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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Macarthur JI, Carlstrom L, Hannan CJ, Wadeson A, Driscoll C, Neff B, Carlson ML, Rutherford SA, Link MJ, van Gompel JJ. Radiation-Associated Vestibular Schwannomas: Case Series and Literature Review. World Neurosurg 2024; 188:e341-e348. [PMID: 38789032 DOI: 10.1016/j.wneu.2024.05.113] [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: 04/22/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVES Radiation treatment, particularly at a young age, creates theoretical risk for long-term adverse radiation effects, including the development of malignancy. The literature is sparse on radiation-induced vestibular schwannomas (VSs). METHODS A retrospective review was performed for cases of suspected radiation-induced VS at 2 high-volume centers. Only cases where radiation included coverage of the posterior fossa were included with those diagnosed within 3 years of radiation treatment being excluded. Patient and tumor characteristics were collected. A systematic literature review was also performed for any previously published series on radiation-induced VS. RESULTS Eight cases of radiation-induced VS were identified with a median follow-up 125 months (range 7-131). The median age at incident radiation was 15 years (range 2-46). The median age at VS diagnosis was 57 years (range 26-83) with median interval from radiation to diagnosis of 51-years (range 15-66). The median tumor size was 6 mm (range 3-21). Two patients underwent surgical resection. Lesions were described as soft and highly vascular, with medium to high adherence to the facial nerve. Five articles with a total of 52 patients were identified, median age at VS diagnosis was 42-years (range 23-73) with a median interval from radiation to diagnosis of 19 years (range 15-23). CONCLUSIONS The development of VS following radiation exposure appears rare and our understanding of the condition remains incomplete. Further studies are required to determine the best management of these patients and determine whether there is a causative relationship between radiation exposure and the development of VS.
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Affiliation(s)
- Joshua I Macarthur
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK; Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, UK.
| | - Lucas Carlstrom
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Cathal John Hannan
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK; Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, UK
| | - Andrea Wadeson
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK
| | - Colin Driscoll
- Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Brian Neff
- Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew L Carlson
- Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott A Rutherford
- Department of Neurosurgery, Manchester Centre for Clinical Neurosciences, Manchester, UK; Geoffrey Jefferson Brain Research Centre, University of Manchester, Manchester, UK
| | - Michael J Link
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA; Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Jamie J van Gompel
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA; Otolaryngology-Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
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Mochizuki A, Shiraishi K, Honda T, Higashiyama RI, Sunami K, Matsuda M, Shimada Y, Miyazaki Y, Yoshida Y, Watanabe SI, Yatabe Y, Hamamoto R, Kohno T. Passive Smoking-Induced Mutagenesis as a Promoter of Lung Carcinogenesis. J Thorac Oncol 2024; 19:984-994. [PMID: 38382595 DOI: 10.1016/j.jtho.2024.02.006] [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: 09/01/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/23/2024]
Abstract
INTRODUCTION The International Agency for Research on Cancer has classified passive smoking (PS) or secondhand smoke exposure as a group 1 carcinogen linked to lung cancer. However, in contrast to active smoking, the mutagenic properties of PS remain unclear. METHODS A consecutive cohort of 564 lung adenocarcinoma samples from female never-smokers, who provided detailed information about their exposure to PS during adolescence and in their thirties through a questionnaire, was prepared. Of these, all 291 cases for whom frozen tumor tissues were available were subjected to whole exome sequencing to estimate tumor mutational burden, and the top 84 cases who were exposed daily, or not, to PS during adolescence, in their thirties or in both periods, were further subjected to whole genome sequencing. RESULTS A modest yet statistically significant increase in tumor mutational burden was observed in the group exposed to PS compared with the group not exposed to PS (median values = 1.44 versus 1.29 per megabase, respectively; p = 0.020). Instead of inducing driver oncogene mutations, PS-induced substantial subclonal mutations exhibiting APOBEC-type signatures, including SMAD4 and ADGRG6 hotspot mutations. A polymorphic APOBEC3A/3B allele-specific to the Asian population that leads to up-regulated expression of APOBEC3A accentuated the mutational load in individuals exposed daily to PS during adolescence. CONCLUSIONS This study reveals that PS-induced mutagenesis can promote lung carcinogenesis. The APOBEC3A/3B polymorphism may serve as a biomarker for identifying passive nonsmoking individuals at high risk of developing lung cancer.
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Affiliation(s)
- Akifumi Mochizuki
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan; Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Takayuki Honda
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Kuniko Sunami
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Maiko Matsuda
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoko Shimada
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yukihiro Yoshida
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Department of Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan.
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4
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Németh E, Szüts D. The mutagenic consequences of defective DNA repair. DNA Repair (Amst) 2024; 139:103694. [PMID: 38788323 DOI: 10.1016/j.dnarep.2024.103694] [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: 03/22/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
Multiple separate repair mechanisms safeguard the genome against various types of DNA damage, and their failure can increase the rate of spontaneous mutagenesis. The malfunction of distinct repair mechanisms leads to genomic instability through different mutagenic processes. For example, defective mismatch repair causes high base substitution rates and microsatellite instability, whereas homologous recombination deficiency is characteristically associated with deletions and chromosome instability. This review presents a comprehensive collection of all mutagenic phenotypes associated with the loss of each DNA repair mechanism, drawing on data from a variety of model organisms and mutagenesis assays, and placing greatest emphasis on systematic analyses of human cancer datasets. We describe the latest theories on the mechanism of each mutagenic process, often explained by reliance on an alternative repair pathway or the error-prone replication of unrepaired, damaged DNA. Aided by the concept of mutational signatures, the genomic phenotypes can be used in cancer diagnosis to identify defective DNA repair pathways.
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Affiliation(s)
- Eszter Németh
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Dávid Szüts
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
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5
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Jayakrishnan R, Kwiatkowski DJ, Rose MG, Nassar AH. Topography of mutational signatures in non-small cell lung cancer: emerging concepts, clinical applications, and limitations. Oncologist 2024:oyae091. [PMID: 38907669 DOI: 10.1093/oncolo/oyae091] [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: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 06/24/2024] Open
Abstract
The genome of a cell is continuously battered by a plethora of exogenous and endogenous processes that can lead to damaged DNA. Repair mechanisms correct this damage most of the time, but failure to do so leaves mutations. Mutations do not occur in random manner, but rather typically follow a more or less specific pattern due to known or imputed mutational processes. Mutational signature analysis is the process by which the predominant mutational process can be inferred for a cancer and can be used in several contexts to study both the genesis of cancer and its response to therapy. Recent pan-cancer genomic efforts such as "The Cancer Genome Atlas" have identified numerous mutational signatures that can be categorized into single base substitutions, doublet base substitutions, or small insertions/deletions. Understanding these mutational signatures as they occur in non-small lung cancer could improve efforts at prevention, predict treatment response to personalized treatments, and guide the development of therapies targeting tumor evolution. For non-small cell lung cancer, several mutational signatures have been identified that correlate with exposures such as tobacco smoking and radon and can also reflect endogenous processes such as aging, APOBEC activity, and loss of mismatch repair. Herein, we provide an overview of the current knowledge of mutational signatures in non-small lung cancer.
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Affiliation(s)
- Ritujith Jayakrishnan
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - David J Kwiatkowski
- Department of Pulmonary Medicine, Brigham and Women's Hospital, Boston, MA, 02115, United States
| | - Michal G Rose
- Yale University School of Medicine and Cancer Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, United States
- Department of Medicine, Medical Oncology Division, Yale Cancer Center, New Haven, CT, United States
| | - Amin H Nassar
- Yale University School of Medicine and Cancer Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT 06516, United States
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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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7
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Yancoskie MN, Khaleghi R, Gururajan A, Raghunathan A, Gupta A, Diethelm S, Maritz C, Sturla SJ, Krishnan M, Naegeli H. ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction. Nucleic Acids Res 2024:gkae517. [PMID: 38884271 DOI: 10.1093/nar/gkae517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C-containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C->T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Reihaneh Khaleghi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Anirvinya Gururajan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aadarsh Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aryan Gupta
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Sarah Diethelm
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich 8092, Switzerland
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
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8
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Morton LM, Lee OW, Karyadi DM, Bogdanova TI, Stewart C, Hartley SW, Breeze CE, Schonfeld SJ, Cahoon EK, Drozdovitch V, Masiuk S, Chepurny M, Zurnadzhy LY, Dai J, Krznaric M, Yeager M, Hutchinson A, Hicks BD, Dagnall CL, Steinberg MK, Jones K, Jain K, Jordan B, Machiela MJ, Dawson ET, Vij V, Gastier-Foster JM, Bowen J, Mabuchi K, Hatch M, Berrington de Gonzalez A, Getz G, Tronko MD, Thomas GA, Chanock SJ. Genomic characterization of cervical lymph node metastases in papillary thyroid carcinoma following the Chornobyl accident. Nat Commun 2024; 15:5053. [PMID: 38871684 PMCID: PMC11176192 DOI: 10.1038/s41467-024-49292-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2024] [Indexed: 06/15/2024] Open
Abstract
Childhood radioactive iodine exposure from the Chornobyl accident increased papillary thyroid carcinoma (PTC) risk. While cervical lymph node metastases (cLNM) are well-recognized in pediatric PTC, the PTC metastatic process and potential radiation association are poorly understood. Here, we analyze cLNM occurrence among 428 PTC with genomic landscape analyses and known drivers (131I-exposed = 349, unexposed = 79; mean age = 27.9 years). We show that cLNM are more frequent in PTC with fusion (55%) versus mutation (30%) drivers, although the proportion varies by specific driver gene (RET-fusion = 71%, BRAF-mutation = 38%, RAS-mutation = 5%). cLNM frequency is not associated with other characteristics, including radiation dose. cLNM molecular profiling (N = 47) demonstrates 100% driver concordance with matched primary PTCs and highly concordant mutational spectra. Transcriptome analysis reveals 17 differentially expressed genes, particularly in the HOXC cluster and BRINP3; the strongest differentially expressed microRNA also is near HOXC10. Our findings underscore the critical role of driver alterations and provide promising candidates for elucidating the biological underpinnings of PTC cLNM.
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Affiliation(s)
- Lindsay M Morton
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Olivia W Lee
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danielle M Karyadi
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tetiana I Bogdanova
- Laboratory of Morphology of the Endocrine System, V.P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen W Hartley
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles E Breeze
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sara J Schonfeld
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth K Cahoon
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir Drozdovitch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergii Masiuk
- National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Mykola Chepurny
- National Research Center for Radiation Medicine of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Liudmyla Yu Zurnadzhy
- Laboratory of Morphology of the Endocrine System, V.P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Jieqiong Dai
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Marko Krznaric
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London, United Kingdom
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Mia K Steinberg
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Komal Jain
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Ben Jordan
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Bethesda, MD, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric T Dawson
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Nvidia Corporation, Santa Clara, CA, USA
| | - Vibha Vij
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH, USA
- Departments of Pathology and Pediatrics, Ohio State University College of Medicine, Columbus, OH, USA
| | - Jay Bowen
- Nationwide Children's Hospital, Biospecimen Core Resource, Columbus, OH, USA
| | - Kiyohiko Mabuchi
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maureen Hatch
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Berrington de Gonzalez
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mykola D Tronko
- Department of Fundamental and Applied Problems of Endocrinology, V.P. Komisarenko Institute of Endocrinology and Metabolism of the National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - Gerry A Thomas
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital, London, United Kingdom
| | - Stephen J Chanock
- Laboratory of Genetic Susceptibility, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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9
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Tan QX, Shannon NB, Lim WK, Teo JX, Yap DRY, Lek SM, Tan JWS, Tan SJJ, Hendrikson J, Liu Y, Ng G, Chong CYL, Guo W, Koh KKN, Ng CCY, Rajasegaran V, Wong JS, Seo CJ, Ong CK, Lim TKH, Teh BT, Kon OL, Chia CS, Soo KC, Iyer NG, Ong CAJ. Transcriptomic convergence despite genomic divergence drive field cancerization in synchronous squamous tumors. Front Oncol 2024; 14:1272432. [PMID: 38939336 PMCID: PMC11208456 DOI: 10.3389/fonc.2024.1272432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
Introduction Field cancerization is suggested to arise from imbalanced differentiation in individual basal progenitor cells leading to clonal expansion of mutant cells that eventually replace the epithelium, although without evidence. Methods We performed deep sequencing analyses to characterize the genomic and transcriptomic landscapes of field change in two patients with synchronous aerodigestive tract tumors. Results Our data support the emergence of numerous genetic alterations in cancer-associated genes but refutes the hypothesis that founder mutation(s) underpin this phenomenon. Mutational signature analysis identified defective homologous recombination as a common underlying mutational process unique to synchronous tumors. Discussion Our analyses suggest a common etiologic factor defined by mutational signatures and/or transcriptomic convergence, which could provide a therapeutic opportunity.
