for length maintenance and stability of human telomeres in vivo.
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Affiliation(s)
- Alexis Bertrand
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Ibrahima Ba
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Génétique, Université Paris Diderot, Paris 75018, France
| | - Laëtitia Kermasson
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Vithura Pirabakaran
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Noémie Chable
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Elodie Lainey
- Hematology Laboratory, Robert Debré Hospital-AssistancePublique-Hôpitaux de Paris (APHP), INSERM UMR 1131-Hematology University Institute-Denis Diderot School of Medicine, Paris 75019, France
| | - Christelle Ménard
- Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Génétique, Université Paris Diderot, Paris 75018, France
| | - Faten Kallel
- Hematology Department, Hedi Chaker Hospital, 3029, Sfax, Tunisia
| | - Capucine Picard
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, (APHP), Paris 75015, France
- Centre de références des déficits immunitaires Héréditaires (CEREDIH), Necker-Enfants Malades Hospital APHP, Paris 75015, France
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, Inserm UMR 1163, Institut Imagine, Paris 75015, France
| | - Sondes Hadiji
- Hematology Department, Hedi Chaker Hospital, 3029, Sfax, Tunisia
| | - Nathalie Coolen-Allou
- Service de Pneumologie, Hôpital Félix Guyon, CHU Réunion, Saint-Denis de la Réunion 97400, France
| | - Elodie Blanchard
- Service de Pneumologie, Hôpital Haut-Lévêque, CHU Bordeaux, Bordeaux 33604, France
| | - Jean-Pierre de Villartay
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
| | - Despina Moshous
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Department of Pediatric Immunology, Hematology and Rheumatology, Necker-Enfants Malades Hospital, (APHP), Paris 75015, France
| | - Marie Roelens
- Université Paris Cité, Imagine Institute, Paris 75015, France
- Centre de références des déficits immunitaires Héréditaires (CEREDIH), Necker-Enfants Malades Hospital APHP, Paris 75015, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris 75005, France
| | - Caroline Kannengiesser
- Assistance Publique des Hôpitaux de Paris, Hôpital Bichat, Service de Génétique, Université Paris Diderot, Paris 75018, France
| | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue contre le Cancer, INSERM UMR 1163, Imagine Institute, 24 boulevard du Montparnasse, Paris 75015, France
- Université Paris Cité, Imagine Institute, Paris 75015, France
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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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Phillips GS, Mengden-Koon S, Dhossche J, LeBoit PE, Goldstein AM, Lee I, Raffeld M, Papanicolau-Sengos A, Sargen MR, Chung J. Atypical Spitz tumor with SQSTM1::NTRK2 fusion: Report of a case with unique spindled cell features. J Cutan Pathol 2024; 51:198-204. [PMID: 38031352 DOI: 10.1111/cup.14565] [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: 07/01/2023] [Revised: 10/28/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023]
Abstract
A host of signature genetic alterations have been demonstrated in Spitz neoplasms, most notably fusions of kinase genes (including BRAF, ALK, ROS1, NTRK1, NTRK3, RET, MET, MAP3K8) or variants in HRAS. While there are multiple reports of rearrangements involving NTRK1 and NTRK3 in Spitz tumors, there are very few reports of NTRK2-rearranged Spitz nevi in the literature. This report presents an NTRK2-rearranged atypical Spitz tumor with spindled cell features. The patient was a 6-year-old female with a growing pigmented papule on the back. Histopathological evaluation revealed an asymmetric, biphasic, compound proliferation of melanocytes featuring an epithelioid cell population arranged as variably sized nests and single cells along the basal layer with extension down adnexa, as well as a population of spindled melanocytes with desmoplastic features and loss of Melan-A expression in the dermis. There was partial loss of p16 expression in the epidermal component and diffuse loss in the dermal component. Immunohistochemistry for PRAME, ALK, NTRK1, HRAS Q61R, p53, and BRAF V600E were negative. A SQSTM1::NTRK2 fusion was identified by RNA sequencing. No TERT promoter hotspot variants were detected. This case report expands the known histopathologic spectrum of genetic alterations in Spitz neoplasms.
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Affiliation(s)
- Gregory S Phillips
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, USA
| | | | - Julie Dhossche
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, USA
| | - Philip E LeBoit
- Dermatopathology and Oral Pathology Service, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Ina Lee
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark Raffeld
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Antonios Papanicolau-Sengos
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael R Sargen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Jina Chung
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, USA
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Marrapodi R, Bellei B. The Keratinocyte in the Picture Cutaneous Melanoma Microenvironment. Cancers (Basel) 2024; 16:913. [PMID: 38473275 DOI: 10.3390/cancers16050913] [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: 01/22/2024] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Melanoma progression is a multistep evolution from a common melanocytic nevus through a radial superficial growth phase, the invasive vertical growth phase finally leading to metastatic dissemination into distant organs. Melanoma aggressiveness largely depends on the propensity to metastasize, which means the capacity to escape from the physiological microenvironment since tissue damage due to primary melanoma lesions is generally modest. Physiologically, epidermal melanocytes are attached to the basement membrane, and their adhesion/migration is under the control of surrounding keratinocytes. Thus, the epidermal compartment represents the first microenvironment responsible for melanoma spread. This complex process involves cell-cell contact and a broad range of secreted bioactive molecules. Invasion, or at the beginning of the microinvasion, implies the breakdown of the dermo-epidermal basement membrane followed by the migration of neoplastic melanocytic cells in the superficial papillary dermis. Correspondingly, several experimental evidences documented the structural and functional rearrangement of the entire tissue surrounding neoplasm that in some way reflects the atypia of tumor cells. Lastly, the microenvironment must support the proliferation and survival of melanocytes outside the normal epidermal-melanin units. This task presumably is mostly delegated to fibroblasts and ultimately to the self-autonomous capacity of melanoma cells. This review will discuss remodeling that occurs in the epidermis during melanoma formation as well as skin changes that occur independently of melanocytic hyperproliferation having possible pro-tumoral features.
