1
|
Castejón-Griñán M, Cerdido S, Sánchez-Beltrán J, Lambertos A, Abrisqueta M, Herraiz C, Jiménez-Cervantes C, García-Borrón JC. Melanoma-associated melanocortin 1 receptor variants confer redox signaling-dependent protection against oxidative DNA damage. Redox Biol 2024; 72:103135. [PMID: 38565069 PMCID: PMC11002308 DOI: 10.1016/j.redox.2024.103135] [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: 02/12/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Cutaneous melanoma, a lethal skin cancer, arises from malignant transformation of melanocytes. Solar ultraviolet radiation (UVR) is a major environmental risk factor for melanoma since its interaction with the skin generates DNA damage, either directly or indirectly via oxidative stress. Pheomelanin pigments exacerbate oxidative stress in melanocytes by UVR-dependent and independent mechanisms. Thus, oxidative stress is considered to contribute to melanomagenesis, particularly in people with pheomelanic pigmentation. The melanocortin 1 receptor gene (MC1R) is a major melanoma susceptibility gene. Frequent MC1R variants (varMC1R) associated with fair skin and red or yellow hair color display hypomorphic signaling to the cAMP pathway and are associated with higher melanoma risk. This association is thought to be due to production of photosensitizing pheomelanins as well as deficient induction of DNA damage repair downstream of varMC1R. However, the data on modulation of oxidative DNA damage repair by MC1R remain scarce. We recently demonstrated that varMC1R accelerates clearance of reactive oxygen species (ROS)-induced DNA strand breaks in an AKT-dependent manner. Here we show that varMC1R also protects against ROS-dependent formation of 8-oxodG, the most frequent oxidative DNA lesion. Since the base excision repair (BER) pathway mediates clearance of these DNA lesions, we analyzed induction of BER enzymes in human melanoma cells of varMC1R genotype. Agonist-mediated activation of both wildtype (wtMC1R) and varMC1R significantly induced OGG and APE-1/Ref1, the rate-limiting BER enzymes responsible for repair of 8-oxodG. Moreover, we found that NADPH oxidase (NOX)-dependent generation of ROS was responsible for AKT activation and oxidative DNA damage repair downstream of varMC1R. These observations provide a better understanding of the functional properties of melanoma-associated MC1R alleles and may be useful for the rational development of strategies to correct defective varMC1R responses for efficient photoprotection and melanoma prevention in fair-skinned individuals.
Collapse
Affiliation(s)
- María Castejón-Griñán
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| | - Sonia Cerdido
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| | - José Sánchez-Beltrán
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| | - Ana Lambertos
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| | - Marta Abrisqueta
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| | - Cecilia Herraiz
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| | - Celia Jiménez-Cervantes
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| | - José Carlos García-Borrón
- Department of Biochemistry, Molecular Biology and Immunology, School of Medicine, University of Murcia and Biomedical Research Institute of Murcia (Instituto Murciano de Investigación Biosanitaria, IMIB), El Palmar, Murcia, Spain.
| |
Collapse
|
2
|
Xu H, Huang K, Shi M, Gong H, Han M, Tian W, Wang X, Zhang D. MicroRNAs in Helicobacter pylori-infected gastric cancer: Function and clinical application. Pharmacol Res 2024; 205:107216. [PMID: 38761883 DOI: 10.1016/j.phrs.2024.107216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
Gastric cancer (GC) is the leading cause of cancer-related death worldwide, and it is associated with a combination of genetic, environmental, and microbial risk factors. Helicobacter pylori (H. pylori) is classified as a type I carcinogen, however, the exact regulatory mechanisms underlying H. pylori-induced GC are incompletely defined. MicroRNAs (miRNAs), one of small non-coding RNAs, negatively regulate gene expression through binding to their target genes. Dysregulation of miRNAs is crucial in human cancer. A noteworthy quantity of aberrant miRNAs induced by H. pylori through complex regulatory networks have been identified. These miRNAs substantially affect genetic instability, cell proliferation, apoptosis, invasion, metastasis, autophagy, chemoresistance, and the tumor microenvironment, leading to GC development and progression. Importantly, some H. pylori-associated miRNAs hold promise as therapeutic tools and biomarkers for GC prevention, diagnosis, and prognosis. Nonetheless, clinical application of miRNAs remains in its infancy with multiple issues, including sensitivity and specificity, stability, reliable delivery systems, and off-target effects. Additional research on the specific molecular mechanisms and more clinical data are still required. This review investigated the biogenesis, regulatory mechanisms, and functions of miRNAs in H. pylori-induced GC, offering novel insights into the potential clinical applications of miRNA-based therapeutics and biomarkers.
Collapse
Affiliation(s)
- Huimei Xu
- Department of Gastroenterology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; Key Laboratory of Digestive Diseases, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Ke Huang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730030, China; Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China
| | - Mingxuan Shi
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China
| | - Hang Gong
- Department of Gastroenterology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; Key Laboratory of Digestive Diseases, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Mengyu Han
- Department of Gastroenterology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; Key Laboratory of Digestive Diseases, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Wenji Tian
- Department of Gastroenterology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; Key Laboratory of Digestive Diseases, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China
| | - Xiaoying Wang
- Department of Emergency, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China.
| | - Dekui Zhang
- Department of Gastroenterology, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China; Key Laboratory of Digestive Diseases, The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou 730030, China.
| |
Collapse
|
3
|
Tuffaha MZ, Castellano D, Colome CS, Gutenkunst RN, Wahl LM. Non-hypermutator cancers access driver mutations through reversals in germline mutational bias. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591900. [PMID: 38746331 PMCID: PMC11092619 DOI: 10.1101/2024.04.30.591900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cancer is an evolutionary disease driven by mutations in asexually-reproducing somatic cells. In asexual microbes, bias reversals in the mutation spectrum can speed adaptation by increasing access to previously undersampled beneficial mutations. By analyzing tumors from 20 tissues, along with normal tissue and the germline, we demonstrate this effect in cancer. Non-hypermutated tumors reverse the germline mutation bias and have consistent spectra across tissues. These spectra changes carry the signature of hypoxia, and they facilitate positive selection in cancer genes. Hypermutated and non-hypermutated tumors thus acquire driver mutations differently: hypermutated tumors by higher mutation rates and non-hypermutated tumors by changing the mutation spectrum to reverse the germline mutation bias.
Collapse
Affiliation(s)
- Marwa Z. Tuffaha
- Department of Mathematics, Western University, London, Ontario N6A 5B7, Canada
| | - David Castellano
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Claudia Serrano Colome
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Lindi M. Wahl
- Department of Mathematics, Western University, London, Ontario N6A 5B7, Canada
| |
Collapse
|
4
|
Ju X, Rokohl AC, Li X, Guo Y, Yao K, Fan W, Heindl LM. A UV-related risk analysis in ophthalmic malignancies: Increased UV exposure may cause ocular malignancies. ADVANCES IN OPHTHALMOLOGY PRACTICE AND RESEARCH 2024; 4:98-105. [PMID: 38707995 PMCID: PMC11066588 DOI: 10.1016/j.aopr.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/08/2024] [Accepted: 04/02/2024] [Indexed: 05/07/2024]
Abstract
Purpose To explore the role of ultraviolet radiation (UVR) in the occurrence and development of various ocular malignancies. Methods In this article, we retrieved ocular malignancy data from the Global Cancer Observatory (GCO) and performed correlation analysis with the global UV index and sunshine duration. We searched for associated studies using the following databases: Embase, Pubmed, Cochrane Library, and Google Scholar. We conducted the literature by searching the Mesh terms denoting an exposure of interest ("UV radiation", "ultraviolet rays", and "ocular malignancies", All studies included are published until December 30, 2023 without language restrictions. Results The mechanisms and epidemiological statistics of UVR on the onset and progression of eyelid malignancies are the most studied and clear. The role of UVR in conjunctival melanoma is similar to that in eyelid melanoma. The relationship between uveal melanoma and UVR is controversial, however, it may have at least a certain impact on its prognosis. UVR causes ocular surface squamous neoplasia by further activating HPV infection. Conclusions UVR is a decisive risk factor for ocular malignancies, but the incidence of ultraviolet-induced tumors is also affected by many other factors. A correct and comprehensive understanding of the mechanisms of UVR in the pathogenesis of ocular malignant tumors can provide patients with more effective and selective immune regulation strategies.
Collapse
Affiliation(s)
- Xiaojun Ju
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Alexander C. Rokohl
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Aachen-Bonn-Cologne-Duesseldorf, Cologne, Germany
| | - Xueting Li
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Yongwei Guo
- Eye Center, The Second Affiliated Hospital of Zhejiang University School of Medicine; Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, Zhejiang, China
| | - Ke Yao
- Eye Center, The Second Affiliated Hospital of Zhejiang University School of Medicine; Zhejiang Provincial Key Laboratory of Ophthalmology, Zhejiang Provincial Clinical Research Center for Eye Diseases, Zhejiang Provincial Engineering Institute on Eye Diseases, Hangzhou, Zhejiang, China
| | - Wanlin Fan
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Ludwig M. Heindl
- Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Aachen-Bonn-Cologne-Duesseldorf, Cologne, Germany
| |
Collapse
|
5
|
Grigore A, Oproiu AM, Iancu I, Florescu IP. The Immune Response of Cutaneous Basosquamous- and Squamous-Cell Carcinoma Associated with Sun Exposure. Curr Oncol 2024; 31:2481-2487. [PMID: 38785466 PMCID: PMC11120243 DOI: 10.3390/curroncol31050185] [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: 03/25/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
In recent years, there has been an observed increase in the frequency of cutaneous carcinoma, which correlates with sun exposure. This study aims to explore the variances of tumor characteristics and immune response markers among patients diagnosed with cutaneous squamous-cell carcinoma (SCC) and basosquamous-cell carcinoma (BSC) with varying levels of sun exposure. The objective is to elucidate the potential influence of sun exposure on tumor progression and immune response in these types of carcinomas. We conducted a retrospective observational study that included 132 patients diagnosed with SCC and BSC. Participants were separated into high- and low-sun exposure groups. Tumor characteristics and immune response markers, including lymphocyte percentage (LY%), neutrophil-to-lymphocyte ratio (NLR), and lymphocyte-to-monocyte ratio (LMR), were assessed using the Mann-Whitney U test. Our findings revealed the interplay between sun exposure, inflammation, aging, and immune response. In 80% of cases, it was found that individuals had high sun exposure throughout their lifetime. Patients in the high sun exposure category had a significantly higher LY% than those with low sun exposure (24.22 ± 7.64 vs. 20.71 ± 8.10, p = 0.041). Also, the NLR was lower in patients with high sun exposure (3.08 ± 1.47 vs. 3.94 ± 2.43, p = 0.023). Regarding inflammatory markers, the erythrocyte sedimentation rate (ESR), LY%, NLR, and LMR showed significant differences between the two groups. Patients who were diagnosed with SCC had higher ESR values (p = 0.041), higher LY% (p = 0.037), higher NLR (p = 0.041), and lower LMR (p = 0.025). This study provides evidence supporting distinct tumor characteristics and immune response patterns in patients diagnosed with SCC and BSC with a high sun exposure history. These findings imply that sun exposure may contribute to tumor progression and influence the immune response in individuals with SCC and BSC.
