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Tolezano GC, Bastos GC, da Costa SS, Freire BL, Homma TK, Honjo RS, Yamamoto GL, Passos-Bueno MR, Koiffmann CP, Kim CA, Vianna-Morgante AM, de Lima Jorge AA, Bertola DR, Rosenberg C, Krepischi ACV. Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature. J Autism Dev Disord 2024; 54:1181-1212. [PMID: 36502452 DOI: 10.1007/s10803-022-05853-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] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Celia Priszkulnik Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Angela Maria Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
- Institute of Biosciences, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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Sarma K, Akther MH, Ahmad I, Afzal O, Altamimi ASA, Alossaimi MA, Jaremko M, Emwas AH, Gautam P. Adjuvant Novel Nanocarrier-Based Targeted Therapy for Lung Cancer. Molecules 2024; 29:1076. [PMID: 38474590 DOI: 10.3390/molecules29051076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 03/14/2024] Open
Abstract
Lung cancer has the lowest survival rate due to its late-stage diagnosis, poor prognosis, and intra-tumoral heterogeneity. These factors decrease the effectiveness of treatment. They release chemokines and cytokines from the tumor microenvironment (TME). To improve the effectiveness of treatment, researchers emphasize personalized adjuvant therapies along with conventional ones. Targeted chemotherapeutic drug delivery systems and specific pathway-blocking agents using nanocarriers are a few of them. This study explored the nanocarrier roles and strategies to improve the treatment profile's effectiveness by striving for TME. A biofunctionalized nanocarrier stimulates biosystem interaction, cellular uptake, immune system escape, and vascular changes for penetration into the TME. Inorganic metal compounds scavenge reactive oxygen species (ROS) through their photothermal effect. Stroma, hypoxia, pH, and immunity-modulating agents conjugated or modified nanocarriers co-administered with pathway-blocking or condition-modulating agents can regulate extracellular matrix (ECM), Cancer-associated fibroblasts (CAF),Tyro3, Axl, and Mertk receptors (TAM) regulation, regulatory T-cell (Treg) inhibition, and myeloid-derived suppressor cells (MDSC) inhibition. Again, biomimetic conjugation or the surface modification of nanocarriers using ligands can enhance active targeting efficacy by bypassing the TME. A carrier system with biofunctionalized inorganic metal compounds and organic compound complex-loaded drugs is convenient for NSCLC-targeted therapy.
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Affiliation(s)
- Kangkan Sarma
- School of Pharmaceutical and Population Health Informatics (SoPPHI), DIT University, Dehradun 248009, India
| | - Md Habban Akther
- School of Pharmaceutical and Population Health Informatics (SoPPHI), DIT University, Dehradun 248009, India
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62521, Saudi Arabia
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Abdulmalik S A Altamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Manal A Alossaimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Preety Gautam
- School of Pharmaceutical and Population Health Informatics (SoPPHI), DIT University, Dehradun 248009, India
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Zhu H, Lu X, Jiang H, Yang Z, Xu T. Descriptive Statistics and Genome-Wide Copy Number Analysis of Milk Production Traits of Jiangsu Chinese Holstein Cows. Animals (Basel) 2023; 14:17. [PMID: 38200748 PMCID: PMC10778490 DOI: 10.3390/ani14010017] [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: 10/24/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Milk production traits are the most important quantitative economic traits in dairy cow production; improving the yield and quality of milk is an important way to ensure the production efficiency of the dairy industry. This study carried out a series of in-depth statistical genetics studies and molecular analyses on the Chinese Holstein cows in the Jiangsu Province, such as descriptive statistics and copy number variation analysis. A genetic correlation, phenotypic correlation, and descriptive statistical analysis of five milk production traits (milk yield, milk fat percentage, milk fat yield, milk protein percentage, and milk protein yield) of the dairy cows were analyzed using the SPSS and DMU software. Through quality control, 4173 cows and their genomes were used for genomic study. Then, SNPs were detected using DNA chips, and a copy number variation (CNV) analysis was carried out to locate the quantitative trait loci (QTL) of the milk production traits by Perl program software Penn CNV and hidden Markov model (HMM). The phenotypic means of the milk yield, milk fat percentage, milk fat mass, milk protein percentage, and milk protein mass at the first trimester were lower than those at the other trimesters by 8.821%, 1.031%, 0.930%, 0.003%, and 0.826%, respectively. The five milk production traits showed a significant phenotypic positive correlation (p < 0.01) and a high genetic positive correlation among the three parities. Based on the GGPBovine 100 K SNP data, QTL-detecting research on the fist-parity milk performance of dairy cows was carried out via the CNV. We identified 1731 CNVs and 236 CNVRs in the 29 autosomes of 984 Holstein dairy cows, and 19 CNVRs were significantly associated with the milk production traits (p < 0.05). These CNVRs were analyzed via a bioinformatics analysis; a total of 13 gene ontology (GO) terms and 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched (p < 0.05), and these terms and pathways are mainly related to lipid metabolism, amino acid metabolism, and cellular catabolic processes. This study provided a theoretical basis for the molecular-marker-assisted selection of dairy cows by developing descriptive statistics on the milk production traits of dairy cows and by locating the QTL and functional genes that affect the milk production traits of first-born dairy cows. The results describe the basic status of the milk production traits of the Chinese Holstein cows in Jiangsu and locate the QTL and functional genes that affect the milk production traits of the first-born cows, providing a theoretical basis for the molecular-marker-assisted selection of dairy cows.