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Affiliation(s)
- Qiu Xuan Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Nicholas B. Shannon
- Department of Head and Neck Surgery, Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Singapore
- Cancer and Stem Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Singapore
| | - Daniel R. Y. Yap
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Sze Min Lek
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Joey W. S. Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Shih Jia J. Tan
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Josephine Hendrikson
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Ying Liu
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Gillian Ng
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Clara Y. L. Chong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Wanyu Guo
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Kelvin K. N. Koh
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Cedric C. Y. Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Vikneswari Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Jolene S.M. Wong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
| | - Chin Jin Seo
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
| | - Choon Kiat Ong
- Cancer and Stem Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Lymphoma Genomics Translational Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Tony K. H. Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
- Pathology Academic Clinical Program, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Bin Tean Teh
- Cancer and Stem Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, ASTAR Research Entities, Singapore, Singapore
| | - Oi Lian Kon
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Claramae S. Chia
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Khee Chee Soo
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - N. Gopalakrishna Iyer
- Department of Head and Neck Surgery, Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Cancer and Stem Biology Program, Duke-NUS Medical School, Singapore, Singapore
- Cancer Therapeutics Research Laboratory, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Chin-Ann J. Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, ASTAR Research Entities, Singapore, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
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10
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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11
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Gou X, Shao Y, Wang X, Shi H, Yu J, Li X, Guo T. Evolutionary patterns of DNA base composition at polymorphic sites highlight the role of the environment in shaping barley and rice genomes. THE PLANT GENOME 2024; 17:e20456. [PMID: 38688857 DOI: 10.1002/tpg2.20456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/20/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
Abstract
Insights into changes in genome base composition underlying crop domestication can be gained by using comparative genomics. With this approach, previous studies have reported that crop genomes during domestication accumulate more nucleotides adenine (A) and thymine (T) (termed as [AT]-increase) across polymorphic sites. However, the potential influence of the environment or its factors, for example, solar ultraviolet (UV) radiation and temperature, on the [AT]-increase has not been well elucidated. Here, we investigated the [AT]-increase in barley (Hordeum vulgare L.) and rice (Oryza sativa L.) and the association with natural environments, where accessions are distributed. With 12,798,376 and 2,861,535 single-nucleotide polymorphisms from 368 barley and 1375 rice accessions, respectively, we discovered that [AT] increases from wild accessions to improved cultivars, and genomic regions with larger [AT]-increase tend to have higher UV-related motif frequencies, suggesting solar UV radiation as a potential factor in driving genome variation. To link [AT] change with the geographic distribution, we gathered georeferenced accessions and examined their local environments. Interestingly, negative correlations between [AT] and environmental factors were observed (r = -0.39 ∼ -0.75) and modern accessions with higher [AT] values, as compared with wild relatives, are from the environments with lower solar UV radiation or lower temperature. With [AT] and environmental factors as phenotypes, genome-wide association mapping identified three candidate genes that have the potential to contribute to [AT] variation under the effect of environmental conditions. Our findings provide genomic and environmental insights into evolutionary pattern of DNA base composition and underlying mechanisms.
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Affiliation(s)
- Xiangjian Gou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yang Shao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Haoran Shi
- Chengdu Academy of Agricultural and Forestry Sciences, Wenjiang, China
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Xianran Li
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, Washington, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Tingting Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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12
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Benedict B, Kristensen SM, Duxin JP. What are the DNA lesions underlying formaldehyde toxicity? DNA Repair (Amst) 2024; 138:103667. [PMID: 38554505 DOI: 10.1016/j.dnarep.2024.103667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 04/01/2024]
Abstract
Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.
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Affiliation(s)
- Bente Benedict
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Stella Munkholm Kristensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Julien P Duxin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark.
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13
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Zhou D, Li Y, Liu Q, Deng X, Chen L, Li M, Zhang J, Lu X, Zheng H, Dai J. Integrated whole-exome and bulk transcriptome sequencing delineates the dynamic evolution from preneoplasia to invasive lung adenocarcinoma featured with ground-glass nodules. Cancer Med 2024; 13:e7383. [PMID: 38864483 PMCID: PMC11167609 DOI: 10.1002/cam4.7383] [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: 10/03/2023] [Revised: 04/15/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
OBJECTIVE The genomic and molecular ecology involved in the stepwise continuum progression of lung adenocarcinoma (LUAD) from adenocarcinoma in situ (AIS) to minimally invasive adenocarcinoma (MIA) and subsequent invasive adenocarcinoma (IAC) remains unclear and requires further elucidation. We aimed to characterize gene mutations and expression landscapes, and explore the association between differentially expressed genes (DEGs) and significantly mutated genes (SMGs) during the dynamic evolution from AIS to IAC. METHODS Thirty-five patients with ground-glass nodules (GGNs) lung adenocarcinomas were enrolled. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-Seq) were conducted on all patients, encompassing both tumor samples and corresponding noncancerous tissues. Data obtained from WES and RNA-Seq were subsequently analyzed. RESULTS The findings from WES delineated that the predominant mutations were observed in EGFR (49%) and ANKRD36C (17%). SMGs, including EGFR and RBM10, were associated with the dynamic evolution from AIS to IAC. Meanwhile, DEGs, including GPR143, CCR9, ADAMTS16, and others were associated with the entire process of invasive LUAD. We found that the signaling pathways related to cell migration and invasion were upregulated, and the signaling pathways of angiogenesis were downregulated across the pathological stages. Furthermore, we found that the messenger RNA (mRNA) levels of FAM83A, MAL2, DEPTOR, and others were significantly correlated with CNVs. Gene set enrichment analysis (GSEA) showed that heme metabolism and cholesterol homeostasis pathways were significantly upregulated in patients with EGFR/RBM10 co-mutations, and these patients may have poorer overall survival than those with EGFR mutations. Based on the six calculation methods for the immune infiltration score, NK/CD8+ T cells decreased, and Treg/B cells increased with the progression of early LUAD. CONCLUSIONS Our findings offer valuable insights into the unique genomic and molecular features of LUAD, facilitating the identification and advancement of precision medicine strategies targeting the invasive progression of LUAD from AIS to IAC.
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Affiliation(s)
- Dong Zhou
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Yan‐qi Li
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Quan‐xing Liu
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Xu‐feng Deng
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Liang Chen
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Man‐yuan Li
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Jiao Zhang
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Xiao Lu
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Hong Zheng
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
| | - Ji‐gang Dai
- Department of Thoracic SurgeryXinqiao Hospital, Third Military Medical University (Army Medical University)ChongqingChina
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14
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Garcia GL, Orellana T, Gorecki G, Frisbie LG, Baruwal R, Goldfield E, Beddows I, MacFawn IP, Britt AK, Hale MM, Shen H, Buckanovich R, Finkel T, Drapkin R, Soong TR, Bruno TC, Atiya HI, Coffman L. Stromal mediated DNA damage promotes high grade serous ovarian cancer initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595550. [PMID: 38853994 PMCID: PMC11160569 DOI: 10.1101/2024.05.23.595550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The fundamental steps in high-grade serous ovarian cancer (HGSOC) initiation are unclear, thus providing critical barriers to the development of prevention or early detection strategies for this deadly disease. Increasing evidence demonstrates most HGSOC starts in the fallopian tube epithelium (FTE). Current models propose HGSOC initiates when FTE cells acquire increasing numbers of mutations allowing cells to evolve into serous tubal intraepithelial carcinoma (STIC) precursors and then to full blown cancer. Here we report that epigenetically altered mesenchymal stem cells (termed high risk MSC-hrMSCs) can be detected prior to the formation of ovarian cancer precursor lesions. These hrMSCs drive DNA damage in the form of DNA double strand breaks in FTE cells while also promoting the survival of FTE cells in the face of DNA damage. Indicating the hrMSC may actually drive cancer initiation, we find hrMSCs induce full malignant transformation of otherwise healthy, primary FTE resulting in metastatic cancer in vivo . Further supporting a role for hrMSCs in cancer initiation in humans, we demonstrate that hrMSCs are highly enriched in BRCA1/2 mutation carriers and increase with age. Combined these findings indicate that hrMSCs may incite ovarian cancer initiation. These findings have important implications for ovarian cancer detection and prevention.
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15
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Zhu T, Tong H, Du Z, Beck S, Teschendorff AE. An improved epigenetic counter to track mitotic age in normal and precancerous tissues. Nat Commun 2024; 15:4211. [PMID: 38760334 PMCID: PMC11101651 DOI: 10.1038/s41467-024-48649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC's mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.
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Affiliation(s)
- Tianyu Zhu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Zhaozhen Du
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, WC1E 6BT, London, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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16
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Díaz-Gay M, Zhang T, Hoang PH, Khandekar A, Zhao W, Steele CD, Otlu B, Nandi SP, Vangara R, Bergstrom EN, Kazachkova M, Pich O, Swanton C, Hsiung CA, Chang IS, Wong MP, Leung KC, Sang J, McElderry J, Yang L, Nowak MA, Shi J, Rothman N, Wedge DC, Homer R, Yang SR, Lan Q, Zhu B, Chanock SJ, Alexandrov LB, Landi MT. The mutagenic forces shaping the genomic landscape of lung cancer in never smokers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307318. [PMID: 38798417 PMCID: PMC11118654 DOI: 10.1101/2024.05.15.24307318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Lung cancer in never smokers (LCINS) accounts for up to 25% of all lung cancers and has been associated with exposure to secondhand tobacco smoke and air pollution in observational studies. Here, we evaluate the mutagenic exposures in LCINS by examining deep whole-genome sequencing data from a large international cohort of 871 treatment-naïve LCINS recruited from 28 geographical locations within the Sherlock-Lung study. KRAS mutations were 3.8-fold more common in adenocarcinomas of never smokers from North America and Europe, while a 1.6-fold higher prevalence of EGFR and TP53 mutations was observed in adenocarcinomas from East Asia. Signature SBS40a, with unknown cause, was found in most samples and accounted for the largest proportion of single base substitutions in adenocarcinomas, being enriched in EGFR-mutated cases. Conversely, the aristolochic acid signature SBS22a was almost exclusively observed in patients from Taipei. Even though LCINS exposed to secondhand smoke had an 8.3% higher mutational burden and 5.4% shorter telomeres, passive smoking was not associated with driver mutations in cancer driver genes or the activities of individual mutational signatures. In contrast, patients from regions with high levels of air pollution were more likely to have TP53 mutations while exhibiting shorter telomeres and an increase in most types of somatic mutations, including a 3.9-fold elevation of signature SBS4 (q-value=3.1 × 10-5), previously linked mainly to tobacco smoking, and a 76% increase of clock-like signature SBS5 (q-value=5.0 × 10-5). A positive dose-response effect was observed with air pollution levels, which correlated with both a decrease in telomere length and an elevation in somatic mutations, notably attributed to signatures SBS4 and SBS5. Our results elucidate the diversity of mutational processes shaping the genomic landscape of lung cancer in never smokers.