Collapse
Affiliation(s)
- Anamaria Grigore
- Plastic Surgery Department, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Ana-Maria Oproiu
- Plastic Surgery Department, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Plastic Surgery Department, Emergency University Hospital, 050098 Bucharest, Romania
| | - Ioana Iancu
- Manchester Centre for Clinical Neuroscience, Manchester M6 8HD, UK;
| | - Ioan-Petre Florescu
- Plastic Surgery Department, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| |
Collapse
|
6
|
Paulin LF, Fan J, O'Neill K, Pleasance E, Porter VL, Jones SJM, Sedlazeck FJ. The benefit of a complete reference genome for cancer structural variant analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.15.24304369. [PMID: 38562786 PMCID: PMC10984048 DOI: 10.1101/2024.03.15.24304369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The complexities of cancer genomes are becoming more easily interpreted due to advancements in sequencing technologies and improved bioinformatic analysis. Structural variants (SVs) represent an important subset of somatic events in tumors. While detection of SVs has been markedly improved by the development of long-read sequencing, somatic variant identification and annotation remains challenging. We hypothesized that use of a completed human reference genome (CHM13-T2T) would improve somatic SV calling. Our findings in a tumour/normal matched benchmark sample and two patient samples show that the CHM13-T2T improves SV detection and prioritization accuracy compared to GRCh38, with a notable reduction in false positive calls. We also overcame the lack of annotation resources for CHM13-T2T by lifting over CHM13-T2T-aligned reads to the GRCh38 genome, therefore combining both improved alignment and advanced annotations. In this process, we assessed the current SV benchmark set for COLO829/COLO829BL across four replicates sequenced at different centers with different long-read technologies. We discovered instability of this cell line across these replicates; 346 SVs (1.13%) were only discoverable in a single replicate. We identify 49 somatic SVs, which appear to be stable as they are consistently present across the four replicates. As such, we propose this consensus set as an updated benchmark for somatic SV calling and include both GRCh38 and CHM13-T2T coordinates in our benchmark. The benchmark is available at: 10.5281/zenodo.10819636 Our work demonstrates new approaches to optimize somatic SV prioritization in cancer with potential improvements in other genetic diseases.
Collapse
Affiliation(s)
- Luis F Paulin
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Jeremy Fan
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Vanessa L Porter
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| |
Collapse
|
7
|
Shen Y, Shi K, Li D, Wang Q, Wu K, Feng C. Prognostic analysis of mutated genes and insight into effects of DNA damage and repair on mutational strand asymmetries in gastric cancer. Biochem Biophys Rep 2024; 37:101597. [PMID: 38371526 PMCID: PMC10873876 DOI: 10.1016/j.bbrep.2023.101597] [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: 08/09/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024] Open
Abstract
Gastric cancer (GACA) is a complex and multifaceted disease influenced by a variety of environmental and genetic factors. Somatic mutations play a major role in its development, and their characteristics, including the asymmetry between two DNA strands, are of great interest and appear as a signal of information and guidance, revealing mechanisms of DNA damage and repair. Here, we analyzed the impact of High-frequency mutated genes on patient prognosis and found that the effect of expression levels of tumor protein p53 (TP53) and lysine methyltransferase 2C (KMT2C) genes remained high throughout the development of GACA, with similar expression patterns. After investigating mutation asymmetry across mutagenic processes, we found that transcriptional asymmetry was dominated by T > G mutations under the influence of transcription couples repair and damage. The apolipoprotein B mRNA editing enzyme catalytic polypeptide like (APOBEC) enzyme that induces mutations during DNA replication has been identified here and we identified a replicative asymmetry, which was dominated by C > A mutations in left-replicating. Strand bias in different mutation classes at transcription factor binding sites and enhancer regions were also confirmed, which implies the important role of non-coding regulatory elements in the occurrence of mutations. This work systematically describes mutational strand asymmetries in specific genomic regions, shedding light on the DNA damage and repair mechanisms underlying somatic mutations in cohorts of GACA patients with gastric cancer.
Collapse
Affiliation(s)
- Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Institute of Animal Science, Jiangsu Academy of Agriculture Science, Nanjing, China
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qiang Wang
- Department of Urology, Peking University People's Hospital, Beijing, China
| | - Kangkang Wu
- Department of Infectious Disease, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
Collapse
|
10
|
Sharif R, Ooi TC. Understanding exposomes and its relation with cancer risk in Malaysia based on epidemiological evidence: a narrative review. Genes Environ 2024; 46:5. [PMID: 38326915 PMCID: PMC10851543 DOI: 10.1186/s41021-024-00300-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
The prevalence of cancer is increasing globally, and Malaysia is no exception. The exposome represents a paradigm shift in cancer research, emphasizing the importance of a holistic approach that considers the cumulative effect of diverse exposures encountered throughout life. The exposures include dietary factors, air and water pollutants, occupational hazards, lifestyle choices, infectious agents and social determinants of health. The exposome concept acknowledges that each individual's cancer risk is shaped by not only their genetic makeup but also their unique life experiences and environmental interactions. This comprehensive review was conducted by systematically searching scientific databases such as PubMed, Scopus and Google Scholar, by using the keywords "exposomes (environmental exposures AND/OR physical exposures AND/OR chemical exposures) AND cancer risk AND Malaysia", for relevant articles published between 2010 and 2023. Articles addressing the relationship between exposomes and cancer risk in the Malaysian population were critically evaluated and summarized. This review aims to provide an update on the epidemiological evidence linking exposomes with cancer risk in Malaysia. This review will provide an update for current findings and research in Malaysia related to identified exposomes-omics interaction and gap in research area related to the subject matter. Understanding the interplay between complex exposomes and carcinogenesis holds the potential to unveil novel preventive strategies that may be beneficial for public health.
Collapse
Affiliation(s)
- Razinah Sharif
- Centre of Healthy Ageing and Wellness, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Bangi, Malaysia.
| | - Theng Choon Ooi
- Centre of Healthy Ageing and Wellness, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| |
Collapse
|
11
|
Taraszka K, Groha S, King D, Tell R, White K, Ziv E, Zaitlen N, Gusev A. A comprehensive analysis of clinical and polygenic germline influences on somatic mutational burden. Am J Hum Genet 2024; 111:242-258. [PMID: 38211585 PMCID: PMC10870141 DOI: 10.1016/j.ajhg.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024] Open
Abstract
Tumor mutational burden (TMB), the total number of somatic mutations in the tumor, and copy number burden (CNB), the corresponding measure of aneuploidy, are established fundamental somatic features and emerging biomarkers for immunotherapy. However, the genetic and non-genetic influences on TMB/CNB and, critically, the manner by which they influence patient outcomes remain poorly understood. Here, we present a large germline-somatic study of TMB/CNB with >23,000 individuals across 17 cancer types, of which 12,000 also have extensive clinical, treatment, and overall survival (OS) measurements available. We report dozens of clinical associations with TMB/CNB, observing older age and male sex to have a strong effect on TMB and weaker impact on CNB. We additionally identified significant germline influences on TMB/CNB, including fine-scale European ancestry and germline polygenic risk scores (PRSs) for smoking, tanning, white blood cell counts, and educational attainment. We quantify the causal effect of exposures on somatic mutational processes using Mendelian randomization. Many of the identified features associated with TMB/CNB were additionally associated with OS for individuals treated at a single tertiary cancer center. For individuals receiving immunotherapy, we observed a complex relationship between PRSs for educational attainment, self-reported college attainment, TMB, and survival, suggesting that the influence of this biomarker may be substantially modified by socioeconomic status. While the accumulation of somatic alterations is a stochastic process, our work demonstrates that it can be shaped by host characteristics including germline genetics.
Collapse
Affiliation(s)
- Kodi Taraszka
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA; Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA 02215, USA.
| | - Stefan Groha
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA 02215, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - David King
- Tempus Labs, Inc, Chicago, IL 60654, USA
| | | | | | - Elad Ziv
- Department of Medicine, University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, CA 90095, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA 02215, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.
| |
Collapse
|
12
|
Yang Z, Verghese M, Yang S, Shah P, He YY. The m 6 A reader YTHDC2 regulates UVB-induced DNA damage repair and histone modification. Photochem Photobiol 2024. [PMID: 38190286 DOI: 10.1111/php.13904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Ultraviolet B (UVB) radiation represents a major carcinogen for the development of all skin cancer types. Mechanistically, UVB induces damage to DNA in the form of lesions, including cyclobutane pyrimidine dimers (CPDs). Disruption of the functional repair processes, such as nucleotide excision repair (NER), allows persistence of DNA damage and contributes to skin carcinogenesis. Recent work has implicated m6 A RNA methylation and its regulatory proteins as having critical roles in facilitating UVB-induced DNA damage repair. However, the biological functions of the m6 A reader YTHDC2 are unknown in this context. Here, we show that YTHDC2 inhibition enhances the repair of UVB-induced DNA damage. We discovered that YTHDC2 inhibition increased the expression of PTEN while it decreased the expression of the PRC2 component SUZ12 and the levels of the histone modification H3K27me3. However, none of these functions were causally linked to the improvements in DNA repair, suggesting that the mechanism utilized by YTHDC2 may be unconventional. Moreover, inhibition of the m6 A writer METTL14 reversed the effect of YTHDC2 inhibition on DNA repair while inhibition of the m6 A eraser FTO mimicked the effect of YTHDC2 inhibition, indicating that YTHDC2 may regulate DNA repair through the m6 A pathway. Finally, compared to normal human skin, YTHDC2 expression was upregulated in human cutaneous squamous cell carcinomas (cSCC), suggesting that it may function as a tumor-promoting factor in skin cancer. Taken together, our findings demonstrate that the m6 A reader YTHDC2 plays a role in regulating UVB-induced DNA damage repair and may serve as a potential biomarker in cSCC.
Collapse
Affiliation(s)
- Zizhao Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois, USA
| | - Michelle Verghese
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois, USA
- Committee on Cancer Biology, University of Chicago, Chicago, Illinois, USA
| | - Seungwon Yang
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois, USA
| | - Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois, USA
- Committee on Molecular Pathogenesis and Molecular Medicine, University of Chicago, Chicago, Illinois, USA
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, Illinois, USA
- Committee on Cancer Biology, University of Chicago, Chicago, Illinois, USA
- Committee on Molecular Pathogenesis and Molecular Medicine, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
13
|
Lu H, Hu Z, Faraudo J, Martí J. In silico design of a lipid-like compound targeting KRAS4B-G12D through non-covalent bonds. NANOSCALE 2023; 15:19359-19368. [PMID: 38014474 DOI: 10.1039/d3nr04513g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
One of the most common drivers in human cancer is the peripheral membrane protein KRAS4B, able to promote oncogenic signalling. To signal, oncogenic KRAS4B not only requires a sufficient nucleotide exchange, but also needs to recruit effectors by exposing its effector-binding sites while anchoring to the phospholipid bilayer where KRAS4B-mediated signalling events occur. The enzyme phosphodiesterase-δ plays an important role in sequestering KRAS4B from the cytoplasm and targeting it to cellular membranes of different cell species. In this work, we present an in silico design of a lipid-like compound that has the remarkable feature of being able to target both an oncogenic KRAS4B-G12D mutant and the phosphodiesterase-δ enzyme. This double action is accomplished by adding a lipid tail (analogous to the farnesyl group of the KRAS4B protein) to an previously known active compound (2H-1,2,4-benzothiadiazine, 3,4-dihydro-,1,1-dioxide). The proposed lipid-like molecule was found to lock KRAS4B-G12D in its GDP-bound state by adjusting the effector-binding domain to be blocked by the interface of the lipid bilayer. Meanwhile, it can tune GTP-bound KRAS4B-G12D to shift from the active orientation state to the inactive state. The proposed compound is also observed to stably accommodate itself in the prenyl-binding pocket of phosphodiesterase-δ, which impairs KRAS4B enrichment at the lipid bilayer, potentially reducing the proliferation of KRAS4B inside the cytoplasm and its anchoring at the bilayer. In conclusion, we report a potential inhibitor of KRAS4B-G12D with a lipid tail attached to a specific warhead, a compound which has not yet been considered for drugs targeting RAS mutants. Our work provides new ways to target KRAS4B-G12D and can also foster drug discovery efforts for the targeting of oncogenes of the RAS family and beyond.