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Affiliation(s)
- Ramona Marrapodi
- Laboratory of Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatological Institute, IRCCS, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Barbara Bellei
- Laboratory of Cutaneous Physiopathology and Integrated Center of Metabolomics Research, San Gallicano Dermatological Institute, IRCCS, Via Elio Chianesi 53, 00144 Rome, Italy
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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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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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Lorbeer FK, Rieser G, Goel A, Wang M, Oh A, Yeh I, Bastian BC, Hockemeyer D. Distinct senescence mechanisms restrain progression of dysplastic nevi. PNAS NEXUS 2024; 3:pgae041. [PMID: 38371417 PMCID: PMC10873501 DOI: 10.1093/pnasnexus/pgae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
Telomerase reverse transcriptase (TERT) promoter mutations (TPMs) are frequently found in different cancer types, including ∼70% of sun-exposed skin melanomas. In melanoma, TPMs are among the earliest mutations and can be present during the transition from nevus to melanoma. However, the specific factors that contribute to the selection of TPMs in certain nevi subsets are not well understood. To investigate this, we analyzed a group of dysplastic nevi (DN) by sequencing genes commonly mutated in melanocytic neoplasms. We examined the relationship between the identified mutations, patient age, telomere length, histological features, and the expression of p16. Our findings reveal that TPMs are more prevalent in DN from older patients and are associated with shorter telomeres. Importantly, these TPMs were not found in nevi with BRAF V600E mutations. Conversely, DN with BRAF V600E mutations were observed in younger patients, had longer telomeres and a higher proportion of p16-positive cells. This suggests that these nevi arrest growth independently of telomere shortening through a mechanism known as oncogene-induced senescence (OIS). These characteristics extend to melanoma-sequencing datasets, where melanomas with BRAF V600E mutations were more likely to have a CDKN2A inactivation, overriding OIS. In contrast, melanomas without BRAF V600E mutations showed a higher frequency of TPMs. Our data imply that TPMs are selected to bypass replicative senescence (RS) in cells that were not arrested by OIS. Overall, our results indicate that a subset of melanocytic neoplasms face constraints from RS, while others encounter OIS and RS. The order in which these barriers are overcome during progression to melanoma depends on the mutational context.
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Affiliation(s)
- Franziska K Lorbeer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabrielle Rieser
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aditya Goel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Meng Wang
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Areum Oh
- Rebus Biosystems, Santa Clara, CA 95050, USA
| | - Iwei Yeh
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
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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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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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Liu M, Zhang Y, Jian Y, Gu L, Zhang D, Zhou H, Wang Y, Xu ZX. The regulations of telomerase reverse transcriptase (TERT) in cancer. Cell Death Dis 2024; 15:90. [PMID: 38278800 PMCID: PMC10817947 DOI: 10.1038/s41419-024-06454-7] [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: 09/22/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
Abnormal activation of telomerase occurs in most cancer types, which facilitates escaping from cell senescence. As the key component of telomerase, telomerase reverse transcriptase (TERT) is regulated by various regulation pathways. TERT gene changing in its promoter and phosphorylation respectively leads to TERT ectopic expression at the transcription and protein levels. The co-interacting factors play an important role in the regulation of TERT in different cancer types. In this review, we focus on the regulators of TERT and these downstream functions in cancer regulation. Determining the specific regulatory mechanism will help to facilitate the development of a cancer treatment strategy that targets telomerase and cancer cell senescence. As the most important catalytic subunit component of telomerase, TERT is rapidly regulated by transcriptional factors and PTM-related activation. These changes directly influence TERT-related telomere maintenance by regulating telomerase activity in telomerase-positive cancer cells, telomerase assembly with telomere-binding proteins, and recruiting telomerase to the telomere. Besides, there are also non-canonical functions that are influenced by TERT, including the basic biological functions of cancer cells, such as proliferation, apoptosis, cell cycle regulation, initiating cell formation, EMT, and cell invasion. Other downstream effects are the results of the influence of transcriptional factors by TERT. Currently, some small molecular inhibitors of TERT and TERT vaccine are under research as a clinical therapeutic target. Purposeful work is in progress.
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Affiliation(s)
- Mingdi Liu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, Jilin, China
| | - Yuning Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, Jilin, China
| | - Yongping Jian
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, Jilin, China
| | - Liting Gu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, Jilin, China
| | - Dan Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, Jilin, China
| | - Honglan Zhou
- Department of Urology, The First Hospital of Jilin University, Changchun, 130021, Jilin, China.
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, Jilin, China.
| | - Zhi-Xiang Xu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, 130021, Jilin, China.
- Department of Urology, The First Hospital of Jilin University, Changchun, 130021, Jilin, China.
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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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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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