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Affiliation(s)
- Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher D. Steele
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Shuvro P. Nandi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Mariya Kazachkova
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Chao Agnes Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Maria Pik Wong
- Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Kin Chung Leung
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Lixing Yang
- Ben May Department for Cancer Research, Department of Human Genetics, Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| | - Martin A Nowak
- Department of Mathematics, Harvard University, Cambridge, MA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
- Manchester NIHR Biomedical Research Centre, Manchester, UK
| | - Robert Homer
- Yale Surgery Pathology Department, Yale University, New Haven, CT, USA
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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17
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Manghrani A, Rangadurai AK, Szekely O, Liu B, Guseva S, Al-Hashimi HM. Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594415. [PMID: 38798635 PMCID: PMC11118333 DOI: 10.1101/2024.05.15.594415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The propensities to form lowly-populated short-lived conformations of DNA could vary with sequence, providing an important source of sequence-specificity in biochemical reactions. However, comprehensively measuring how these dynamics vary with sequence is challenging. Using 1H CEST and 13C R 1 ρ NMR, we measured Watson-Crick to Hoogsteen dynamics for an A-T base pair in thirteen trinucleotide sequence contexts. The Hoogsteen population and exchange rate varied 4-fold and 16-fold, respectively, and were dependent on both the 3'- and 5'-neighbors but only weakly dependent on monovalent ion concentration (25 versus 100 mM NaCl) and pH (6.8 versus 8.0). Flexible TA and CA dinucleotide steps exhibited the highest Hoogsteen populations, and their kinetics rates strongly depended on the 3'-neighbor. In contrast, the stiffer AA and GA steps had the lowest Hoogsteen population, and their kinetics were weakly dependent on the 3'-neighbor. The Hoogsteen lifetime was especially short when G-C neighbors flanked the A-T base pair. The Hoogsteen dynamics had a distinct sequence-dependence compared to duplex stability and minor groove width. Thus, our results uncover a unique source of sequence-specificity hidden within the DNA double helix in the form of A-T Hoogsteen dynamics and establish the utility of 1H CEST to quantitively measure sequence-dependent DNA dynamics.
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Affiliation(s)
- Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Atul Kaushik Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, M5G 0A4, Canada
| | - Or Szekely
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27705, United States
| | - Serafima Guseva
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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18
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Conway JR, Gillani R, Crowdis J, Reardon B, Park J, Han S, Titchen B, Benamar M, Haq R, Van Allen EM. Somatic structural variants drive distinct modes of oncogenesis in melanoma. J Clin Invest 2024; 134:e177270. [PMID: 38758740 PMCID: PMC11213511 DOI: 10.1172/jci177270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
The diversity of structural variants (SVs) in melanoma and how they impact oncogenesis are incompletely known. We performed harmonized analysis of SVs across melanoma histologic and genomic subtypes, and we identified distinct global properties between subtypes. These included the frequency and size of SVs and SV classes, their relation to chromothripsis events, and the impact on cancer-related genes of SVs that alter topologically associated domain (TAD) boundaries. Following our prior identification of double-stranded break repair deficiency in a subset of triple-wild-type cutaneous melanoma, we identified MRE11 and NBN loss-of-function SVs in melanomas with this mutational signature. Experimental knockouts of MRE11 and NBN, followed by olaparib cell viability assays in melanoma cells, indicated that dysregulation of each of these genes may cause sensitivity to PARP inhibitors in cutaneous melanomas. Broadly, harmonized analysis of melanoma SVs revealed distinct global genomic properties and molecular drivers, which may have biological and therapeutic impact.
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Affiliation(s)
- Jake R. Conway
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Riaz Gillani
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Jett Crowdis
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Brendan Reardon
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jihye Park
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Seunghun Han
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Breanna Titchen
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Rizwan Haq
- Center for Cancer Precision Medicine and
| | - Eliezer M. Van Allen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Center for Cancer Precision Medicine and
- Parker Institute for Cancer Immunotherapy, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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19
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Pancotti C, Rollo C, Codicè F, Birolo G, Fariselli P, Sanavia T. MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification. Bioinformatics 2024; 40:btae320. [PMID: 38754097 PMCID: PMC11139523 DOI: 10.1093/bioinformatics/btae320] [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: 11/28/2023] [Revised: 04/08/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024] Open
Abstract
MOTIVATION Mutational signatures are a critical component in deciphering the genetic alterations that underlie cancer development and have become a valuable resource to understand the genomic changes during tumorigenesis. Therefore, it is essential to employ precise and accurate methods for their extraction to ensure that the underlying patterns are reliably identified and can be effectively utilized in new strategies for diagnosis, prognosis, and treatment of cancer patients. RESULTS We present MUSE-XAE, a novel method for mutational signature extraction from cancer genomes using an explainable autoencoder. Our approach employs a hybrid architecture consisting of a nonlinear encoder that can capture nonlinear interactions among features, and a linear decoder which ensures the interpretability of the active signatures. We evaluated and compared MUSE-XAE with other available tools on both synthetic and real cancer datasets and demonstrated that it achieves superior performance in terms of precision and sensitivity in recovering mutational signature profiles. MUSE-XAE extracts highly discriminative mutational signature profiles by enhancing the classification of primary tumour types and subtypes in real world settings. This approach could facilitate further research in this area, with neural networks playing a critical role in advancing our understanding of cancer genomics. AVAILABILITY AND IMPLEMENTATION MUSE-XAE software is freely available at https://github.com/compbiomed-unito/MUSE-XAE.
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Affiliation(s)
- Corrado Pancotti
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Cesare Rollo
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Francesco Codicè
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Giovanni Birolo
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Piero Fariselli
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
| | - Tiziana Sanavia
- Computational Biomedicine Unit, Department of Medical Sciences, University of Torino, via Santena 19, Torino 10126, Italy
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20
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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [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: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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21
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Xu Y, Liu K, Li C, Li M, Zhou X, Sun M, Zhang L, Wang S, Liu F, Xu Y. Microsatellite instability in mismatch repair proficient colorectal cancer: clinical features and underlying molecular mechanisms. EBioMedicine 2024; 103:105142. [PMID: 38691939 PMCID: PMC11070601 DOI: 10.1016/j.ebiom.2024.105142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Both defects in mismatch repair (dMMR) and high microsatellite instability (MSI-H) have been recognised as crucial biomarkers that guide treatment strategies and disease management in colorectal cancer (CRC). As MMR and MSI tests are being widely conducted, an increasing number of MSI-H tumours have been identified in CRCs with mismatch repair proficiency (pMMR). The objective of this study was to assess the clinical features of patients with pMMR/MSI-H CRC and elucidate the underlying molecular mechanism in these cases. METHODS From January 2015 to December 2018, 1684 cases of pMMR and 401 dMMR CRCs were enrolled. Of those patients, 93 pMMR/MSI-H were identified. The clinical phenotypes and prognosis were analysed. Frozen and paraffin-embedded tissue were available in 35 patients with pMMR/MSI-H, for which comprehensive genomic and transcriptomic analyses were performed. FINDINGS In comparison to pMMR/MSS CRCs, pMMR/MSI-H CRCs exhibited significantly less tumour progression and better long-term prognosis. The pMMR/MSI-H cohorts displayed a higher presence of CD8+ T cells and NK cells when compared to the pMMR/MSS group. Mutational signature analysis revealed that nearly all samples exhibited deficiencies in MMR genes, and we also identified deleterious mutations in MSH3-K383fs. INTERPRETATION This study revealed pMMR/MSI-H CRC as a distinct subgroup within CRC, which manifests diverse clinicopathological features and long-term prognostic outcomes. Distinct features in the tumour immune-microenvironment were observed in pMMR/MSI-H CRCs. Pathogenic deleterious mutations in MSH3-K383fs were frequently detected, suggesting another potential biomarker for identifying MSI-H. FUNDING This work was supported by the Science and Technology Commission of Shanghai Municipality (20DZ1100101).
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Affiliation(s)
- Yun Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Kai Liu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Cong Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Minghan Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Menghong Sun
- Department of Pathology, Tissue Bank, Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Sheng Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China.
| | - Fangqi Liu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, PR China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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22
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Xu Y, Jiao Y, Liu C, Miao R, Liu C, Wang Y, Ma C, Liu J. R-loop and diseases: the cell cycle matters. Mol Cancer 2024; 23:84. [PMID: 38678239 PMCID: PMC11055327 DOI: 10.1186/s12943-024-02000-3] [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: 02/11/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
The cell cycle is a crucial biological process that is involved in cell growth, development, and reproduction. It can be divided into G1, S, G2, and M phases, and each period is closely regulated to ensure the production of two similar daughter cells with the same genetic material. However, many obstacles influence the cell cycle, including the R-loop that is formed throughout this process. R-loop is a triple-stranded structure, composed of an RNA: DNA hybrid and a single DNA strand, which is ubiquitous in organisms from bacteria to mammals. The existence of the R-loop has important significance for the regulation of various physiological processes. However, aberrant accumulation of R-loop due to its limited resolving ability will be detrimental for cells. For example, DNA damage and genomic instability, caused by the R-loop, can activate checkpoints in the cell cycle, which in turn induce cell cycle arrest and cell death. At present, a growing number of factors have been proven to prevent or eliminate the accumulation of R-loop thereby avoiding DNA damage and mutations. Therefore, we need to gain detailed insight into the R-loop resolution factors at different stages of the cell cycle. In this review, we review the current knowledge of factors that play a role in resolving the R-loop at different stages of the cell cycle, as well as how mutations of these factors lead to the onset and progression of diseases.
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Affiliation(s)
- Yuqin Xu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yue Jiao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunming Ma
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China.
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23
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Eoli A, Ibing S, Schurmann C, Nadkarni GN, Heyne HO, Böttinger E. A clustering approach to improve our understanding of the genetic and phenotypic complexity of chronic kidney disease. Sci Rep 2024; 14:9642. [PMID: 38671065 PMCID: PMC11053134 DOI: 10.1038/s41598-024-59747-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic kidney disease (CKD) is a complex disorder that causes a gradual loss of kidney function, affecting approximately 9.1% of the world's population. Here, we use a soft-clustering algorithm to deconstruct its genetic heterogeneity. First, we selected 322 CKD-associated independent genetic variants from published genome-wide association studies (GWAS) and added association results for 229 traits from the GWAS catalog. We then applied nonnegative matrix factorization (NMF) to discover overlapping clusters of related traits and variants. We computed cluster-specific polygenic scores and validated each cluster with a phenome-wide association study (PheWAS) on the BioMe biobank (n = 31,701). NMF identified nine clusters that reflect different aspects of CKD, with the top-weighted traits signifying areas such as kidney function, type 2 diabetes (T2D), and body weight. For most clusters, the top-weighted traits were confirmed in the PheWAS analysis. Results were found to be more significant in the cross-ancestry analysis, although significant ancestry-specific associations were also identified. While all alleles were associated with a decreased kidney function, associations with CKD-related diseases (e.g., T2D) were found only for a smaller subset of variants and differed across genetic ancestry groups. Our findings leverage genetics to gain insights into the underlying biology of CKD and investigate population-specific associations.