Collapse
Affiliation(s)
- Huixia Lu
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, Barcelona E-08193, Spain.
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Zheyao Hu
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, Barcelona E-08193, Spain.
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| |
Collapse
|
14
|
Lee SS, Oudjedi F, Kirk AG, Paliouras M, Trifiro MA. Photothermal therapy of papillary thyroid cancer tumor xenografts with targeted thyroid stimulating hormone receptor antibody functionalized multiwalled carbon nanotubes. Cancer Nanotechnol 2023. [DOI: 10.1186/s12645-023-00184-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023] Open
Abstract
AbstractMultiwalled carbon nanotubes (MWCNTs) are being widely investigated in multiple biomedical applications including, and not limited to, drug delivery, gene therapy, imaging, biosensing, and tissue engineering. Their large surface area and aspect ratio in addition to their unique structural, optical properties, and thermal conductivity also make them potent candidates for novel hyperthermia therapy. Here we introduce thyroid hormone stimulating receptor (TSHR) antibody–conjugate–MWCNT formulation as an enhanced tumor targeting and light-absorbing device for the photoablation of xenografted BCPAP papillary thyroid cancer tumors. To ensure successful photothermal tumor ablation, we determined three key criteria that needed to be addressed: (1) predictive pre-operational modeling; (2) real-time monitoring of the tumor ablation process; and (3) post-operational follow-up to assess the efficacy and ensure complete response with minimal side effects. A COMSOL-based model of spatial temperature distributions of MWCNTs upon selected laser irradiation of the tumor was prepared to accurately predict the internal tumor temperature. This modeling ensured that 4.5W of total laser power delivered over 2 min, would cause an increase of tumor temperature above 45 ℃, and be needed to completely ablate the tumor while minimizing the damage to neighboring tissues. Experimentally, our temperature monitoring results were in line with our predictive modeling, with effective tumor photoablation leading to a significantly reduced post 5-week tumor recurrence using the TSHR-targeted MWCNTs. Ultimately, the results from this study support a utility for photosensitive biologically modified MWCNTs as a cancer therapeutic modality. Further studies will assist with the transition of photothermal therapy from preclinical studies to clinical evaluations.
Collapse
|
15
|
Monti P, Solazzo G, Bollati V. Effect of environmental exposures on cancer risk: Emerging role of non-coding RNA shuttled by extracellular vesicles. ENVIRONMENT INTERNATIONAL 2023; 181:108255. [PMID: 37839267 DOI: 10.1016/j.envint.2023.108255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/11/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Environmental and lifestyle exposures have a huge impact on cancer risk; nevertheless, the biological mechanisms underlying this association remain poorly understood. Extracellular vesicles (EVs) are membrane-enclosed particles actively released by all living cells, which play a key role in intercellular communication. EVs transport a variegate cargo of biomolecules, including non-coding RNA (ncRNA), which are well-known regulators of gene expression. Once delivered to recipient cells, EV-borne ncRNAs modulate a plethora of cancer-related biological processes, including cell proliferation, differentiation, and motility. In addition, the ncRNA content of EVs can be altered in response to outer stimuli. Such changes can occur either as an active attempt to adapt to the changing environment or as an uncontrolled consequence of cell homeostasis loss. In either case, such environmentally-driven alterations in EV ncRNA might affect the complex crosstalk between malignant cells and the tumor microenvironment, thus modulating the risk of cancer initiation and progression. In this review, we summarize the current knowledge about EV ncRNAs at the interface between environmental and lifestyle determinants and cancer. In particular, we focus on the effect of smoking, air and water pollution, diet, exercise, and electromagnetic radiation. In addition, we have conducted a bioinformatic analysis to investigate the biological functions of the genes targeted by environmentally-regulated EV microRNAs. Overall, we draw a comprehensive picture of the role of EV ncRNA at the interface between external factors and cancer, which could be of great interest to the development of novel strategies for cancer prevention, diagnosis, and therapy.
Collapse
Affiliation(s)
- Paola Monti
- EPIGET Lab, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Giulia Solazzo
- EPIGET Lab, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Valentina Bollati
- EPIGET Lab, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy; CRC, Center for Environmental Health, University of Milan, Milan, Italy; Occupational Health Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| |
Collapse
|
16
|
Majidian S, Agustinho DP, Chin CS, Sedlazeck FJ, Mahmoud M. Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biol 2023; 24:221. [PMID: 37798733 PMCID: PMC10552390 DOI: 10.1186/s13059-023-03061-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.
Collapse
Affiliation(s)
- Sina Majidian
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | | | | | - Fritz J Sedlazeck
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, 77030, USA.
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
| | - Medhat Mahmoud
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
17
|
Liu C, Wang Z, Wang J, Liu C, Wang M, Ngo V, Wang W. Predicting regional somatic mutation rates using DNA motifs. PLoS Comput Biol 2023; 19:e1011536. [PMID: 37782656 PMCID: PMC10569533 DOI: 10.1371/journal.pcbi.1011536] [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: 04/02/2023] [Revised: 10/12/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
How the locus-specificity of epigenetic modifications is regulated remains an unanswered question. A contributing mechanism is that epigenetic enzymes are recruited to specific loci by DNA binding factors recognizing particular sequence motifs (referred to as epi-motifs). Using these motifs to predict biological outputs depending on local epigenetic state such as somatic mutation rates would confirm their functionality. Here, we used DNA motifs including known TF motifs and epi-motifs as a surrogate of epigenetic signals to predict somatic mutation rates in 13 cancers at an average 23kbp resolution. We implemented an interpretable neural network model, called contextual regression, to successfully learn the universal relationship between mutations and DNA motifs, and uncovered motifs that are most impactful on the regional mutation rates such as TP53 and epi-motifs associated with H3K9me3. Furthermore, we identified genomic regions with significantly higher mutation rates than the expected values in each individual tumor and demonstrated that such cancer-related regions can accurately predict cancer types. Interestingly, we found that the same mutation signatures often have different contributions to cancer-related and cancer-independent regions, and we also identified the motifs with the most contribution to each mutation signature.
Collapse
Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Jun Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Chengyu Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Vu Ngo
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| |
Collapse
|
18
|
Miao H, Kuruoğlu EE, Xu T. Non-homogeneous Poisson and renewal processes as spatial models for cancer mutation. Comput Biol Chem 2023; 106:107922. [PMID: 37499435 DOI: 10.1016/j.compbiolchem.2023.107922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023]
Abstract
Advances in sequencing technology assisted biologists in revealing signatures of DNA cancer mutation process and in demonstrating the mutagenesis behind. However, most of these signatures proposed by majority of work focus only on the type and frequency of mutations, without considering spatial information which is non-negligible in exploring mechanisms of mutation occurrence, e.g., Kataegis. Statistical characterization of the distance between consecutive mutations can give us relative spatial information; however, it ignores location information which is as important as distance information. In this work, we assume that DNA cancer mutations are location-dependent and that integrating the two variables, location and inter-distance, is beneficial to study DNA cancer mutation processes more accurately. Particularly, instead of following a specific distribution over the whole DNA sequence, we found out that the distribution of distance between successive mutations alternates between exponential and power-law distributions. Apart from this, the parameters of either of the two distributions vary with DNA locations. The cancers with kataegis phenomenon, a specific mutation pattern caused by abnormal activity of APOBEC protein family, are more likely to be accompanied by higher parameter values of distance distribution, implying higher occurrence rate of mutation. Therefore, we propose non-homogeneous Poisson and Renewal processes to spatially model DNA cancer mutations and to describe mutation patterns quantitatively and more accurately through a statistical perspective.
Collapse
Affiliation(s)
- Hengyuan Miao
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
| | - Ercan Engin Kuruoğlu
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China; Institute of Data and Information, Tsinghua University, Shenzhen, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
| | - Tao Xu
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Bio-intelligent Manufacturing and Living Matter Bioprinting Center, Research Institute of Tsinghua University in Shenzhen, Tsinghua University, Shenzhen, China; Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.
| |
Collapse
|
19
|
Alshahrani SH, Rakhimov N, Rana A, Alsaab HO, Hjazi A, Adile M, Abosaooda M, Abdulhussien Alazbjee AA, Alsalamy A, Mahmoudi R. Dishevelled: An emerging therapeutic oncogene in human cancers. Pathol Res Pract 2023; 250:154793. [PMID: 37683388 DOI: 10.1016/j.prp.2023.154793] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/24/2023] [Accepted: 09/02/2023] [Indexed: 09/10/2023]
Abstract
Cancer is a multifaceted and complex disorder characterized by uncontrolled rates of cell proliferation and its ability to spread and attack other organs. Emerging data indicated several pathways and molecular targets are engaged in cancer progression. Among them, the Wnt signaling pathway was shown to have a crucial role in cancer onset and progression. Dishevelled (DVL) acts in a branch point of canonical and non-canonical Wnt pathway. DVL not only acts in the cytoplasm to inactivate the destruction complex of β-catenin but is also transported into the nucleus to affect the transcription of target genes. Available data revealed that the expression levels of DVL increased in cell and clinical specimens of various cancers, proposing that it may have an oncogenic role. DVL promoted cell invasion, migration, cell cycle, survival, proliferation, 3D-spheroid formation, stemness, and epithelial mesenchymal transition (EMT) and it suppressed cell apoptosis. The higher levels of DVL is associated with the clinicopathological characteristic of cancer-affected patients, including lymph node metastasis, tumor grade, histological type, and age. In addition, the higher levels of DVL could be a promising diagnostic and prognostic biomarker in cancer as well as it could be a mediator in cancer chemoresistance to Methotrexate, paclitaxel, and 5-fluorouracil. This study aimed to investigate the underlying molecular mechanism of DVL in cancer pathogenesis as well as to explore its importance in cancer diagnosis and prognosis as well as its role as a mediator in cancer chemotherapy.