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Affiliation(s)
- A Eoli
- Digital Engineering Faculty, University of Potsdam, Potsdam, Germany, Prof.-Dr.-Helmert-Str. 2-3, 14482.
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.
- Hasso Plattner Institute for Digital Engineering gGmbH, Prof.-Dr.-Helmert-Str. 2-3, 14482, Potsdam, Germany.
| | - S Ibing
- Digital Engineering Faculty, University of Potsdam, Potsdam, Germany, Prof.-Dr.-Helmert-Str. 2-3, 14482
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Hasso Plattner Institute for Digital Engineering gGmbH, Prof.-Dr.-Helmert-Str. 2-3, 14482, Potsdam, Germany
| | - C Schurmann
- Digital Engineering Faculty, University of Potsdam, Potsdam, Germany, Prof.-Dr.-Helmert-Str. 2-3, 14482
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Hasso Plattner Institute for Digital Engineering gGmbH, Prof.-Dr.-Helmert-Str. 2-3, 14482, Potsdam, Germany
| | - G N Nadkarni
- Windreich Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- The Charles Bronfman Institute of Personalized Medicine, New York City, NY, USA
| | - H O Heyne
- Digital Engineering Faculty, University of Potsdam, Potsdam, Germany, Prof.-Dr.-Helmert-Str. 2-3, 14482
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Windreich Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Hasso Plattner Institute for Digital Engineering gGmbH, Prof.-Dr.-Helmert-Str. 2-3, 14482, Potsdam, Germany
| | - E Böttinger
- Digital Engineering Faculty, University of Potsdam, Potsdam, Germany, Prof.-Dr.-Helmert-Str. 2-3, 14482
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Windreich Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Hasso Plattner Institute for Digital Engineering gGmbH, Prof.-Dr.-Helmert-Str. 2-3, 14482, Potsdam, Germany
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24
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McCauley KB, Kukreja K, Tovar Walker AE, Jaffe AB, Klein AM. A map of signaling responses in the human airway epithelium. Cell Syst 2024; 15:307-321.e10. [PMID: 38508187 PMCID: PMC11031335 DOI: 10.1016/j.cels.2024.02.005] [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] [Received: 12/20/2022] [Revised: 11/14/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal cell and secretory cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell-cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Katherine B McCauley
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA; Disease Area X, Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Kalki Kukreja
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Aron B Jaffe
- Respiratory Diseases, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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25
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Luo Z, Liu X, Chen Y, Shen L, Qin H, Zha Q, Hu F, Wang Y. Gene features of tumor-specific T cells relevant to immunotherapy, targeted therapy and chemotherapy in lung cancer. Heliyon 2024; 10:e28374. [PMID: 38590880 PMCID: PMC10999884 DOI: 10.1016/j.heliyon.2024.e28374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
1 Background In lung cancer, the use of small-molecule inhibitors, chemotherapy and immunotherapy has led to unprecedented survival benefits in selected patients. Considering most patients will experience a relapse within a short period of time due to single drug resistance, combination therapy is also particularly important to improve patient prognosis. Therefore, more robust biomarkers to predict responses to immunotherapy, targeted therapy, chemotherapy and rationally drug combination therapies may be helpful in clinical treatment choices. 2 Methods We defined tumor-specific T cells (TSTs) and their features (TSTGs) by single-cell RNA sequencing. We applied LASSO regression to filter out the most survival-relevant TSTGs to form the Tumor-specific T cell score (TSTS). Immunological characteristics, enriched pathways, and mutation were evaluated in high- and low TSTS groups. 3 Results We identified six clusters of T cells as TSTs in lung cancer, and four most robust genes from 9 feature genes expressed only on tumor-specific T cells were screened to construct a tumor-specific T cells score (TSTS). TSTS was positively correlated with immune infiltration and angiogenesis and negatively correlated with malignant cell proliferation. Moreover, potential vascular-immune crosstalk in lung cancer provides the theoretical basis for combined anti-angiogenic and immunotherapy. Noticeable, patients in high TSTS had better response to ICB and targeted therapy and patients in the low TSTS group often benefit from chemotherapy. 4 Conclusion The proposed TSTS is a promising indicator to predict immunotherapy, targeted therapy and chemotherapy responses in lung cancer patients for helping clinical treatment choices.
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Affiliation(s)
- Ziwei Luo
- Department of Respiratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200120, China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xuefei Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- Shenzhen Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, 518038, China
| | - Ying Chen
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Lize Shen
- LC-Bio Technology Co.ltd, Hangzhou, 310018, China
| | - Hui Qin
- Department of Respiratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200120, China
| | - Qiongfang Zha
- Department of Respiratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200120, China
| | - Feng Hu
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200120, China
| | - Yali Wang
- Department of Respiratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200120, China
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26
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Han Z, Song C, Li D, Zhu W, Sun J, Yao J, Gan W, Wang F, Yang X, Zhu L. KMT2A Mutations and High Prevalence of dMMR-associated Mutational Signatures as Prognostic Indicators in Metastatic Colorectal Cancer. J Cancer 2024; 15:3140-3150. [PMID: 38706918 PMCID: PMC11064249 DOI: 10.7150/jca.94410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/17/2024] [Indexed: 05/07/2024] Open
Abstract
The conventional treatment strategies for patients with metastatic colorectal cancer (mCRC) are predominantly guided by the status of RAS and BRAF mutations. Although patients may exhibit analogous pathological characteristics and undergo similar treatment regimens, notable disparities in their prognostic outcomes can be observed. Therefore, tissue and plasma samples from 40 mCRC patients underwent next-generation sequencing targeting 425 cancer-relevant genes. Genomic variations and canonical oncogenic pathways were investigated for their prognostic effects in association with progression-free survival (PFS) of these patients. We found that patients with BRCA2 and KMT2A mutations exhibited worse prognostic outcomes after chemotherapy-based treatment (univariate, P < 0.01). Further pathway analysis indicated that alterations in the homologous recombination pathway and in the KMT2A signaling network were also significantly associated with shortened PFS (univariate, P < 0.01). Additionally, mutation signature analysis showed that patients with higher proportions of defective mismatch repair (dMMR)-related mutational signatures. Had a worse prognosis (univariate, P = 0.02). KMT2A mutations (hazard ratio [HR], 4.47; 95% confidence interval [CI], 1-19.93; P =0.050) and dMMR signature proportions (HR, 3.57; 95% CI, 1.42-8.96; P = 0.007) remained independently associated with PFS after multivariate analysis and the results were further externally validated. These findings may enhance our understanding of this disease and may potentially facilitate the optimization of its treatment approaches.
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Affiliation(s)
- Zhihang Han
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
| | - Chuanjun Song
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
- Xinghua People's Hospital Affiliated to Yangzhou University, No. 419 Yingwu South Road, Xinghua, Jiangsu, 225700, China
| | - Dongqing Li
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
| | - Weiyou Zhu
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
| | - Jiukang Sun
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
| | - Jialing Yao
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
| | - Wenyuan Gan
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
| | - Fufeng Wang
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu Province, 210018, China
| | - Xiaodong Yang
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
| | - Lingjun Zhu
- The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, Jiangsu Province,210029, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, 210029, China
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Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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Lee D, Hua M, Wang D, Song L, Zhang T, Hua X, Yu K, Yang XR, Chanock SJ, Shi J, Landi MT, Zhu B. Pan-cancer mutational signature analysis of 111,711 targeted sequenced tumors using SATS. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.05.18.23290188. [PMID: 37425683 PMCID: PMC10327246 DOI: 10.1101/2023.05.18.23290188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Tumor mutational signatures have the potential to inform cancer diagnosis and treatment. However, their detection in targeted sequenced tumors is hampered by sparse mutations and variability in targeted gene panels. Here we present SATS, a scalable mutational signature analyzer addressing these challenges by leveraging tumor mutational burdens from targeted gene panels. Through analyzing simulated data, pseudo-targeted sequencing data generated by down-sampling whole exome and genome data, and samples with matched whole genome sequencing and targeted sequencing, we showed that SATS can accurately detect common mutational signatures and estimate signature burdens. Applying SATS to 111,711 targeted sequenced tumors from the AACR Project GENIE, we generated a pan-cancer catalogue of mutational signatures tailored to targeted sequencing, enabling estimation of signature burdens within individual tumors. Integrating signatures with clinical data, we demonstrated SATS's clinical utility, including identifying signatures enriched in early-onset hypermutated colorectal cancers and signatures associated with cancer prognosis and immunotherapy response.
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Affiliation(s)
- Donghyuk Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Statistics, Pusan National University, Busan, Korea
| | - Min Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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29
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Qin Q, Zhou Y, Guo J, Chen Q, Tang W, Li Y, You J, Li Q. Conserved methylation signatures associate with the tumor immune microenvironment and immunotherapy response. Genome Med 2024; 16:47. [PMID: 38566132 PMCID: PMC10985907 DOI: 10.1186/s13073-024-01318-3] [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: 03/16/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Aberrant DNA methylation is a major characteristic of cancer genomes. It remains unclear which biological processes determine epigenetic reprogramming and how these processes influence the variants in the cancer methylome, which can further impact cancer phenotypes. METHODS We performed pairwise permutations of 381,900 loci in 569 paired DNA methylation profiles of cancer tissue and matched normal tissue from The Cancer Genome Atlas (TCGA) and defined conserved differentially methylated positions (DMPs) based on the resulting null distribution. Then, we derived independent methylation signatures from 2,465 cancer-only methylation profiles from the TCGA and 241 cell line-based methylation profiles from the Genomics of Drug Sensitivity in Cancer (GDSC) cohort using nonnegative matrix factorization (NMF). We correlated DNA methylation signatures with various clinical and biological features, including age, survival, cancer stage, tumor immune microenvironment factors, and immunotherapy response. We inferred the determinant genes of these methylation signatures by integrating genomic and transcriptomic data and evaluated the impact of these signatures on cancer phenotypes in independent bulk and single-cell RNA/methylome cohorts. RESULTS We identified 7,364 differentially methylated positions (2,969 Hyper-DMPs and 4,395 Hypo-DMPs) in nine cancer types from the TCGA. We subsequently retrieved three highly conserved, independent methylation signatures (Hyper-MS1, Hypo-MS1, and Hypo-MS4) from cancer tissues and cell lines based on these Hyper and Hypo-DMPs. Our data suggested that Hypo-MS4 activity predicts poor survival and is associated with immunotherapy response and distant tumor metastasis, and Hypo-MS4 activity is related to TP53 mutation and FOXA1 binding specificity. In addition, we demonstrated a correlation between the activities of Hypo-MS4 in cancer cells and the fractions of regulatory CD4 + T cells with the expression levels of immunological genes in the tumor immune microenvironment. CONCLUSIONS Our findings demonstrated that the methylation signatures of distinct biological processes are associated with immune activity in the cancer microenvironment and predict immunotherapy response.
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Affiliation(s)
- Qingqing Qin
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Ying Zhou
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jintao Guo
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Qinwei Chen
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
| | - Weiwei Tang
- Department of Medical Oncology, School of Medicine, The First Affiliated Hospital of Xiamen University and Institute of Hematology, Xiamen University, Xiamen, 361003, China
- Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, The School of Clinical Medicine of Fujian, Medical University, Xiamen, 361003, China
| | - Yuchen Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Jun You
- Department of Gastrointestinal Oncology Surgery, The First Affiliated Hospital of Xiamen University, Cancer Center, Xiamen, 361003, China
| | - Qiyuan Li
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, 361003, China.
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China.
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China.
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30
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Unger M, Kather JN. Deep learning in cancer genomics and histopathology. Genome Med 2024; 16:44. [PMID: 38539231 PMCID: PMC10976780 DOI: 10.1186/s13073-024-01315-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/13/2024] [Indexed: 07/08/2024] Open
Abstract
Histopathology and genomic profiling are cornerstones of precision oncology and are routinely obtained for patients with cancer. Traditionally, histopathology slides are manually reviewed by highly trained pathologists. Genomic data, on the other hand, is evaluated by engineered computational pipelines. In both applications, the advent of modern artificial intelligence methods, specifically machine learning (ML) and deep learning (DL), have opened up a fundamentally new way of extracting actionable insights from raw data, which could augment and potentially replace some aspects of traditional evaluation workflows. In this review, we summarize current and emerging applications of DL in histopathology and genomics, including basic diagnostic as well as advanced prognostic tasks. Based on a growing body of evidence, we suggest that DL could be the groundwork for a new kind of workflow in oncology and cancer research. However, we also point out that DL models can have biases and other flaws that users in healthcare and research need to know about, and we propose ways to address them.
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Affiliation(s)
- Michaela Unger
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
- Department of Medicine I, University Hospital Dresden, Dresden, Germany.
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany.
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31
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Zeng PYF, Prokopec SD, Lai SY, Pinto N, Chan-Seng-Yue MA, Clifton-Bligh R, Williams MD, Howlett CJ, Plantinga P, Cecchini MJ, Lam AK, Siddiqui I, Wang J, Sun RX, Watson JD, Korah R, Carling T, Agrawal N, Cipriani N, Ball D, Nelkin B, Rooper LM, Bishop JA, Garnis C, Berean K, Nicolson NG, Weinberger P, Henderson YC, Lalansingh CM, Tian M, Yamaguchi TN, Livingstone J, Salcedo A, Patel K, Vizeacoumar F, Datti A, Xi L, Nikiforov YE, Smallridge R, Copland JA, Marlow LA, Hyrcza MD, Delbridge L, Sidhu S, Sywak M, Robinson B, Fung K, Ghasemi F, Kwan K, MacNeil SD, Mendez A, Palma DA, Khan MI, Shaikh M, Ruicci KM, Wehrli B, Winquist E, Yoo J, Mymryk JS, Rocco JW, Wheeler D, Scherer S, Giordano TJ, Barrett JW, Faquin WC, Gill AJ, Clayman G, Boutros PC, Nichols AC. The genomic and evolutionary landscapes of anaplastic thyroid carcinoma. Cell Rep 2024; 43:113826. [PMID: 38412093 PMCID: PMC11077417 DOI: 10.1016/j.celrep.2024.113826] [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: 04/11/2023] [Revised: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.
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Affiliation(s)
- Peter Y F Zeng
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Stephenie D Prokopec
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole Pinto
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | | | - Roderick Clifton-Bligh
- Division of Endocrinology, Royal North Shore Hospital, and University of Sydney, Sydney, NSW, Australia
| | - Michelle D Williams
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Paul Plantinga
- Department of Pathology, Western University, London, ON, Canada
| | - Matthew J Cecchini
- Department of Pathology, School of Medicine, Griffith University, Gold Coast, QLD, Australia
| | - Alfred K Lam
- Department of Pathology, School of Medicine, Griffith University, Gold Coast, QLD, Australia
| | - Iram Siddiqui
- Department of Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Jianxin Wang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ren X Sun
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - John D Watson
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Reju Korah
- Department of Surgery, Yale University, New Haven, CT, USA
| | - Tobias Carling
- Department of Surgery, Yale University, New Haven, CT, USA
| | - Nishant Agrawal
- Department of Otolaryngology - Head and Neck Surgery, University of Chicago, Chicago, IL, USA
| | - Nicole Cipriani
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Douglas Ball
- Division of Endocrinology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Barry Nelkin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa M Rooper
- Division of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern, Dallas, TX, USA
| | | | | | | | - Paul Weinberger
- Department of Otolaryngology - Head and Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA, USA; Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Ying C Henderson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mao Tian
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Takafumi N Yamaguchi
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julie Livingstone
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Salcedo
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Krupal Patel
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Alessandro Datti
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Liu Xi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Robert Smallridge
- Division of Endocrinology, Department of Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Laura A Marlow
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Martin D Hyrcza
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Leigh Delbridge
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Stan Sidhu
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Mark Sywak
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Bruce Robinson
- University of Sydney, Sydney, NWS, Australia; Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Farhad Ghasemi
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Keith Kwan
- Department of Pathology, Western University, London, ON, Canada
| | - S Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Adrian Mendez
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - David A Palma
- London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Mohammed I Khan
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Mushfiq Shaikh
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Kara M Ruicci
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Bret Wehrli
- Department of Pathology, Western University, London, ON, Canada
| | - Eric Winquist
- London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada; Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - James W Rocco
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - David Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steve Scherer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anthony J Gill
- University of Sydney, Sydney, NWS, Australia; Cancer Diagnosis and Pathology Group, Kolling Institute of Medicine, Royal North Shore Hospital, Sydney, NSW, Australia; NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Gary Clayman
- The Clayman Thyroid Surgery and Thyroid Cancer Center, The Thyroid Institute, Tampa General Hospital, Tampa, FL, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada.
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Chancharoen M, Yang Z, Dalvie ED, Gubina N, Ruchirawat M, Croy RG, Fedeles BI, Essigmann JM. 5-Chloro-2'-deoxycytidine Induces a Distinctive High-Resolution Mutational Spectrum of Transition Mutations In Vivo. Chem Res Toxicol 2024; 37:486-496. [PMID: 38394377 PMCID: PMC10952010 DOI: 10.1021/acs.chemrestox.3c00358] [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: 11/09/2023] [Revised: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 02/25/2024]
Abstract
The biomarker 5-chlorocytosine (5ClC) appears in the DNA of inflamed tissues. Replication of a site-specific 5ClC in a viral DNA genome results in C → T mutations, which is consistent with 5ClC acting as a thymine mimic in vivo. Direct damage of nucleic acids by immune-cell-derived hypochlorous acid is one mechanism by which 5ClC could appear in the genome. A second, nonmutually exclusive mechanism involves damage of cytosine nucleosides or nucleotides in the DNA precursor pool, with subsequent utilization of the 5ClC deoxynucleotide triphosphate as a precursor for DNA synthesis. The present work characterized the mutagenic properties of 5ClC in the nucleotide pool by exposing cells to the nucleoside 5-chloro-2'-deoxycytidine (5CldC). In both Escherichia coli and mouse embryonic fibroblasts (MEFs), 5CldC in the growth media was potently mutagenic, indicating that 5CldC enters cells and likely is erroneously incorporated into the genome from the nucleotide pool. High-resolution sequencing of DNA from MEFs derived from the gptΔ C57BL/6J mouse allowed qualitative and quantitative characterization of 5CldC-induced mutations; CG → TA transitions in 5'-GC(Y)-3' contexts (Y = a pyrimidine) were dominant, while TA → CG transitions appeared at a much lower frequency. The high-resolution mutational spectrum of 5CldC revealed a notable similarity to the Catalogue of Somatic Mutations in Cancer mutational signatures SBS84 and SBS42, which appear in human lymphoid tumors and in occupationally induced cholangiocarcinomas, respectively. SBS84 is associated with the expression of activation-induced cytidine deaminase (AID), a cytosine deaminase associated with inflammation, as well as immunoglobulin gene diversification during antibody maturation. The similarity between the spectra of AID activation and 5CldC could be coincidental; however, the administration of 5CldC did induce some AID expression in MEFs, which have no inherent expression of its gene. In summary, this work shows that 5CldC induces a distinct pattern of mutations in cells. Moreover, that pattern resembles human mutational signatures induced by inflammatory processes, such as those triggered in certain malignancies.
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Affiliation(s)
- Marisa Chancharoen
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- Chulabhorn
Research Institute and Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | - Zhiyu Yang
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Esha D. Dalvie
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Gubina
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Mathuros Ruchirawat
- Chulabhorn
Research Institute and Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | - Robert G. Croy
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Bogdan I. Fedeles
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - John M. Essigmann
- Departments
of Biological Engineering and Chemistry, and Center for Environmental
Health Sciences, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
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Cheng X, An J, Lou J, Gu Q, Ding W, Droby GN, Wang Y, Wang C, Gao Y, Anand JR, Shelton A, Satterlee AB, Mann B, Hsiao YC, Liu CW, Lu K, Hingtgen S, Wang J, Liu Z, Miller CR, Wu D, Vaziri C, Yang Y. Trans-lesion synthesis and mismatch repair pathway crosstalk defines chemoresistance and hypermutation mechanisms in glioblastoma. Nat Commun 2024; 15:1957. [PMID: 38438348 PMCID: PMC10912752 DOI: 10.1038/s41467-024-45979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/08/2024] [Indexed: 03/06/2024] Open
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides an aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
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Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Qisheng Gu
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Nabil Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jay Ramanlal Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Breanna Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - C Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
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Jin H, Gulhan DC, Geiger B, Ben-Isvy D, Geng D, Ljungström V, Park PJ. Accurate and sensitive mutational signature analysis with MuSiCal. Nat Genet 2024; 56:541-552. [PMID: 38361034 PMCID: PMC10937379 DOI: 10.1038/s41588-024-01659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present Mutational Signature Calculator (MuSiCal), a rigorous analytical framework with algorithms that solve major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing more than 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous 'flat' signatures and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
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Affiliation(s)
- Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedikt Geiger
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniel Ben-Isvy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - David Geng
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Kaufmann TL, Schwarz RF. Improved identification of cancer mutational processes. Nat Genet 2024; 56:365-366. [PMID: 38454020 DOI: 10.1038/s41588-024-01679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Affiliation(s)
- Tom L Kaufmann
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Department of Electrical Engineering and Computer Science, Technische Universität Berlin, Berlin, Germany.
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
| | - Roland F Schwarz
- BIFOLD - Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
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36
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Yang Z, Zhou B, Guo W, Peng Y, Tian H, Xu J, Wang S, Chen X, Hu B, Liu C, Wang Z, Li C, Gao S, He J. Genomic characteristics and immune landscape of super multiple primary lung cancer. EBioMedicine 2024; 101:105019. [PMID: 38364701 PMCID: PMC10878856 DOI: 10.1016/j.ebiom.2024.105019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND In recent years, a growing number of patients with multiple primary lung cancer (MPLC) are being diagnosed, and a subset of these patients is found to have a large number of lesions at the time of diagnosis, which are referred to as 'super MPLC'. METHODS Here, we perform whole exome sequencing (WES) and immunohistochemistry (IHC) analysis of PD-L1 and CD8 on 212 tumor samples from 42 patients with super MPLC. FINDINGS We report the genomic alteration landscape of super MPLC. EGFR, RBM10 and TP53 mutation and TERT amplification are important molecular events in the evolution of super MPLC. We propose the conception of early intrapulmonary metastasis, which exhibits different clinical features from conventional metastasis. The IHC analyses of PD-L1 and CD8 reveal a less inflamed microenvironment of super MPLC than that of traditional non-small cell lung cancer (NSCLC). We identify the potentially susceptible germline mutations for super MPLC. INTERPRETATION Our study depicts the genomic characteristics and immune landscape, providing insights into the pathogenesis and possible therapeutic guidance of super MPLC. FUNDING A full list of funding bodies that supported this study can be found in the Acknowledgements section.