Collapse
Affiliation(s)
| | - Nodir Rakhimov
- Department of Oncology, Samarkand State Medical University, Amir Temur Street 18, Samarkand, Uzbekistan; Department of Scientific Affairs,Tashkent State Dental Institute, Makhtumkuli 103, Tashkent, Uzbekistan
| | - Arti Rana
- Uttaranchal Institute of Technology, Uttaranchal University, Dehradun 248007, India
| | - Hashem O Alsaab
- Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mohaned Adile
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | | | | | - Ali Alsalamy
- College of Technical Engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
| | - Reza Mahmoudi
- Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
20
|
Xia Y, Jin Z, Zhang C, Ouyang L, Dong Y, Li J, Guo L, Jing B, Shi Y, Miao S, Xi R. TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing. Nat Commun 2023; 14:5935. [PMID: 37741817 PMCID: PMC10518008 DOI: 10.1038/s41467-023-41649-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
Single-molecule Real-time Isoform Sequencing (Iso-seq) of transcriptomes by PacBio can generate very long and accurate reads, thus providing an ideal platform for full-length transcriptome analysis. We present an integrated computational toolkit named TAGET for Iso-seq full-length transcript data analyses, including transcript alignment, annotation, gene fusion detection, and quantification analyses such as differential expression gene analysis and differential isoform usage analysis. We evaluate the performance of TAGET using a public Iso-seq dataset and newly sequenced Iso-seq datasets from tumor patients. TAGET gives significantly more precise novel splice site prediction and enables more accurate novel isoform and gene fusion discoveries, as validated by experimental validations and comparisons with RNA-seq data. We identify and experimentally validate a differential isoform usage gene ECM1, and further show that its isoform ECM1b may be a tumor-suppressor in laryngocarcinoma. Our results demonstrate that TAGET provides a valuable computational toolkit and can be applied to many full-length transcriptome studies.
Collapse
Affiliation(s)
- Yuchao Xia
- College of Science, Beijing Information Science and Technology University, 100192, Beijing, China
- Beijing GeneX Health Co.,Ltd, 100195, Beijing, China
| | - Zijie Jin
- Peking University International Cancer Institute, Health Science Center, Peking University, 100191, Beijing, China
- School of Mathematical Sciences, Peking University, 100871, Beijing, China
| | | | - Linkun Ouyang
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Yuhao Dong
- Beijing GeneX Health Co.,Ltd, 100195, Beijing, China
| | - Juan Li
- Department of Biomedical Engineering, College of Future Technology, Peking University, 100871, Beijing, China
| | - Lvze Guo
- Beijing GeneX Health Co.,Ltd, 100195, Beijing, China
| | - Biyang Jing
- Beijing GeneX Health Co.,Ltd, 100195, Beijing, China
| | - Yang Shi
- BeiGene (Beijing) Co., Ltd., Beijing, China
| | - Susheng Miao
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, 150081, Harbin, China.
| | - Ruibin Xi
- School of Mathematical Sciences, Peking University, 100871, Beijing, China.
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China.
- Center for Statistical Science, Peking University, 100871, Beijing, China.
| |
Collapse
|
21
|
Liakos A, Synacheri AC, Konstantopoulos D, Stefos G, Lavigne M, Fousteri M. Enhanced frequency of transcription pre-initiation complexes assembly after exposure to UV irradiation results in increased repair activity and reduced probabilities for mutagenesis. Nucleic Acids Res 2023; 51:8575-8586. [PMID: 37470822 PMCID: PMC10484669 DOI: 10.1093/nar/gkad593] [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: 04/13/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.
Collapse
Affiliation(s)
- Anastasios Liakos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Anna-Chloe Synacheri
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Dimitris Konstantopoulos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Georgios C Stefos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Matthieu D Lavigne
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Maria Fousteri
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| |
Collapse
|
22
|
Poulsgaard GA, Sørensen SG, Juul RI, Nielsen MM, Pedersen JS. Sequence dependencies and mutation rates of localized mutational processes in cancer. Genome Med 2023; 15:63. [PMID: 37592287 PMCID: PMC10436389 DOI: 10.1186/s13073-023-01217-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: 02/21/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes. METHODS We count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs. RESULTS We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average. CONCLUSIONS We summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.
Collapse
Affiliation(s)
- Gustav Alexander Poulsgaard
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Simon Grund Sørensen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Randi Istrup Juul
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Morten Muhlig Nielsen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Jakob Skou Pedersen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark.
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
- Bioinformatics Research Centre (BiRC), Aarhus University, University City 81, Building 1872, 3Rd Floor, 8000, Aarhus C, Denmark.
| |
Collapse
|
23
|
Liu Z, Zhang R, Jiang X, Ji L, Sun P, Ji Y, Zhang Y, Ding Y, Li K, Pu Z, Zhou F, Zou J. Highly Sensitive Enrichment of Low-Frequency Variants by Hairpin Competition Amplification. Anal Chem 2023; 95:12015-12023. [PMID: 37527514 DOI: 10.1021/acs.analchem.3c01803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Gene mutations are inevitably accumulated in cells of the human body. It is of great significance to detect mutations at the earliest possible time in physiological and pathological processes. However, genotyping low-copy tumor DNA (ctDNA) in patients is challenging due to abundant wild DNA backgrounds. One novel strategy to enrich rare mutations at low variant allele fractions (VAFs) with quantitative polymerase chain reaction (qPCR) and Sanger sequencing was contrived by introducing artificial hairpins into amplicons to compete with primers, coined as the hairpin competition amplification (HCA) system. The influence imposed by artificial hairpins on primer-binding in a high-temperature PCR system was investigated for the first time in this work, paving the way for the optimization of HCA. HCA differs from the previously reported work in which hairpins are formed to inhibit extension of wild-type DNA using 5-exonuclease-negative polymerase, where the readout is dependent on melting curve analysis after asymmetric PCR. Targeted at six different variants, HCA qPCR and HCA Sanger-enriched mutant DNA at VAFs as low as 0.1 or 0.01% were performed. HCA demonstrated advantages in multiplex reaction and temperature robustness. In profiling gene status from 12 lung cancer ctDNA samples and 16 thyroid cancer FNA DNA samples, HCA demonstrated a 100% concordance rate compared to ddPCR and commercial ARMS kit. HCA qPCR and Sanger sequencing can enrich low-abundance variants with high sensitivity and temperature robustness, presenting a novel and effective tool for precision diagnosis and treatment of rare variant diseases.
Collapse
Affiliation(s)
- Zhaocheng Liu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Rui Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Xixi Jiang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Li Ji
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi 214023, Jiangsu, China
| | - Yong Ji
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Yu Zhang
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Yan Ding
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Koukou Li
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Fengsheng Zhou
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| |
Collapse
|
24
|
Vardi-Yaacov O, Yaacov A, Rosenberg S, Simon I. Both cell autonomous and non-autonomous processes modulate the association between replication timing and mutation rate. Sci Rep 2023; 13:13143. [PMID: 37573368 PMCID: PMC10423235 DOI: 10.1038/s41598-023-39463-1] [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: 02/27/2023] [Accepted: 07/26/2023] [Indexed: 08/14/2023] Open
Abstract
Cancer somatic mutations are the product of multiple mutational and repair processes, some of which are tightly associated with DNA replication. Mutation rates (MR) are known to be higher in late replication timing (RT) regions, but different processes can affect this association. Systematic analysis of the mutational landscape of 2787 tumors from 32 tumor types revealed that approximately one third of the tumor samples show weak association between replication timing and mutation rate. Further analyses revealed that those samples have unique mutational signatures and are enriched with mutations in genes involved in DNA replication, DNA repair and chromatin structure. Surprisingly, analysis of differentially expressed genes between weak and strong RT-MR association groups revealed that tumors with weak association are enriched with genes associated with cell-cell communication and the immune system, suggesting a non-autonomous response to DNA damage.
Collapse
Affiliation(s)
- Oriya Vardi-Yaacov
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adar Yaacov
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Sharett Institute for Oncology, The Gaffin Center for Neuro-Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shai Rosenberg
- Sharett Institute for Oncology, The Gaffin Center for Neuro-Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
25
|
Shiraishi Y, Koya J, Chiba K, Okada A, Arai Y, Saito Y, Shibata T, Kataoka K. Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv. Nucleic Acids Res 2023; 51:e74. [PMID: 37336583 PMCID: PMC10415145 DOI: 10.1093/nar/gkad526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023] Open
Abstract
We present our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. The current version of nanomonsv includes two detection modules, Canonical SV module, and Single breakend SV module. Using tumor/control paired long-read sequencing data from three cancer and their matched lymphoblastoid lines, we demonstrate that Canonical SV module can identify somatic SVs that can be captured by short-read technologies with higher precision and recall than existing methods. In addition, we have developed a workflow to classify mobile element insertions while elucidating their in-depth properties, such as 5' truncations, internal inversions, as well as source sites for 3' transductions. Furthermore, Single breakend SV module enables the detection of complex SVs that can only be identified by long-reads, such as SVs involving highly-repetitive centromeric sequences, and LINE1- and virus-mediated rearrangements. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to a better understanding of mutational processes and functional consequences of somatic SVs.
Collapse
Affiliation(s)
- Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
- Department of Hematology, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
26
|
Baker BH, Zhang S, Simon JM, McLarnan SM, Chung WK, Pearson BL. Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Front Neurosci 2023; 17:1106573. [PMID: 37599994 PMCID: PMC10435087 DOI: 10.3389/fnins.2023.1106573] [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: 11/23/2022] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction De novo mutations contribute to a large proportion of sporadic psychiatric and developmental disorders, yet the potential role of environmental carcinogens as drivers of causal de novo mutations in neurodevelopmental disorders is poorly studied. Methods To explore environmental mutation vulnerability of disease-associated gene sets, we analyzed publicly available whole genome sequencing datasets of mutations in human induced pluripotent stem cell clonal lines exposed to 12 classes of environmental carcinogens, and human lung cancers from individuals living in highly polluted regions. We compared observed rates of exposure-induced mutations in disease-related gene sets with the expected rates of mutations based on control genes randomly sampled from the genome using exact binomial tests. To explore the role of sequence characteristics in mutation vulnerability, we modeled the effects of sequence length, gene expression, and percent GC content on mutation rates of entire genes and gene coding sequences using multivariate Quasi-Poisson regressions. Results We demonstrate that several mutagens, including radiation and polycyclic aromatic hydrocarbons, disproportionately mutate genes related to neurodevelopmental disorders including autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder. Other disease genes including amyotrophic lateral sclerosis, Alzheimer's disease, congenital heart disease, orofacial clefts, and coronary artery disease were generally not mutated more than expected. Longer sequence length was more strongly associated with elevated mutations in entire genes compared with mutations in coding sequences. Increased expression was associated with decreased coding sequence mutation rate, but not with the mutability of entire genes. Increased GC content was associated with increased coding sequence mutation rates but decreased mutation rates in entire genes. Discussion Our findings support the possibility that neurodevelopmental disorder genetic etiology is partially driven by a contribution of environment-induced germ line and somatic mutations.
Collapse
Affiliation(s)
- Brennan H. Baker
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shaoyi Zhang
- Master of Public Health Program, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeremy M. Simon
- Department of Genetics and Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah M. McLarnan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Brandon L. Pearson
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| |
Collapse
|
27
|
Laughery MF, Plummer DA, Wilson HE, Vandenberg BN, Mitchell D, Mieczkowski PA, Roberts SA, Wyrick JJ. Genome-wide maps of UVA and UVB mutagenesis in yeast reveal distinct causative lesions and mutational strand asymmetries. Genetics 2023; 224:iyad086. [PMID: 37170598 PMCID: PMC10324949 DOI: 10.1093/genetics/iyad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
Ultraviolet (UV) light primarily causes C > T substitutions in lesion-forming dipyrimidine sequences. However, many of the key driver mutations in melanoma do not fit this canonical UV signature, but are instead caused by T > A, T > C, or C > A substitutions. To what extent exposure to the UVB or UVA spectrum of sunlight can induce these noncanonical mutation classes, and the molecular mechanism involved is unclear. Here, we repeatedly exposed wild-type or repair-deficient yeast (Saccharomyces cerevisiae) to UVB or UVA light and characterized the resulting mutations by whole genome sequencing. Our data indicate that UVB induces C > T and T > C substitutions in dipyrimidines, and T > A substitutions that are often associated with thymine-adenine (TA) sequences. All of these mutation classes are induced in nucleotide excision repair-deficient cells and show transcriptional strand asymmetry, suggesting they are caused by helix-distorting UV photoproducts. In contrast, UVA exposure induces orders of magnitude fewer mutations with a distinct mutation spectrum. UVA-induced mutations are elevated in Ogg1-deficient cells, and the resulting spectrum consists almost entirely of C > A/G > T mutations, indicating they are likely derived from oxidative guanine lesions. These mutations show replication asymmetry, with elevated G > T mutations on the leading strand, suggesting there is a strand bias in the removal or bypass of guanine lesions during replication. Finally, we develop a mutation reporter to show that UVA induces a G > T reversion mutation in yeast that mimics the oncogenic NRAS Q61K mutation in melanoma. Taken together, these findings indicate that UVA and UVB exposure can induce many of the noncanonical mutation classes that cause driver mutations in melanoma.