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Affiliation(s)
- Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Bolun Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Yue Peng
- Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China; Guangdong Provincial People's Hospital/Guangdong Provincial Academy of Medical Sciences, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangdong, 519041, China
| | - Shuaibo Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Xiaowei Chen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Bin Hu
- Department of Thoracic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Chengming Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Zhijie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, China.
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37
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Rashid M, Rashid R, Gadewal N, Carethers JM, Koi M, Brim H, Ashktorab H. High-throughput sequencing and in-silico analysis confirm pathogenicity of novel MSH3 variants in African American colorectal cancer. Neoplasia 2024; 49:100970. [PMID: 38281411 PMCID: PMC10840101 DOI: 10.1016/j.neo.2024.100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/19/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024]
Abstract
The maintenance of DNA sequence integrity is critical to avoid accumulation of cancer-causing mutations. Inactivation of DNA Mismatch Repair (MMR) genes (e.g., MLH1 and MSH2) is common among many cancers, including colorectal cancer (CRC) and is the driver of classic microsatellite instability (MSI) in tumors. Somatic MSH3 alterations have been linked to a specific form of MSI called elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) that is associated with patient poor prognosis and elevated among African American (AA) rectal cancer patients. Genetic variants of MSH3 and their pathogenicity vary among different populations, such as among AA, which are not well-represented in publicly available databases. Targeted exome sequencing of MSH3 among AA CRC samples followed by computational bioinformatic pipeline and molecular dynamic simulation analysis approach confirmed six identified MSH3 variants (c.G1237A, c.C2759T, c.G1397A, c.G2926A, c.C3028T, c.G3241A) that corresponded to MSH3 amino-acid changes (p.E413K; p.S466N; p.S920F; p.E976K; p.H1010Y; p.E1081K). All identified MSH3 variants were non-synonymous, novel, pathogenic, and show loss or gain of hydrogen bonding, ionic bonding, hydrophobic bonding, and disulfide bonding and have a deleterious effect on the structure of MSH3 protein. Some variants were located within the ATPase site of MSH3, affecting ATP hydrolysis that is critical for MSH3's function. Other variants were in the MSH3-MSH2 interacting domain, important for MSH3's binding to MSH2. Overall, our data suggest that these variants among AA CRC patients affect the function of MSH3 making them pathogenic and likely contributing to the development or advancement of CRC among AA. Further clarifying functional studies will be necessary to fully understand the impact of these variants on MSH3 function and CRC development in AA patients.
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Affiliation(s)
- Mudasir Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Rumaisa Rashid
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Nikhil Gadewal
- Bioinformatics and Computational Biology Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210, India
| | - John M Carethers
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA; Moores Cancer Center, and Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Minoru Koi
- Division of Gastroenterology and Hepatology, Department of Medicine, UC San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Hassan Brim
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division, Department of Pathology and Cancer Center, Howard University College of Medicine, Washington, DC 20059, USA.
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Simpson JT. Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582089. [PMID: 38464143 PMCID: PMC10925087 DOI: 10.1101/2024.02.26.582089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DNA sequencing of tumours to identify somatic mutations has become a critical tool to guide the type of treatment given to cancer patients. The gold standard for mutation calling is comparing sequencing data from the tumour to a matched normal sample to avoid mis-classifying inherited SNPs as mutations. This procedure works extremely well, but in certain situations only a tumour sample is available. While approaches have been developed to find mutations without a matched normal, they have limited accuracy or require specific types of input data (e.g. ultra-deep sequencing). Here we explore the application of single molecule long read sequencing to calling somatic mutations without matched normal samples. We develop a simple theoretical framework to show how haplotype phasing is an important source of information for determining whether a variant is a somatic mutation. We then use simulations to assess the range of experimental parameters (tumour purity, sequencing depth) where this approach is effective. These ideas are developed into a prototype somatic mutation caller, smrest, and its use is demonstrated on two highly mutated cancer cell lines. Finally, we argue that this approach has potential to measure clinically important biomarkers that are based on the genome-wide distribution of mutations: tumour mutation burden and mutation signatures.
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Affiliation(s)
- Jared T. Simpson
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
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Gatz SA, Harttrampf AC, Brard C, Bautista F, André N, Abbou S, Rubino J, Rondof W, Deloger M, Rübsam M, Marshall LV, Hübschmann D, Nebchi S, Aerts I, Thebaud E, De Carli E, Defachelles AS, Paoletti X, Godin R, Miah K, Mortimer PGS, Vassal G, Geoerger B. Phase I/II Study of the WEE1 Inhibitor Adavosertib (AZD1775) in Combination with Carboplatin in Children with Advanced Malignancies: Arm C of the AcSé-ESMART Trial. Clin Cancer Res 2024; 30:741-753. [PMID: 38051741 DOI: 10.1158/1078-0432.ccr-23-2959] [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: 09/27/2023] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
PURPOSE AcSé-ESMART Arm C aimed to define the recommended dose and activity of the WEE1 inhibitor adavosertib in combination with carboplatin in children and young adults with molecularly enriched recurrent/refractory malignancies. PATIENTS AND METHODS Adavosertib was administered orally, twice every day on Days 1 to 3 and carboplatin intravenously on Day 1 of a 21-day cycle, starting at 100 mg/m2/dose and AUC 5, respectively. Patients were enriched for molecular alterations in cell cycle and/or homologous recombination (HR). RESULTS Twenty patients (median age: 14.0 years; range: 3.4-23.5) were included; 18 received 69 treatment cycles. Dose-limiting toxicities were prolonged grade 4 neutropenia and grade 3/4 thrombocytopenia requiring transfusions, leading to two de-escalations to adavosertib 75 mg/m2/dose and carboplatin AUC 4; no recommended phase II dose was defined. Main treatment-related toxicities were hematologic and gastrointestinal. Adavosertib exposure in children was equivalent to that in adults; both doses achieved the cell kill target. Overall response rate was 11% (95% confidence interval, 0.0-25.6) with partial responses in 2 patients with neuroblastoma. One patient with medulloblastoma experienced unconfirmed partial response and 5 patients had stable disease beyond four cycles. Seven of these eight patients with clinical benefit had alterations in HR, replication stress, and/or RAS pathway genes with or without TP53 alterations, whereas TP53 pathway alterations alone (8/10) or no relevant alterations (2/10) were present in the 10 patients without benefit. CONCLUSIONS Adavosertib-carboplatin combination exhibited significant hematologic toxicity. Activity signals and identified potential biomarkers suggest further studies with less hematotoxic DNA-damaging therapy in molecularly enriched pediatric cancers.
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Affiliation(s)
- Susanne A Gatz
- Institute of Cancer and Genomic Sciences, University of Birmingham; Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Anne C Harttrampf
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, Villejuif, France
- Gustave Roussy Cancer Campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Caroline Brard
- Gustave Roussy Cancer Campus, Biostatistics and Epidemiology Unit, INSERM U1018, CESP, Université Paris-Saclay, Université Paris-Sud, UVSQ, Villejuif, France
| | - Francisco Bautista
- Hospital Niño Jesús, Department of Pediatric Oncology, Hematology and Stem Cell Transplantation, Madrid, Spain
| | - Nicolas André
- Hôpital de la Timone, AP-HM, Department of Pediatric Oncology, Marseille, France
- UMR INSERM 1068, CNRS UMR 7258, Aix Marseille Université U105, Marseille, Cancer Research Center (CRCM), Marseille, France
| | - Samuel Abbou
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, Villejuif, France
| | - Jonathan Rubino
- Gustave Roussy Cancer Campus, Clinical Research Direction, Villejuif, France
| | - Windy Rondof
- Gustave Roussy Cancer Campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
- Gustave Roussy Cancer Campus, Bioinformatics platform, Université Paris-Saclay, Villejuif, France
| | - Marc Deloger
- Gustave Roussy Cancer Campus, Bioinformatics platform, Université Paris-Saclay, Villejuif, France
| | - Marc Rübsam
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center
| | - Lynley V Marshall
- Royal Marsden Hospital & The Institute of Cancer Research, Paediatric and Adolescent Oncology Drug Development Unit, London, United Kingdom
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem cell Technology and Experimental Medicine (HI-STEM); German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Souad Nebchi
- Gustave Roussy Cancer Campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
| | - Isabelle Aerts
- Institut Curie, SIREDO Oncology Center (Care, Innovation and research for children and AYA with cancer), PSL Research University, Paris, France
| | - Estelle Thebaud
- Centre Hospitalier Universitaire, Department of Pediatric Oncology, Nantes, France
| | - Emilie De Carli
- Centre Hospitalier Universitaire, Department of Pediatric Oncology, Angers, France
| | | | - Xavier Paoletti
- Gustave Roussy Cancer Campus, Biostatistics and Epidemiology Unit, INSERM U1018, CESP, Université Paris-Saclay, Université Paris-Sud, UVSQ, Villejuif, France
| | - Robert Godin
- AstraZeneca Oncology External R&D, Waltham, Massachusetts
| | - Kowser Miah
- Clinical Pharmacology and Quantitative Pharmacology, AstraZeneca, Waltham, Massachusetts
| | | | - Gilles Vassal
- Gustave Roussy Cancer Campus, Clinical Research Direction, Villejuif, France
| | - Birgit Geoerger
- Gustave Roussy Cancer Campus, Department of Pediatric and Adolescent Oncology, Villejuif, France
- Gustave Roussy Cancer Campus, INSERM U1015, Université Paris-Saclay, Villejuif, France
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40
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Youk J, Kwon HW, Lim J, Kim E, Kim T, Kim R, Park S, Yi K, Nam CH, Jeon S, An Y, Choi J, Na H, Lee ES, Cho Y, Min DW, Kim H, Kang YR, Choi SH, Bae MJ, Lee CG, Kim JG, Kim YS, Yu T, Lee WC, Shin JY, Lee DS, Kim TY, Ku T, Kim SY, Lee JH, Koo BK, Lee H, Yi OV, Han EC, Chang JH, Kim KS, Son TG, Ju YS. Quantitative and qualitative mutational impact of ionizing radiation on normal cells. CELL GENOMICS 2024; 4:100499. [PMID: 38359788 PMCID: PMC10879144 DOI: 10.1016/j.xgen.2024.100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing (WGS) of clones expanded from irradiated murine and human single cells, we revealed that IR induces a characteristic spectrum of short insertions or deletions (indels) and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Our findings suggest that 1 Gy IR exposure causes an average of 2.33 mutational events per Gb genome, comprising 2.15 indels, 0.17 SVs, and 0.01 CGRs, despite a high level of inter-cellular stochasticity. The mutational burden was dependent on total irradiation dose, regardless of dose rate or cell type. The findings were further validated in IR-induced secondary cancers and single cells without clonalization. Overall, our study highlights a comprehensive and clear picture of IR effects on normal mammalian genomes.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyun Woo Kwon
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joonoh Lim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Eunji Kim
- Department of Radiation Oncology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, 20, Boramae-ro 5 Gil, Dongjak-gu, Seoul 07061, Republic of Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sara Jeon
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yohan An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jinwook Choi
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Hyelin Na
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Eon-Seok Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Youngwon Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Dong-Wook Min
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - HyoJin Kim
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Yeong-Rok Kang
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Min Ji Bae
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Chang Geun Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Joon-Goon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Tosol Yu
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Dongnam Institute of Radiological and Medical Science, Busan 46033, Republic of Korea
| | | | | | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Su Yeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Joo-Hyeon Lee
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - On Vox Yi
- Department of Breast Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Eon Chul Han
- Department of Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kyung Su Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Tae Gen Son
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea.
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA.
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Ohno M, Takano N, Hidaka K, Sasaki F, Yamauchi K, Aoki Y, Nohmi T, Nakabeppu Y, Nakatsu Y, Tsuzuki T. Oxidative stress accelerates intestinal tumorigenesis by enhancing 8-oxoguanine-mediated mutagenesis in MUTYH-deficient mice. Genome Res 2024; 34:47-56. [PMID: 38290979 PMCID: PMC10904009 DOI: 10.1101/gr.278326.123] [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: 07/25/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
Oxidative stress-induced DNA damage and its repair systems are related to cancer etiology; however, the molecular basis triggering tumorigenesis is not well understood. Here, we aimed to explore the causal relationship between oxidative stress, somatic mutations in pre-tumor-initiated normal tissues, and tumor incidence in the small intestines of MUTYH-proficient and MUTYH-deficient mice. MUTYH is a base excision repair enzyme associated with human colorectal cancer. Mice were administered different concentrations of potassium bromate (KBrO3; an oxidizing agent)-containing water for 4 wk for mutagenesis studies or 16 wk for tumorigenesis studies. All Mutyh -/- mice treated with >0.1% KBrO3 developed multiple tumors, and the average tumor number increased dose dependently. Somatic mutation analysis of Mutyh -/-/rpsL transgenic mice revealed that G:C > T:A transversion was the only mutation type correlated positively with KBrO3 dose and tumor incidence. These mutations preferentially occurred at 5'G in GG and GAA sequences in rpsL This characteristic mutation pattern was also observed in the genomic region of Mutyh -/- tumors using whole-exome sequencing. It closely corresponded to signature 18 and SBS36, typically caused by 8-oxo-guanine (8-oxoG). 8-oxoG-induced mutations were sequence context dependent, yielding a biased amino acid change leading to missense and stop-gain mutations. These mutations frequently occurred in critical amino acid codons of known cancer drivers, Apc or Ctnnb1, known for activating Wnt signal pathway. Our results indicate that oxidative stress contributes to increased tumor incidence by elevating the likelihood of gaining driver mutations by increasing 8-oxoG-mediated mutagenesis, particularly under MUTYH-deficient conditions.
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Affiliation(s)
- Mizuki Ohno
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan;
| | - Noriko Takano
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Kyoko Hidaka
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Center for Fundamental Education, The University of Kitakyushu, Kitakyushu, Fukuoka 802-8577, Japan
| | - Fumiko Sasaki
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Kazumi Yamauchi
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Department of Radiobiology, Institute for Environmental Sciences, Kamikita, Aomori 039-3212, Japan
| | - Yasunobu Aoki
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Japan Society for the Promotion of Science, San Francisco Office, Berkeley, California 94704, USA
| | - Yoshimichi Nakatsu
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Teruhisa Tsuzuki
- Department of Medical Biophysics and Radiation Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
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42
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Richau CS, Scherer NDM, Matta BP, de Armas EM, de Barros Moreira FC, Bergmann A, Pereira Chaves CB, Boroni M, dos Santos ACE, Moreira MAM. BRCA1, BRCA2, and TP53 germline and somatic variants and clinicopathological characteristics of Brazilian patients with epithelial ovarian cancer. Cancer Med 2024; 13:e6729. [PMID: 38308422 PMCID: PMC10905552 DOI: 10.1002/cam4.6729] [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: 06/21/2023] [Revised: 10/20/2023] [Accepted: 11/07/2023] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Approximately 3/4 of ovarian cancers are diagnosed in advanced stages, with the high-grade epithelial ovarian carcinoma (EOC) accounting for 90% of the cases. EOC present high genomic instability and somatic loss-of-function variants in genes associated with homologous recombination mutational repair pathway (HR), such as BRCA1 and BRCA2, and in TP53. The identification of germline variants in HR genes in EOC is relevant for treatment of platinum resistant tumors and relapsed tumors with therapies based in synthetic lethality such as PARP inhibitors. Patients with somatic variants in HR genes may also benefit from these therapies. In this work was analyzed the frequency of somatic variants in BRCA1, BRCA2, and TP53 in an EOC cohort of Brazilian patients, estimating the proportion of variants in tumoral tissue and their association with progression-free survival and overall survival. METHODS The study was conducted with paired blood/tumor samples from 56 patients. Germline and tumoral sequences of BRCA1, BRCA2, and TP53 were obtained by massive parallel sequencing. The HaplotypeCaller method was used for calling germline variants, and somatic variants were called with Mutect2. RESULTS A total of 26 germline variants were found, and seven patients presented germline pathogenic or likely pathogenic variants in BRCA1 or BRCA2. The analysis of tumoral tissue identified 52 somatic variants in 41 patients, being 43 somatic variants affecting or likely affecting protein functionality. Survival analyses showed that tumor staging was associated with overall survival (OS), while the presence of somatic mutation in TP53 was not associated with OS or progression-free survival. CONCLUSION Frequency of pathogenic or likely pathogenic germline variants in BRCA1 and BRCA2 (12.5%) was lower in comparison with other studies. TP53 was the most altered gene in tumors, with 62.5% presenting likely non-functional or non-functional somatic variants, while eight 14.2% presented likely non-functional or non-functional somatic variants in BRCA1 or BRCA2.
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Affiliation(s)
| | | | - Bruna Palma Matta
- Tumoral Genetics and Virology ProgramInstituto Nacional de CâncerRio de JaneiroBrazil
- Present address:
Hospital BP ‐ A Beneficência Portuguesa de São PauloSão PauloBrazil
| | | | | | - Anke Bergmann
- Clinical EpidemiologyInstituto Nacional de CâncerRio de JaneiroBrazil
| | | | - Mariana Boroni
- Bioinformatics and Computational Biology LaboratoryInstituto Nacional de CâncerRio de JaneiroBrazil
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43
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Zhang L, Lee M, Maslov AY, Montagna C, Vijg J, Dong X. Analyzing somatic mutations by single-cell whole-genome sequencing. Nat Protoc 2024; 19:487-516. [PMID: 37996541 DOI: 10.1038/s41596-023-00914-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/18/2023] [Indexed: 11/25/2023]
Abstract
Somatic mutations are the cause of cancer and have been implicated in other, noncancerous diseases and aging. While clonally expanded mutations can be studied by deep sequencing of bulk DNA, very few somatic mutations expand clonally, and most are unique to each cell. We describe a detailed protocol for single-cell whole-genome sequencing to discover and analyze somatic mutations in tissues and organs. The protocol comprises single-cell multiple displacement amplification (SCMDA), which ensures efficiency and high fidelity in amplification, and the SCcaller software tool to call single-nucleotide variations and small insertions and deletions from the sequencing data by filtering out amplification artifacts. With SCMDA and SCcaller at its core, this protocol describes a complete procedure for the comprehensive analysis of somatic mutations in a single cell, covering (1) single-cell or nucleus isolation, (2) single-cell or nucleus whole-genome amplification, (3) library preparation and sequencing, and (4) computational analyses, including alignment, variant calling, and mutation burden estimation. Methods are also provided for mutation annotation, hotspot discovery and signature analysis. The protocol takes 12-15 h from single-cell isolation to library preparation and 3-7 d of data processing. Compared with other single-cell amplification methods or single-molecular sequencing, it provides high genomic coverage, high accuracy in single-nucleotide variation and small insertions and deletion calling from the same single-cell genome, and fewer processing steps. SCMDA and SCcaller require basic experience in molecular biology and bioinformatics. The protocol can be utilized for studying mutagenesis and genome mosaicism in normal and diseased human and animal tissues under various conditions.
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Affiliation(s)
- Lei Zhang
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technology, Voronezh, Russia
| | - Cristina Montagna
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
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Cornejo KM, Hutchinson L, O'Donnell P, Meng X, Tomaszewicz K, Shalin SC, Cassarino DS, Chan MP, Quinn TR, Googe PB, Nazarian RM. Molecular Profiling of Syringocystadenocarcinoma Papilliferum Reveals RAS-Activating Mutations. Arch Pathol Lab Med 2024; 148:215-222. [PMID: 37074845 DOI: 10.5858/arpa.2022-0474-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 04/20/2023]
Abstract
CONTEXT.— Syringocystadenocarcinoma papilliferum (SCACP) is a rare adnexal carcinoma and the malignant counterpart of syringocystadenoma papilliferum (SCAP), which is commonly located on the head and neck and may arise in association with a nevus sebaceus. RAS mutations have been identified in both SCAP and nevus sebaceus. OBJECTIVE.— To evaluate the clinicopathologic and molecular features of SCACPs, which have not been previously explored. DESIGN.— We obtained 11 SCACPs from 6 institutions and reviewed the clinicopathologic features. We also performed molecular profiling using next-generation sequencing. RESULTS.— The cohort comprised 6 women and 5 men with ages ranging from 29 to 96 years (mean, 73.6 years). The neoplasms occurred on the head and neck (n = 8; 73%) and extremities (n = 3; 27%). Three tumors possibly arose in a nevus sebaceus. A total of 4 cases showed at least carcinoma in situ (adenocarcinoma, n = 3; squamous cell carcinoma [SCC], n = 1), and 7 cases were invasive (SCC, n = 5; mixed adenocarcinoma + SCC, n = 2). A total of 8 of 11 cases (73%) had hot spot mutations consisting of HRAS (n = 4), KRAS (n = 1), BRAF (n = 1), TP53 (n = 4), ATM (n = 2), FLT3 (n = 1), CDKN2A (n = 1), and PTEN (n = 1). All 4 cases with HRAS mutations occurred on the head and neck, whereas the KRAS mutation occurred on the extremity. CONCLUSIONS.— RAS-activating mutations were detected in 50% of the cases, of which most (80%) involved HRAS and occurred on the head and neck, which shows overlapping features with SCAP, supporting that a subset may arise as a result of malignant transformation and likely an early oncogenic event.
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Affiliation(s)
- Kristine M Cornejo
- From the Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts (Cornejo, Nazarian)
| | - Lloyd Hutchinson
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Patrick O'Donnell
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Xiuling Meng
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Keith Tomaszewicz
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts (Hutchinson, O'Donnell, Meng, Tomaszewicz)
| | - Sara C Shalin
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas (Shalin)
| | - David S Cassarino
- Southern California Permanente Medical Group, Sunset Medical Center, Department of Pathology, Los Angeles, California (Cassarino)
| | - May P Chan
- Department of Pathology, University of Michigan Health System, Ann Arbor, Michigan (Chan)
| | - Timothy R Quinn
- Massachusetts General Physicians Organization Dermatopathology Associates, Newton, Massachusetts (Quinn)
| | - Paul B Googe
- the Department of Dermatology, University of North Carolina School of Medicine, Chapel Hill, North Carolina (Googe)
| | - Rosalynn M Nazarian
- From the Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts (Cornejo, Nazarian)
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45
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Maekawa S, Takata R, Obara W. Molecular Mechanisms of Prostate Cancer Development in the Precision Medicine Era: A Comprehensive Review. Cancers (Basel) 2024; 16:523. [PMID: 38339274 PMCID: PMC10854717 DOI: 10.3390/cancers16030523] [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: 11/24/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
The progression of prostate cancer (PCa) relies on the activation of the androgen receptor (AR) by androgens. Despite efforts to block this pathway through androgen deprivation therapy, resistance can occur through several mechanisms, including the abnormal activation of AR, resulting in castration-resistant PCa following the introduction of treatment. Mutations, amplifications, and splicing variants in AR-related genes have garnered attention in this regard. Furthermore, recent large-scale next-generation sequencing analysis has revealed the critical roles of AR and AR-related genes, as well as the DNA repair, PI3K, and cell cycle pathways, in the onset and progression of PCa. Moreover, research on epigenomics and microRNA has increasingly become popular; however, it has not translated into the development of effective therapeutic strategies. Additionally, treatments targeting homologous recombination repair mutations and the PI3K/Akt pathway have been developed and are increasingly accessible, and multiple clinical trials have investigated the efficacy of immune checkpoint inhibitors. In this comprehensive review, we outline the status of PCa research in genomics and briefly explore potential future developments in the field of epigenetic modifications and microRNAs.