Collapse
Affiliation(s)
- Marian F Laughery
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Hannah E Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Brittany N Vandenberg
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Debra Mitchell
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| |
Collapse
|
28
|
Nigam M, Mishra AP, Deb VK, Dimri DB, Tiwari V, Bungau SG, Bungau AF, Radu AF. Evaluation of the association of chronic inflammation and cancer: Insights and implications. Biomed Pharmacother 2023; 164:115015. [PMID: 37321055 DOI: 10.1016/j.biopha.2023.115015] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
Among the most extensively researched processes in the development and treatment of cancer is inflammatory condition. Although acute inflammation is essential for the wound healing and reconstruction of tissues that have been damaged, chronic inflammation may contribute to the onset and growth of a number of diseases, including cancer. By disrupting the signaling processes of cells, which result in cancer induction, invasion, and development, a variety of inflammatory molecules are linked to the development of cancer. The microenvironment surrounding the tumor is greatly influenced by inflammatory cells and their subsequent secretions, which also contribute significantly to the tumor's growth, survivability, and potential migration. These inflammatory variables have been mentioned in several publications as prospective diagnostic tools for anticipating the onset of cancer. Targeting inflammation with various therapies can reduce the inflammatory response and potentially limit or block the proliferation of cancer cells. The scientific medical literature from the past three decades has been studied to determine how inflammatory chemicals and cell signaling pathways related to cancer invasion and metastasis are related. The current narrative review updates the relevant literature while highlighting the specifics of inflammatory signaling pathways in cancer and their possible therapeutic possibilities.
Collapse
Affiliation(s)
- Manisha Nigam
- Department of Biochemistry, Hemvati Nandan Bahuguna Garhwal University, 246174 Srinagar Garhwal, Uttarakhand, India
| | - Abhay Prakash Mishra
- Department of Pharmacology, Faculty of Health Science, University of Free State, 9300 Bloemfontein, South Africa.
| | - Vishal Kumar Deb
- Dietetics and Nutrition Technology Division, CSIR Institute of Himalayan Bioresource Technology, 176061 Palampur, Himanchal Pradesh, India
| | - Deen Bandhu Dimri
- Department of Biochemistry, Hemvati Nandan Bahuguna Garhwal University, 246174 Srinagar Garhwal, Uttarakhand, India
| | - Vinod Tiwari
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology BHU, Varanasi 221005, Uttar Pradesh, India
| | - Simona Gabriela Bungau
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania.
| | - Alexa Florina Bungau
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Andrei-Flavius Radu
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania; Department of Preclinical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| |
Collapse
|
29
|
Song T, He N, Hao Z, Yang Y. Upregulation of ENKD1 disrupts cellular homeostasis to promote lymphoma development. J Cell Physiol 2023; 238:1308-1323. [PMID: 36960713 DOI: 10.1002/jcp.31012] [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: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023]
Abstract
Diffuse large B cell lymphoma (DLBCL) is a common and aggressive form of B cell lymphoma. Approximately 40% of DLBCL patients are incurable despite modern therapeutic approaches. To explore the molecular mechanisms driving the growth and progression of DLBCL, we analyzed genes with differential expression in DLBCL using the Gene Expression Profiling Interactive Analysis database. Enkurin domain-containing protein 1 (ENKD1), a centrosomal protein-encoding gene, was found to be highly expressed in DLBCL samples compared with normal samples. The phylogenetic analysis revealed that ENKD1 is evolutionarily conserved. Depletion of ENKD1 in cultured DLBCL cells induced apoptosis, suppressed cell proliferation, and blocked cell cycle progression in the G2/M phase. Moreover, ENKD1 expression positively correlates with the expression levels of a number of cellular homeostatic regulators, including Sperm-associated antigen 5, a gene encoding an important mitotic regulator. These findings thus demonstrate a critical function for ENKD1 in regulating the cellular homeostasis and suggest a potential value of targeting ENKD1 for the treatment of DLBCL.
Collapse
Affiliation(s)
- Ting Song
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, China
| | - Na He
- Department of Hematology, Qilu Hospital of Shandong University, Jinan, China
| | - Ziqian Hao
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yunfan Yang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, China
| |
Collapse
|
30
|
Selvam K, Sivapragasam S, Poon GMK, Wyrick JJ. Detecting recurrent passenger mutations in melanoma by targeted UV damage sequencing. Nat Commun 2023; 14:2702. [PMID: 37169747 PMCID: PMC10175485 DOI: 10.1038/s41467-023-38265-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Sequencing of melanomas has identified hundreds of recurrent mutations in both coding and non-coding DNA. These include a number of well-characterized oncogenic driver mutations, such as coding mutations in the BRAF and NRAS oncogenes, and non-coding mutations in the promoter of telomerase reverse transcriptase (TERT). However, the molecular etiology and significance of most of these mutations is unknown. Here, we use a new method known as CPD-capture-seq to map UV-induced cyclobutane pyrimidine dimers (CPDs) with high sequencing depth and single nucleotide resolution at sites of recurrent mutations in melanoma. Our data reveal that many previously identified drivers and other recurrent mutations in melanoma occur at CPD hotspots in UV-irradiated melanocytes, often associated with an overlapping binding site of an E26 transformation-specific (ETS) transcription factor. In contrast, recurrent mutations in the promoters of a number of known or suspected cancer genes are not associated with elevated CPD levels. Our data indicate that a subset of recurrent protein-coding mutations are also likely caused by ETS-induced CPD hotspots. This analysis indicates that ETS proteins profoundly shape the mutation landscape of melanoma and reveals a method for distinguishing potential driver mutations from passenger mutations whose recurrence is due to elevated UV damage.
Collapse
Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA.
- Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
| |
Collapse
|
31
|
Lodde GC, Jansen P, Herbst R, Terheyden P, Utikal J, Pföhler C, Ulrich J, Kreuter A, Mohr P, Gutzmer R, Meier F, Dippel E, Weichenthal M, Sucker A, Placke JM, Zaremba A, Albrecht LJ, Kowall B, Galetzka W, Becker JC, Tasdogan A, Zimmer L, Livingstone E, Hadaschik E, Schadendorf D, Ugurel S, Griewank K. Characterisation and outcome of RAC1 mutated melanoma. Eur J Cancer 2023; 183:1-10. [PMID: 36773463 DOI: 10.1016/j.ejca.2023.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
BACKGROUND Activating hot spot R29S mutations in RAC1, a small GTPase influencing several cellular processes including cell proliferation and cytoskeleton rearrangement, have been reported in up to 9% of sun-exposed melanomas. Clinical characteristics and treatment implications of RAC1 mutations in melanoma remain unclear. METHODS We investigated the largest set (n = 64) of RAC1 mutated melanoma patients reported to date, including a retrospective single institution cohort (n = 34) from the University Hospital Essen and a prospective multicentre cohort (n = 30) from the translational study Tissue Registry in Melanoma (TRIM; CA209-578), for patient and tumour characteristics as well as therapy outcomes. RESULTS From 3037 sequenced melanoma samples screened RAC1 mutations occurred in ∼2% of samples (64/3037). The most common RAC1 mutation was P29S (95%, 61/64). The majority of tumours had co-occuring MAP kinase mutations (88%, 56/64); mostly activating NRAS (47%, 30/64) mutations, followed by activating BRAF (28%, 18/64) and NF1 (25%, 16/64) mutations. RAC1 mutated melanomas were almost exclusively of cutaneous origin (84%, 54/64) or of unknown primary (MUP, 14%, 9/64). C > T alterations were the most frequent mutation type identified demonstrating a UV-signature for RAC1 mutated melanoma. Most patients with unresectable disease (39) received immune checkpoint inhibitors (ICI) (77%, 30/39). Objective response rate of first-line treatment in patients with stage III/IV disease was 21%; median overall survival was 47.8 months. CONCLUSIONS RAC1 mutated melanomas are rare, mostly of cutaneous origin and frequently harbour concomitant MAP kinase mutations, particularly in NRAS. Patients with advanced disease benefit from systemic treatment with ICI.
Collapse
Affiliation(s)
- Georg C Lodde
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Philipp Jansen
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany; Department of Dermatology and Allergology, UK Bonn, Bonn, Germany.
| | - Rudolf Herbst
- Department of Dermatology, Helios Klinikum Erfurt, Erfurt, Germany.
| | | | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany, Department of Dermatology, Venereology and Allergology, Ruprecht-Karl University of Heidelberg, Mannheim, Germany, DFKZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Claudia Pföhler
- Saarland University Medical School, Homburg, Department of Dermatology, Homburg/Saar, Germany.
| | - Jens Ulrich
- Department of Dermatology and Skin Cancer Center, Harzklinikum Dorothea Christiane Erxleben, Quedlinburg, Germany.
| | - Alexander Kreuter
- Department of Dermatology, Venereology and Allergology, HELIOS St. Elisabeth Klinik Oberhausen, University Witten/Herdecke, Oberhausen, Germany.
| | - Peter Mohr
- Dermatological Center Buxtehude, Elbe Kliniken Buxtehude, Buxtehude, Germany.
| | - Ralf Gutzmer
- Department of Dermatology, Venereology, Allergology and Phlebology, University Hospital Mühlenkreiskliniken Minden, Minden, Germany.
| | - Friedegund Meier
- Skin Cancer Center at the University Cancer Centre Dresden and National Center for Tumor Diseases, Dresden, Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Germany, National Center for Tumor Diseases Dresden (NCT/UCC), Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Edgar Dippel
- Department of Dermatology, Ludwigshafen Medical Center, Ludwigshafen, Germany.
| | - Michael Weichenthal
- Department of Dermatology, Skin Cancer Center, Schleswig-Holstein University Hospital, Campus Kiel, Kiel, Germany.
| | - Antje Sucker
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Jan-Malte Placke
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Anne Zaremba
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Lea Jessica Albrecht
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Bernd Kowall
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany.
| | - Wolfgang Galetzka
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany.
| | - Jürgen C Becker
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany; Translational Skin Cancer Research, University Medicine Essen, Essen, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Alpaslan Tasdogan
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Lisa Zimmer
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Elisabeth Livingstone
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Eva Hadaschik
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| | - Dirk Schadendorf
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Selma Ugurel
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Klaus Griewank
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, Essen, Germany.
| |
Collapse
|
32
|
Zeiger JS, Lally SE, Dalvin LA, Shields CL. Advances in conjunctival melanoma: clinical features, diagnostic modalities, staging, genetic markers, and management. CANADIAN JOURNAL OF OPHTHALMOLOGY 2023:S0008-4182(23)00043-1. [PMID: 36921624 DOI: 10.1016/j.jcjo.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023]
Abstract
Conjunctival melanoma, a rare malignancy of the ocular surface, is increasing in incidence. When small, straightforward excision with "no touch" surgery and cryotherapy at an experienced centre can provide excellent outcomes. When advanced, management is more complex and highly individualized. The risk of metastatic disease from conjunctival melanoma is as high as 30% and depends on tumour origin, American Joint Committee on Cancer (AJCC) classification, biomarkers, and perhaps most important, management technique. Metastatic disease can result in melanoma-associated death. Therefore, early detection and prompt directed treatment at an experienced centre are important for protection from metastasis. In this review, we provide an update on conjunctival melanoma clinical features, diagnostic modalities, AJCC staging, genetic markers, and the most critical, controlled management with minimization of tumour seeding. We detail the new era of characterization of conjunctival melanoma with molecular biomarkers that predict melanoma prognosis. This could lead to precision medicine with targeted approaches to specific mutations that improve patient survival. As we work together, the field of conjunctival melanoma is moving forward.
Collapse
Affiliation(s)
- Jennifer S Zeiger
- From the Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA
| | - Sara E Lally
- From the Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA
| | - Lauren A Dalvin
- Departments of Ophthalmology and Medical Oncology, Mayo Clinic, Rochester, MN
| | - Carol L Shields
- From the Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA.
| |
Collapse
|
33
|
Sousa A, Dugourd A, Memon D, Petursson B, Petsalaki E, Saez-Rodriguez J, Beltrao P. Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival. Mol Syst Biol 2023; 19:e10631. [PMID: 36688815 PMCID: PMC9996241 DOI: 10.15252/msb.202110631] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Genetic alterations in cancer cells trigger oncogenic transformation, a process largely mediated by the dysregulation of kinase and transcription factor (TF) activities. While the mutational profiles of thousands of tumours have been extensively characterised, the measurements of protein activities have been technically limited until recently. We compiled public data of matched genomics and (phospho)proteomics measurements for 1,110 tumours and 77 cell lines that we used to estimate activity changes in 218 kinases and 292 TFs. Co-regulation of kinase and TF activities reflects previously known regulatory relationships and allows us to dissect genetic drivers of signalling changes in cancer. We find that loss-of-function mutations are not often associated with the dysregulation of downstream targets, suggesting frequent compensatory mechanisms. Finally, we identified the activities most differentially regulated in cancer subtypes and showed how these can be linked to differences in patient survival. Our results provide broad insights into the dysregulation of protein activities in cancer and their contribution to disease severity.
Collapse
Affiliation(s)
- Abel Sousa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.,Instituto de Investigação e Inovação em Saúde da Universidade do Porto (i3s), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Graduate Program in Areas of Basic and Applied Biology (GABBA), Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Aurelien Dugourd
- Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.,Faculty of Medicine, Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Danish Memon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Borgthor Petursson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Julio Saez-Rodriguez
- Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.,Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
34
|
Therapy-selected clonal hematopoiesis and its role in myeloid neoplasms. Leuk Res 2023; 126:107020. [PMID: 36696829 DOI: 10.1016/j.leukres.2023.107020] [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: 11/22/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
Therapy-related myeloid neoplasms (t-MN) account for approximately 10-15% of all myeloid neoplasms and are associated with poor prognosis. Genomic characterization of t-MN to date has been limited in comparison to the considerable sequencing efforts performed for de novo myeloid neoplasms. Until recently, targeted deep sequencing (TDS) or whole exome sequencing (WES) have been the primary technologies utilized and thus limited the ability to explore the landscape of structural variants and mutational signatures. In the past decade, population-level studies have identified clonal hematopoiesis as a risk factor for the development of myeloid neoplasms. However, emerging research on clonal hematopoiesis as a risk factor for developing t-MN is evolving, and much is unknown about the progression of CH to t-MN. In this work, we will review the current knowledge of the genomic landscape of t-MN, discuss background knowledge of clonal hematopoiesis gained from studies of de novo myeloid neoplasms, and examine the recent literature studying the role of therapeutic selection of CH and its evolution under the effects of antineoplastic therapy. Finally, we will discuss the potential implications on current clinical practice and the areas of focus needed for future research into therapy-selected clonal hematopoiesis in myeloid neoplasms.
Collapse
|
35
|
Khazaal A, Zandavi SM, Smolnikov A, Fatima S, Vafaee F. Pan-Cancer Analysis Reveals Functional Similarity of Three lncRNAs across Multiple Tumors. Int J Mol Sci 2023; 24:ijms24054796. [PMID: 36902227 PMCID: PMC10003012 DOI: 10.3390/ijms24054796] [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: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as key regulators in many biological processes. The dysregulation of lncRNA expression has been associated with many diseases, including cancer. Mounting evidence suggests lncRNAs to be involved in cancer initiation, progression, and metastasis. Thus, understanding the functional implications of lncRNAs in tumorigenesis can aid in developing novel biomarkers and therapeutic targets. Rich cancer datasets, documenting genomic and transcriptomic alterations together with advancement in bioinformatics tools, have presented an opportunity to perform pan-cancer analyses across different cancer types. This study is aimed at conducting a pan-cancer analysis of lncRNAs by performing differential expression and functional analyses between tumor and non-neoplastic adjacent samples across eight cancer types. Among dysregulated lncRNAs, seven were shared across all cancer types. We focused on three lncRNAs, found to be consistently dysregulated among tumors. It has been observed that these three lncRNAs of interest are interacting with a wide range of genes across different tissues, yet enriching substantially similar biological processes, found to be implicated in cancer progression and proliferation.
Collapse
Affiliation(s)
- Abir Khazaal
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW 2052, Australia
| | - Seid Miad Zandavi
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Andrei Smolnikov
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shadma Fatima
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- Ingham Institute of Applied Medical Research, Sydney, NSW 2170, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW 2052, Australia
- Correspondence:
| |
Collapse
|
36
|
Identification of Cancer Driver Genes by Integrating Multiomics Data with Graph Neural Networks. Metabolites 2023; 13:metabo13030339. [PMID: 36984779 PMCID: PMC10052551 DOI: 10.3390/metabo13030339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Cancer is a heterogeneous disease that is driven by the accumulation of both genetic and nongenetic alterations, so integrating multiomics data and extracting effective information from them is expected to be an effective way to predict cancer driver genes. In this paper, we first generate comprehensive instructive features for each gene from genomic, epigenomic, transcriptomic levels together with protein–protein interaction (PPI)-networks-derived attributes and then propose a novel semisupervised deep graph learning framework GGraphSAGE to predict cancer driver genes according to the impact of the alterations on a biological system. When applied to eight tumor types, experimental results suggest that GGraphSAGE outperforms several state-of-the-art computational methods for driver genes identification. Moreover, it broadens our current understanding of cancer driver genes from multiomics level and identifies driver genes specific to the tumor type rather than pan-cancer. We expect GGraphSAGE to open new avenues in precision medicine and even further predict drivers for other complex diseases.
Collapse
|
37
|
Lee SS, Paliouras M, Trifiro MA. Functionalized Carbon Nanoparticles as Theranostic Agents and Their Future Clinical Utility in Oncology. BIOENGINEERING (BASEL, SWITZERLAND) 2023; 10:bioengineering10010108. [PMID: 36671680 PMCID: PMC9854994 DOI: 10.3390/bioengineering10010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
Over the years, research of nanoparticle applications in pre-clinical and clinical applications has greatly advanced our therapeutic and imaging approaches to many diseases, most notably neoplastic disorders. In particular, the innate properties of inorganic nanomaterials, such as gold and iron oxide, as well as carbon-based nanoparticles, have provided the greatest opportunities in cancer theranostics. Carbon nanoparticles can be used as carriers of biological agents to enhance the therapeutic index at a tumor site. Alternatively, they can also be combined with external stimuli, such as light, to induce irreversible physical damaging effects on cells. In this review, the recent advances in carbon nanoparticles and their use in cancer theranostics will be discussed. In addition, the set of evaluations that will be required during their transition from laboratory investigations toward clinical trials will be addressed.
Collapse
Affiliation(s)
- Seung S. Lee
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research—Jewish General Hospital, Montreal, QC H4A 3J1, Canada
| | - Miltiadis Paliouras
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research—Jewish General Hospital, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Department of Oncology, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence:
| | - Mark A. Trifiro
- Division of Experimental Medicine, McGill University, Montreal, QC H4A 3J1, Canada
- Lady Davis Institute for Medical Research—Jewish General Hospital, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
| |
Collapse
|
38
|
Liu M, Li W, Ma X, Che Y, Wei B, Chen M, Zhong L, Zhao S, Chen A, Pang Y, Zeng J, Guo J. Gradient differences of immunotherapy efficacy in metastatic melanoma related to sunlight exposure pattern: A population-based study. Front Oncol 2023; 12:1086664. [PMID: 36686834 PMCID: PMC9850161 DOI: 10.3389/fonc.2022.1086664] [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: 11/01/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have revolutionized metastatic melanoma (MM) treatment in just a few years. Ultraviolet (UV) in sunlight is the most significant environmental cause of melanoma, which is considered to be the main reason for tumor mutation burden (TMB) increase in melanoma. High TMB usually predicts that PD-1 inhibitors are effective. The sunlight exposure pattern of MM might be a clinical feature that matches TMB. The relationship between sunlight exposure patterns and immunotherapy response in MM is unclear. This study aims to investigate the correlation between sunlight exposure patterns and immunotherapy response in MM and establish nomograms that predict 3- and 5-year overall survival (OS) rate. Methods We searched the Surveillance, Epidemiology, and End Results (SEER) database and enrolled MM cases from 2005-2016. According to the advent of ICIs in 2011, the era was divided into the non-ICIs era (2005-2010) and the ICIs era (2011-2016). Patients were divided into three cohorts according to the primary site sunlight exposure patterns: head and neck in the first cohort, trunk arms and legs in the second cohort, and acral sites in the third cohort. We compared survival differences for each cohort between the two eras, performed stratified analysis, established nomograms for predicting 3- and 5-year OS rate, and performed internal validation. Results Comparing the survival difference between the ICIs and non-ICIs era, head and neck melanoma showed the greatest improvement in survival, with 3- and 5-year OS rate increasing by 10.2% and 9.1%, respectively (P=0.00011). In trunk arms and legs melanoma, the 3- and 5-year OS rate increased by 4.6% and 3.9%, respectively (P<0.0001). There is no improvement in survival in acral melanoma (AM) between the two eras (P=0.78). The receiver operating characteristic (ROC) curve, area under the ROC curve (AUC) and calibration graphs show good discrimination and accuracy of nomograms. Decision curve analysis (DCA) suggests good clinical utility of nomograms. Conclusions Based on the classification of sunlight exposure patterns, there is a gradient difference in immunotherapy efficacy for MM. The degree of sunlight exposure is positively correlated with immunotherapy response. The nomograms are sufficiently accurate to predict 3- and 5-year OS rate for MM, allowing for individualized clinical decisions for future clinical work.