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Affiliation(s)
- Shigekatsu Maekawa
- Department of Urology, Iwate Medical University, Iwate 028-3694, Japan; (R.T.); (W.O.)
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46
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Ramadan WS, Saber-Ayad MM, Saleh E, Abdu-Allah HH, El-Shorbagi ANA, Menon V, Tarazi H, Semreen MH, Soares NC, Hafezi S, Venkatakhalam T, Ahmed S, Kanie O, Hamoudi R, El-Awady R. Design, synthesis and mechanistic anticancer activity of new acetylated 5-aminosalicylate-thiazolinone hybrid derivatives. iScience 2024; 27:108659. [PMID: 38235331 PMCID: PMC10792193 DOI: 10.1016/j.isci.2023.108659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/29/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024] Open
Abstract
The development of hybrid compounds has been widely considered as a promising strategy to circumvent the difficulties that emerge in cancer treatment. The well-established strategy of adding acetyl groups to certain drugs has been demonstrated to enhance their therapeutic efficacy. Based on our previous work, an approach of accommodating two chemical entities into a single structure was implemented to synthesize new acetylated hybrids (HH32 and HH33) from 5-aminosalicylic acid and 4-thiazolinone derivatives. These acetylated hybrids showed potential anticancer activities and distinct metabolomic profile with antiproliferative properties. The in-silico molecular docking predicts a strong binding of HH32 and HH33 to cell cycle regulators, and transcriptomic analysis revealed DNA repair and cell cycle as the main targets of HH33 compounds. These findings were validated using in vitro models. In conclusion, the pleiotropic biological effects of HH32 and HH33 compounds on cancer cells demonstrated a new avenue to develop more potent cancer therapies.
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Affiliation(s)
- Wafaa S. Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Maha M. Saber-Ayad
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ekram Saleh
- Medical Biochemistry and Molecular Biology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo 12613, Egypt
| | | | - Abdel-nasser A. El-Shorbagi
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
- Faculty of Pharmacy, Assiut University, Assiut 16122, Egypt
| | - Varsha Menon
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hamadeh Tarazi
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Nelson C. Soares
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Shirin Hafezi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Thenmozhi Venkatakhalam
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Samrein Ahmed
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Biosciences and Chemistry, College of Health, Wellbeing and Life sciences, University of Sheffield Hallam, Sheffield S1 1WB, United Kingdom
| | - Osamu Kanie
- Department of Applied Biochemistry, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Division of Surgery and Interventional Science, Faculty of Medical Science, University College London, London, United Kingdom
| | - Raafat El-Awady
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
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47
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Otlu B, Alexandrov LB. Evaluating topography of mutational signatures with SigProfilerTopography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574683. [PMID: 38260507 PMCID: PMC10802511 DOI: 10.1101/2024.01.08.574683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The mutations found in a cancer genome are shaped by diverse processes, each displaying a characteristic mutational signature that may be influenced by the genome's architecture. While prior analyses have evaluated the effect of topographical genomic features on mutational signatures, there has been no computational tool that can comprehensively examine this interplay. Here, we present SigProfilerTopography, a Python package that allows evaluating the effect of chromatin organization, histone modifications, transcription factor binding, DNA replication, and DNA transcription on the activities of different mutational processes. SigProfilerTopography elucidates the unique topographical characteristics of mutational signatures, unveiling their underlying biological and molecular mechanisms.
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Affiliation(s)
- Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, 92037, USA
- Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA 92037
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48
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Liu Q, Zhang J, Guo C, Wang M, Wang C, Yan Y, Sun L, Wang D, Zhang L, Yu H, Hou L, Wu C, Zhu Y, Jiang G, Zhu H, Zhou Y, Fang S, Zhang T, Hu L, Li J, Liu Y, Zhang H, Zhang B, Ding L, Robles AI, Rodriguez H, Gao D, Ji H, Zhou H, Zhang P. Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies. Cell 2024; 187:184-203.e28. [PMID: 38181741 DOI: 10.1016/j.cell.2023.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 09/25/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024]
Abstract
We performed comprehensive proteogenomic characterization of small cell lung cancer (SCLC) using paired tumors and adjacent lung tissues from 112 treatment-naive patients who underwent surgical resection. Integrated multi-omics analysis illustrated cancer biology downstream of genetic aberrations and highlighted oncogenic roles of FAT1 mutation, RB1 deletion, and chromosome 5q loss. Two prognostic biomarkers, HMGB3 and CASP10, were identified. Overexpression of HMGB3 promoted SCLC cell migration via transcriptional regulation of cell junction-related genes. Immune landscape characterization revealed an association between ZFHX3 mutation and high immune infiltration and underscored a potential immunosuppressive role of elevated DNA damage response activity via inhibition of the cGAS-STING pathway. Multi-omics clustering identified four subtypes with subtype-specific therapeutic vulnerabilities. Cell line and patient-derived xenograft-based drug tests validated the specific therapeutic responses predicted by multi-omics subtyping. This study provides a valuable resource as well as insights to better understand SCLC biology and improve clinical practice.
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Affiliation(s)
- Qian Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China; Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Chenchen Guo
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mengcheng Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yilv Yan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Liangdong Sun
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Di Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Lele Zhang
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Huansha Yu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Yuming Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Hongwen Zhu
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanting Zhou
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shanhua Fang
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tengfei Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Hu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junqiang Li
- D1 Medical Technology, Shanghai 201800, China
| | - Yansheng Liu
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT 06516, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Daming Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 200120, China.
| | - Hu Zhou
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China.
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49
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Lin YL, Zhu JQ, Ma RQ, Meng W, Wang ZY, Li XB, Ma R, Wu HL, Xu HB, Gao Y, Li Y. Whole-Exome Sequencing Identifies Mutation Profile and Mutation Signature-Based Clustering Associated with Prognosis in Appendiceal Pseudomyxoma Peritonei. Mol Cancer Res 2024; 22:70-81. [PMID: 37768171 DOI: 10.1158/1541-7786.mcr-22-0801] [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: 10/11/2022] [Revised: 01/18/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023]
Abstract
Pseudomyxoma peritonei (PMP) is a rare malignant clinical syndrome with little known about the global mutation profile. In this study, whole-exome sequencing (WES) was performed in 49 appendiceal PMP to investigate mutation profiles and mutation signatures. A total of 4,020 somatic mutations were detected, with a median mutation number of 56 (1-402). Tumor mutation burden (TMB) was generally low (median 1.55 mutations/Mb, 0.12-11.26 mutations/Mb). Mutations were mainly enriched in the function of cancer-related axonogenesis, extracellular matrix-related processes, calcium signaling pathway, and cAMP signaling pathway. Mutations in FCGBP, RBFOX1, SPEG, RTK-RAS, PI3K-AKT, and focal adhesion pathways were associated with high-grade mucinous carcinoma peritonei. These findings revealed distinct mutation profile in appendiceal PMP. Ten mutation signatures were identified, dividing patients into mutation signature cluster (MSC) 1 (N = 28, 57.1%) and MSC 2 (N = 21, 42.9%) groups. MSC (P = 0.007) was one of the four independent factors associated with 3-year survival. TMB (P = 0.003) and microsatellite instability (P = 0.002) were independent factors associated with MSC 2 grouping. Taken together, our findings provided a broader view in the understanding of molecular pathologic mechanism in appendiceal PMP and may be critical to developing an individualized approach to appendiceal PMP treatment. IMPLICATIONS This work describes exhaustive mutation profile of PMP based on WES data and derives ten mutation signatures, which divides patients into two clusters and serve as an independent prognostic factor associated with 3-year survival.
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Affiliation(s)
- Yu-Lin Lin
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | | | - Rui-Qing Ma
- Department of Myxoma, Aerospace Center Hospital, Beijing, China
| | - Wei Meng
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Zi-Yue Wang
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xin-Bao Li
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Ru Ma
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - He-Liang Wu
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Peking University Ninth School of Clinical Medicine, Beijing, China
| | - Hong-Bin Xu
- Department of Myxoma, Aerospace Center Hospital, Beijing, China
| | - Ying Gao
- Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yan Li
- Department of Peritoneal Cancer Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Surgical Oncology, Beijing Tsinghua Changgung Hospital affiliated to Tsinghua University, Beijing, China
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50
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Berrino E, Bellomo SE, Chesta A, Detillo P, Bragoni A, Gagliardi A, Naccarati A, Cereda M, Witel G, Sapino A, Bussolati B, Bussolati G, Marchiò C. Alternative Tissue Fixation Protocols Dramatically Reduce the Impact of DNA Artifacts, Unraveling the Interpretation of Clinical Comprehensive Genomic Profiling. J Transl Med 2024; 104:100280. [PMID: 38345263 DOI: 10.1016/j.labinv.2023.100280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 02/15/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent the cornerstone of tissue-based analysis in precision medicine. Targeted next-generation sequencing panels are routinely used to analyze a limited number of genes to guide treatment decision-making for advanced-stage patients. The number and complexity of genetic alterations to be investigated are rapidly growing; in several instances, a comprehensive genomic profiling analysis is needed. The poor quality of genetic material extracted from FFPE samples may impact the feasibility/reliability of sequencing data. We sampled 9 colorectal cancers to allow 4 parallel fixations: (1) neutral buffered formalin (NBF), (2) acid-deprived formalin fixation (ADF), (3) precooled ADF (coldADF), and (4) glyoxal acid free (GAF). DNA extraction, fragmentation analysis, and sequencing by 2 large next-generation sequencing panels (OCAv3 and TSO500) followed. We comprehensively analyzed library and sequencing quality controls and the quality of sequencing results. Libraries from coldADF samples showed significantly longer reads than the others with both panels. ADF-derived and coldADF-derived libraries showed the lowest level of noise and the highest levels of uniformity with the OCAv3 panel, followed by GAF and NBF samples. The data uniformity was confirmed by the TSO500 results, which also highlighted the best performance in terms of the total region sequenced for the ADF and coldADF samples. NBF samples had a significantly smaller region sequenced and displayed a significantly lower number of evaluable microsatellite loci and a significant increase in single-nucleotide variations compared with other protocols. Mutational signature 1 (aging and FFPE artifact related) showed the highest (37%) and lowest (17%) values in the NBF and coldADF samples, respectively. Most of the identified genetic alterations were shared by all samples in each lesion. Five genes showed a different mutational status across samples and/or panels: 4 discordant results involved NBF samples. In conclusion, acid-deprived fixatives (GAF and ADF) guarantee the highest DNA preservation/sequencing performance, thus allowing more complex molecular profiling of tissue samples.
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Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
| | | | - Anita Chesta
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | | | - Alberto Bragoni
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Amedeo Gagliardi
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Alessio Naccarati
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Matteo Cereda
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Gianluca Witel
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
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