Collapse
Affiliation(s)
- Mengsong Liu
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenyuan Li
- Sichuan Evidence-Based Medicine Center of Traditional Chinese Medicine, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiao Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuhui Che
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Bo Wei
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mulan Chen
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lin Zhong
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Siqi Zhao
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Anjing Chen
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yaobin Pang
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jinhao Zeng
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,Department of Geriatrics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,*Correspondence: Jinhao Zeng, ; Jing Guo,
| | - Jing Guo
- Dermatological Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China,School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China,*Correspondence: Jinhao Zeng, ; Jing Guo,
| |
Collapse
|
39
|
Van Horebeek L, Dedoncker N, Dubois B, Goris A. Frequent somatic mosaicism in T lymphocyte subsets in individuals with and without multiple sclerosis. Front Immunol 2022; 13:993178. [PMID: 36618380 PMCID: PMC9817019 DOI: 10.3389/fimmu.2022.993178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/09/2022] [Indexed: 12/25/2022] Open
Abstract
Background Somatic variants are variations in an individual's genome acquired after the zygotic stadium and result from mitotic errors or not (fully) repaired DNA damage. Objectives To investigate whether somatic mosaicism in T lymphocyte subsets is enriched early in multiple sclerosis (MS). Methods We identified somatic variants with variant allele fractions ≥1% across the whole exome in CD4+ and CD8+ T lymphocytes of 21 treatment-naive MS patients with <5 years of disease duration and 16 partially age-matched healthy controls. We investigated the known somatic STAT3 variant p.Y640F in peripheral blood in a larger cohort of 446 MS patients and 259 controls. Results All subjects carried 1-142 variants in CD4+ or CD8+ T lymphocytes. Variants were more common, more abundant, and increased with age in CD8+ T lymphocytes. Somatic variants were common in the genes DNMT3A and especially STAT3. Overall, the presence or abundance of somatic variants, including the STAT3 p.Y640F variant, did not differ between MS patients and controls. Conclusions Somatic variation in T lymphocyte subsets is widespread in both control individuals and MS patients. Somatic mosaicism in T lymphocyte subsets is not enriched in early MS and thus unlikely to contribute to MS risk, but future research needs to address whether a subset of variants influences disease susceptibility.
Collapse
Affiliation(s)
- Lies Van Horebeek
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Nina Dedoncker
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Bénédicte Dubois
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium,Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - An Goris
- Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium,*Correspondence: An Goris,
| |
Collapse
|
40
|
Kičiatovas D, Guo Q, Kailas M, Pesonen H, Corander J, Kaski S, Pitkänen E, Mustonen V. Identification of multiplicatively acting modulatory mutational signatures in cancer. BMC Bioinformatics 2022; 23:522. [PMID: 36474143 PMCID: PMC9724449 DOI: 10.1186/s12859-022-05060-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A deep understanding of carcinogenesis at the DNA level underpins many advances in cancer prevention and treatment. Mutational signatures provide a breakthrough conceptualisation, as well as an analysis framework, that can be used to build such understanding. They capture somatic mutation patterns and at best identify their causes. Most studies in this context have focused on an inherently additive analysis, e.g. by non-negative matrix factorization, where the mutations within a cancer sample are explained by a linear combination of independent mutational signatures. However, other recent studies show that the mutational signatures exhibit non-additive interactions. RESULTS We carefully analysed such additive model fits from the PCAWG study cataloguing mutational signatures as well as their activities across thousands of cancers. Our analysis identified systematic and non-random structure of residuals that is left unexplained by the additive model. We used hierarchical clustering to identify cancer subsets with similar residual profiles to show that both systematic mutation count overestimation and underestimation take place. We propose an extension to the additive mutational signature model-multiplicatively acting modulatory processes-and develop a maximum-likelihood framework to identify such modulatory mutational signatures. The augmented model is expressive enough to almost fully remove the observed systematic residual patterns. CONCLUSION We suggest the modulatory processes biologically relate to sample specific DNA repair propensities with cancer or tissue type specific profiles. Overall, our results identify an interesting direction where to expand signature analysis.
Collapse
Affiliation(s)
- Dovydas Kičiatovas
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Department of Computer Science, University of Helsinki, 00014 Helsinki, Finland
| | - Qingli Guo
- grid.7737.40000 0004 0410 2071Department of Computer Science, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland
| | - Miika Kailas
- grid.9681.60000 0001 1013 7965Department of Mathematics and Statistics, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Henri Pesonen
- grid.5510.10000 0004 1936 8921Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Jukka Corander
- grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology, University of Helsinki, 00014 Helsinki, Finland ,grid.5510.10000 0004 1936 8921Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, CB10 1SA UK
| | - Samuel Kaski
- grid.5373.20000000108389418Department of Computer Science, Aalto University, 00076 Aalto, Finland ,grid.5379.80000000121662407Department of Computer Science, University of Manchester, Manchester, M13 9PL UK
| | - Esa Pitkänen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071Department of Computer Science, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Organismal and Evolutionary Biology Research Programme, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology, University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
41
|
Newell F, Johansson PA, Wilmott JS, Nones K, Lakis V, Pritchard AL, Lo SN, Rawson RV, Kazakoff SH, Colebatch AJ, Koufariotis LT, Ferguson PM, Wood S, Leonard C, Law MH, Brooks KM, Broit N, Palmer JM, Couts KL, Vergara IA, Long GV, Barbour AP, Nieweg OE, Shivalingam B, Robinson WA, Stretch JR, Spillane AJ, Saw RP, Shannon KF, Thompson JF, Mann GJ, Pearson JV, Scolyer RA, Waddell N, Hayward NK. Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes. Cancer Discov 2022; 12:2856-2879. [PMID: 36098958 PMCID: PMC9716259 DOI: 10.1158/2159-8290.cd-22-0603] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 01/12/2023]
Abstract
Melanoma is a cancer of melanocytes, with multiple subtypes based on body site location. Cutaneous melanoma is associated with skin exposed to ultraviolet radiation; uveal melanoma occurs in the eyes; mucosal melanoma occurs in internal mucous membranes; and acral melanoma occurs on the palms, soles, and nail beds. Here, we present the largest whole-genome sequencing study of melanoma to date, with 570 tumors profiled, as well as methylation and RNA sequencing for subsets of tumors. Uveal melanoma is genomically distinct from other melanoma subtypes, harboring the lowest tumor mutation burden and with significantly mutated genes in the G-protein signaling pathway. Most cutaneous, acral, and mucosal melanomas share alterations in components of the MAPK, PI3K, p53, p16, and telomere pathways. However, the mechanism by which these pathways are activated or inactivated varies between melanoma subtypes. Additionally, we identify potential novel germline predisposition genes for some of the less common melanoma subtypes. SIGNIFICANCE This is the largest whole-genome analysis of melanoma to date, comprehensively comparing the genomics of the four major melanoma subtypes. This study highlights both similarities and differences between the subtypes, providing insights into the etiology and biology of melanoma. This article is highlighted in the In This Issue feature, p. 2711.
Collapse
Affiliation(s)
- Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
| | - Peter A. Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonia L. Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Department of Genetics and Immunology, Division of Biomedical Science, University of the Highlands and Islands, Inverness, Scotland, United Kingdom
| | - Serigne N. Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert V. Rawson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | | | - Andrew J. Colebatch
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | | | - Peter M. Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matthew H. Law
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kelly M. Brooks
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Natasa Broit
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,Q-Gen Cell Therapeutics, Brisbane, Queensland, Australia
| | - Jane M. Palmer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kasey L. Couts
- Center for Rare Melanomas, University of Colorado Cancer Center, Aurora, Colorado
| | - Ismael A. Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Andrew P. Barbour
- Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Omgo E. Nieweg
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Brindha Shivalingam
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Neurosurgery, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.,Department of Neurosurgery, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - William A. Robinson
- Center for Rare Melanomas, University of Colorado Cancer Center, Aurora, Colorado
| | - Jonathan R. Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Robyn P.M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Kerwin F. Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - John F. Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Mater Hospital, North Sydney, New South Wales, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Graham J. Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, New South Wales, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Corresponding Authors: Felicity Newell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3965; E-mail: ; Richard A. Scolyer, Melanoma Institute Australia, 40 Rockland Road, Wollstonecraft, Sydney, NSW 2065, Australia. Phone: 61-2-9515-7011; E-mail: ; and Nicola Waddell, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia. Phone: 61-7-3845-3538;
| | | |
Collapse
|
42
|
Chen L, Deng J. Role of non-coding RNA in immune microenvironment and anticancer therapy of gastric cancer. J Mol Med (Berl) 2022; 100:1703-1719. [PMID: 36329206 DOI: 10.1007/s00109-022-02264-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Gastric cancer remains one of the cancers with the highest mortality in the world; therefore, it is very important to investigate its pathogenesis to improve the prognosis of gastric cancer patients. Recently, noncoding RNAs have become a research hotspot in the field of oncology. These RNA molecules play complex roles in the regulation of tumor cells, immune cells, and the tumor microenvironment. Therefore, studying their ability to regulate the gastric cancer immune microenvironment will provide us with a better perspective to understand their potential role in anticancer therapy. In this review, we discuss the regulatory effects of several common noncoding RNAs on the immune microenvironment of gastric cancer and their prospects in anticancer therapy to provide some novel insight into the identification of valuable diagnostic markers and improving the prognosis of gastric cancer patients.
Collapse
Affiliation(s)
- Liqiao Chen
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China
| | - Jingyu Deng
- Department of Gastric Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, People's Republic of China.
| |
Collapse
|
43
|
Song D, Yang X, Guo X, Sun H. Safety and efficacy analysis of PD-1 inhibitors in combination with chemotherapy for advanced pancreatic cancer. Immunotherapy 2022; 14:1307-1313. [DOI: 10.2217/imt-2022-0196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Objective: To investigate the safety and efficacy of anti-PD-1 antibodies in combination with chemotherapy in the treatment of advanced pancreatic cancer. Methods: The clinical data of 18 patients with advanced pancreatic cancer who received anti-PD-1 antibody combined with chemotherapy were retrospectively analyzed. Safety, objective response rate, disease control rate, progression-free survival and overall survival were analyzed. Results: One patient achieved a complete response, nine patients had a partial response, five patients had stable disease and three patients had progressive disease. Progression-free survival and overall survival were shown to be significantly prolonged in both PD-L1-positive and high microsatellite instability (MSI-H) patients. Conclusion: Anti-PD-1 antibodies in combination with chemotherapy are safe and effective in the treatment of advanced pancreatic cancer.
Collapse
Affiliation(s)
- Dong Song
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, China
| | - Xuejing Yang
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, China
| | - Xin Guo
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, China
| | - Hu Sun
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
- Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, China
| |
Collapse
|
44
|
Wagstaff W, Mwamba RN, Grullon K, Armstrong M, Zhao P, Hendren-Santiago B, Qin KH, Li AJ, Hu DA, Youssef A, Reid RR, Luu HH, Shen L, He TC, Haydon RC. Melanoma: Molecular genetics, metastasis, targeted therapies, immunotherapies, and therapeutic resistance. Genes Dis 2022; 9:1608-1623. [PMID: 36157497 PMCID: PMC9485270 DOI: 10.1016/j.gendis.2022.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 04/10/2022] [Indexed: 02/07/2023] Open
Abstract
Cutaneous melanoma is a common cancer and cases have steadily increased since the mid 70s. For some patients, early diagnosis and surgical removal of melanomas is lifesaving, while other patients typically turn to molecular targeted therapies and immunotherapies as treatment options. Easy sampling of melanomas allows the scientific community to identify the most prevalent mutations that initiate melanoma such as the BRAF, NRAS, and TERT genes, some of which can be therapeutically targeted. Though initially effective, many tumors acquire resistance to the targeted therapies demonstrating the need to investigate compensatory pathways. Immunotherapies represent an alternative to molecular targeted therapies. However, inter-tumoral immune cell populations dictate initial therapeutic response and even tumors that responded to treatment develop resistance in the long term. As the protocol for combination therapies develop, so will our scientific understanding of the many pathways at play in the progression of melanoma. The future direction of the field may be to find a molecule that connects all of the pathways. Meanwhile, noncoding RNAs have been shown to play important roles in melanoma development and progression. Studying noncoding RNAs may help us to understand how resistance - both primary and acquired - develops; ultimately allow us to harness the true potential of current therapies. This review will cover the basic structure of the skin, the mutations and pathways responsible for transforming melanocytes into melanomas, the process by which melanomas metastasize, targeted therapeutics, and the potential that noncoding RNAs have as a prognostic and treatment tool.
Collapse
Affiliation(s)
- William Wagstaff
- The Pritzker School of Medicine, and the Medical Scientist Training Program, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rimel N. Mwamba
- The Pritzker School of Medicine, and the Medical Scientist Training Program, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Karina Grullon
- The Pritzker School of Medicine, and the Medical Scientist Training Program, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Mikhayla Armstrong
- The Pritzker School of Medicine, and the Medical Scientist Training Program, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Piao Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Bryce Hendren-Santiago
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Kevin H. Qin
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Alexander J. Li
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Daniel A. Hu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Andrew Youssef
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R. Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Laboratory of Craniofacial Suture Biology and Development, Department of Surgery Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Hue H. Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Le Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
- Department of Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Rex C. Haydon
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| |
Collapse
|
45
|
Wen Z, Yang C, Zou D, Liu J, Wang S, Liu X, Zhang Y, Zhang Y. Pan-cancer analysis of PSAP identifies its expression and clinical relevance in gastric cancer. Pathol Res Pract 2022; 238:154027. [PMID: 36084426 DOI: 10.1016/j.prp.2022.154027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 11/23/2022]
Abstract
Prosaposin (PSAP) plays a critical role in sphingolipid and cancer metabolism. Reports have shown that PSAP was involved in proliferation, tumorigenesis, and metastasis. However, the expression pattern of PSAP and its prognostic roles in gastric cancer remain elusive. PSAP expression pattern and its prognostic roles in gastric cancer (GC) were explored using data from the TCGA and Kaplan-Meier Plotter. Immunohistochemical staining of GC tissues was performed to validate the prognostic role of PSAP. TISIDB was used to analyze its correlation with immunomodulators. PSAP-associated genes, PDCD1, TGFB1, and CSF1R were used to build a risk model to evaluate immunotherapy outcomes of patients with stomach adenocarcinoma (STAD). Results showed that PSAP was highly expressed in GC. High PSAP expression in GC patients also significantly indicated a poor prognosis. The results of immunohistochemical staining showed that PSAP was an independent prognostic factor in GC patients. Based on three PSAP-associated genes, a risk model that could predict the prognosis and immunotherapy outcome of STAD was bulit. PSAP was an independent prognostic factor in GC. Our results have identified three prognosis-related genes which were useful to evaluate immunotherapy outcomes of STAD patients.
Collapse
Affiliation(s)
- Zhenpeng Wen
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, PR China.
| | - Chunjiao Yang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, PR China.
| | - Dan Zou
- Department of Medical Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Insititute, Shenyang, Liaoning Province 110042, PR China.
| | - Jiaqing Liu
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, PR China.
| | - Song Wang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, PR China.
| | - Xuqin Liu
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, PR China.
| | - Yi Zhang
- Department of Gynecology, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, PR China.
| | - Ye Zhang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, PR China.
| |
Collapse
|
46
|
Effects of replication domains on genome-wide UV-induced DNA damage and repair. PLoS Genet 2022; 18:e1010426. [PMID: 36155646 PMCID: PMC9536635 DOI: 10.1371/journal.pgen.1010426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/06/2022] [Accepted: 09/12/2022] [Indexed: 11/19/2022] Open
Abstract
Nucleotide excision repair is the primary repair mechanism that removes UV-induced DNA lesions in placentals. Unrepaired UV-induced lesions could result in mutations during DNA replication. Although the mutagenesis of pyrimidine dimers is reasonably well understood, the direct effects of replication fork progression on nucleotide excision repair are yet to be clarified. Here, we applied Damage-seq and XR-seq techniques and generated replication maps in synchronized UV-treated HeLa cells. The results suggest that ongoing replication stimulates local repair in both early and late replication domains. Additionally, it was revealed that lesions on lagging strand templates are repaired slower in late replication domains, which is probably due to the imbalanced sequence context. Asymmetric relative repair is in line with the strand bias of melanoma mutations, suggesting a role of exogenous damage, repair, and replication in mutational strand asymmetry.
Collapse
|
47
|
Jin SG, Padron F, Pfeifer GP. UVA Radiation, DNA Damage, and Melanoma. ACS OMEGA 2022; 7:32936-32948. [PMID: 36157735 PMCID: PMC9494637 DOI: 10.1021/acsomega.2c04424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/30/2022] [Indexed: 05/05/2023]
Abstract
Melanoma is a lethal type of skin tumor that has been linked with sunlight exposure chiefly in fair-skinned human populations. Wavelengths from the sun that can reach the earth's surface include UVA radiation (320-400 nm) and UVB radiation (280-320 nm). UVB effectively induces the formation of dimeric DNA photoproducts, preferentially the cyclobutane pyrimidine dimers (CPDs). The characteristic UVB signature mutations in the form of C to T mutations at dipyrimidine sequences are prevalent in melanoma tumor genomes and have been ascribed to deamination of cytosines within CPDs before DNA polymerase bypass. However, evidence from epidemiological, animal, and other experimental studies also suggest that UVA radiation may participate in melanoma formation. The DNA damage relevant for UVA includes specific types of CPDs at TT sequences and perhaps oxidative DNA damage to guanine, both induced by direct or indirect, photosensitization-mediated chemical and biophysical processes. We summarize the evidence for a potential role of UVA in melanoma and discuss some of the mechanistic pathways of how UVA may induce mutagenesis in melanocytes.
Collapse
|
48
|
Rosenquist R, Cuppen E, Buettner R, Caldas C, Dreau H, Elemento O, Frederix G, Grimmond S, Haferlach T, Jobanputra V, Meggendorfer M, Mullighan CG, Wordsworth S, Schuh A. Clinical utility of whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:32-39. [PMID: 34175442 DOI: 10.1016/j.semcancer.2021.06.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022]
Abstract
Precision diagnostics is one of the two pillars of precision medicine. Sequencing efforts in the past decade have firmly established cancer as a primarily genetically driven disease. This concept is supported by therapeutic successes aimed at particular pathways that are perturbed by specific driver mutations in protein-coding domains and reflected in three recent FDA tissue agnostic cancer drug approvals. In addition, there is increasing evidence from studies that interrogate the entire genome by whole-genome sequencing that acquired global and complex genomic aberrations including those in non-coding regions of the genome might also reflect clinical outcome. After addressing technical, logistical, financial and ethical challenges, national initiatives now aim to introduce clinical whole-genome sequencing into real-world diagnostics as a rational and potentially cost-effective tool for response prediction in cancer and to identify patients who would benefit most from 'expensive' targeted therapies and recruitment into clinical trials. However, so far, this has not been accompanied by a systematic and prospective evaluation of the clinical utility of whole-genome sequencing within clinical trials of uniformly treated patients of defined clinical outcome. This approach would also greatly facilitate novel predictive biomarker discovery and validation, ultimately reducing size and duration of clinical trials and cost of drug development. This manuscript is the third in a series of three to review and critically appraise the potential and challenges of clinical whole-genome sequencing in solid tumors and hematological malignancies.
Collapse
Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, The Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States
| | - Geert Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, United States
| | - Sarah Wordsworth
- Nuffield Department of Population Health and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
49
|
Meggendorfer M, Jobanputra V, Wrzeszczynski KO, Roepman P, de Bruijn E, Cuppen E, Buttner R, Caldas C, Grimmond S, Mullighan CG, Elemento O, Rosenquist R, Schuh A, Haferlach T. Analytical demands to use whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:16-22. [PMID: 34119643 DOI: 10.1016/j.semcancer.2021.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Interrogating the tumor genome in its entirety by whole-genome sequencing (WGS) offers an unprecedented insight into the biology and pathogenesis of cancer, with potential impact on diagnostics, prognostication and therapy selection. WGS is able to detect sequence as well as structural variants and thereby combines central domains of cytogenetics and molecular genetics. Given the potential of WGS in directing targeted therapeutics and clinical decision-making, we envision a gradual transition of the method from research to clinical routine. This review is one out of three within this issue aimed at facilitating this effort, by discussing in-depth analytical validation, clinical interpretation and clinical utility of WGS. The review highlights the requirements for implementing, validating and maintaining a clinical WGS pipeline to obtain high-quality patient-specific data in accordance with the local regulatory landscape. Every step of the WGS pipeline, which includes DNA extraction, library preparation, sequencing, bioinformatics analysis, and data storage, is considered with respect to its logistics, necessities, potential pitfalls, and the required quality management. WGS is likely to drive clinical diagnostics and patient care forward, if requirements and challenges of the technique are recognized and met.
Collapse
Affiliation(s)
| | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, USA; Columbia University Medical Center, 650 W 168th St, New York, USA
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, the Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, USA
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
50
|
Anik MI, Mahmud N, Masud AA, Khan MI, Islam MN, Uddin S, Hossain MK. Role of Reactive Oxygen Species in Aging and Age-Related Diseases: A Review. ACS APPLIED BIO MATERIALS 2022; 5:4028-4054. [PMID: 36043942 DOI: 10.1021/acsabm.2c00411] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Research on the role of reactive oxygen species (ROS) in the aging process has advanced significantly over the last two decades. In light of recent findings, ROS takes part in the aging process of cells along with contributing to various physiological signaling pathways. Antioxidants being cells' natural defense mechanism against ROS-mediated alteration, play an imperative role to maintain intracellular ROS homeostasis. Although the complete understanding of the ROS regulated aging process is yet to be fully comprehended, current insights into various sources of cellular ROS and their correlation with the aging process and age-related diseases are portrayed in this review. In addition, results on the effect of antioxidants on ROS homeostasis and the aging process as well as their advances in clinical trials are also discussed in detail. The future perspective in ROS-antioxidant dynamics on antiaging research is also marshaled to provide future directions for ROS-mediated antiaging research fields.
Collapse
Affiliation(s)
- Muzahidul I Anik
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Niaz Mahmud
- Department of Biomedical Engineering, Military Institute of Science and Technology, Dhaka 1216, Bangladesh
| | - Abdullah Al Masud
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Md Ishak Khan
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Md Nurul Islam
- Department of Bioregulatory Sciences, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Shihab Uddin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - M Khalid Hossain
- Institute of Electronics, Atomic Energy Research Establishment, Bangladesh Atomic Energy Commission, Dhaka 1349, Bangladesh
- Interdisciplinary Graduate School of Engineering Science, Kyushu University, Fukuoka 816-8580, Japan
| |
Collapse
|