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Affiliation(s)
- Hao Zhu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.Y.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Hui Jiang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000 Aarhus C, Denmark;
| | - Zhangping Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.Y.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.Y.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
- International Joint Research Laboratory, Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
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Wang Z, Cai H, Li Z, Sun W, Zhao E, Cui H. Histone demethylase KDM4B accelerates the progression of glioblastoma via the epigenetic regulation of MYC stability. Clin Epigenetics 2023; 15:192. [PMID: 38093312 PMCID: PMC10720090 DOI: 10.1186/s13148-023-01608-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most malignant and invasive human brain tumor. Histone demethylase 4B (KDM4B) is abnormally expressed in GBM, but the molecular mechanisms by which KDM4B affects the malignant tumor progression are not well defined. METHODS GBM cell lines and xenograft tumor samples were subjected to quantitative PCR (qPCR), Western blot, immunohistochemical staining (IHC), as well as ubiquitination, immunoprecipitation (IP), and chromatin immunoprecipitation (ChIP) assays to investigate the role of KDM4B in the progression of GBM. RESULTS Here, we report that KDM4B is an epigenetic activator of GBM progression. Abnormal expression of KDM4B is correlated with a poor prognosis in GBM patients. In GBM cell lines, KDM4B silencing significantly inhibited cell survival, proliferation, migration, and invasion, indicating that KDM4B is essential for the anchorage-independent growth and tumorigenic activity of GBM cells. Mechanistically, KDM4B silencing led to downregulation of the oncoprotein MYC and suppressed the expression of cell cycle proteins and epithelial-to-mesenchymal transition (EMT)-related proteins. Furthermore, we found that KDM4B regulates MYC stability through the E3 ligase complex SCFFBXL3+CRY2 and epigenetically activates the transcription of CCNB1 by removing the repressive chromatin mark histone H3 lysine 9 trimethylation (H3K9me3). Finally, we provide evidence that KDM4B epigenetically activates the transcription of miR-181d-5p, which enhances MYC stability. CONCLUSIONS Our study has uncovered a KDM4B-dependent epigenetic mechanism in the control of tumor progression, providing a rationale for utilizing KDM4B as a promising therapeutic target for the treatment of MYC-amplified GBM.
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Affiliation(s)
- Zhongze Wang
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Huarui Cai
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
- Jinfeng Laboratory, Chongqing, 401329, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China
| | - Zekun Li
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
| | - Wei Sun
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China
| | - Erhu Zhao
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Medical Research Institute, Southwest University, No.2 Tiansheng Road, Beibei district, Chongqing, 400715, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Chongqing, 400716, China.
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Xu Z, Wang X, Song X, An Q, Wang D, Zhang Z, Ding X, Yao Z, Wang E, Liu X, Ru B, Xu Z, Huang Y. Association between the copy number variation of CCSER1 gene and growth traits in Chinese Capra hircus (goat) populations. Anim Biotechnol 2023; 34:1377-1383. [PMID: 35108172 DOI: 10.1080/10495398.2022.2025818] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Recently, Coiled-coil serine-rich protein 1 (CCSER1) gene is reported to be related to economic traits in livestock, and become a hotspot. In our study, we detected CCSER1 gene CNV in 693 goats from six breeds (GZB, GZW, AN, BH, HG, TH) by quantitative real-time PCR (qPCR) and the association analysis between the types of CNV and growth traits. Then, CCSER1 gene expression pattern was discovered in seven tissues from NB goats. Our results showed that the CCSER1 gene copy numbers were distributed differently in the aforementioned six breeds. The type of CCSER1 gene CNV was significantly associated with body weight and heart girth traits in GZW goat, in which individuals with deletion type were dominant in body weight trait (P < 0.05), while the normal type individuals were more advantageous in heart girth trait (P < 0.01); and there was a significant association with heart girth in TH goat (P < 0.05), which normal type was the dominant one. The expression profile revealed that CCSER1 gene has the highest level in the lung, followed by the small intestine and heart. In conclusion, our result is dedicated to an in-depth study of the novel CCSER1 gene CNV site and to provide essential information for Chinese goats molecular selective breeding in the future.
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Affiliation(s)
- Zijie Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Xingya Song
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou, People's Republic of China
| | - Dahui Wang
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xiaoting Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
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Shi Y, Shen H. DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma. Front Genet 2023; 14:1231415. [PMID: 37867602 PMCID: PMC10587545 DOI: 10.3389/fgene.2023.1231415] [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: 05/30/2023] [Accepted: 09/05/2023] [Indexed: 10/24/2023] Open
Abstract
Stomach Adenocarcinoma (STAD) is a leading cause of death worldwide. Somatic Copy Number Alterations (SCNAs), which result in Homologous recombination (HR) deficiency in double-strand break repair, are associated with the progression of STAD. However, the landscape of frequent breakpoints of SCNAs (hotspots) and their functional impacts remain poorly understood. In this study, we aimed to explore the frequency and impact of these hotspots in 332 STAD patients and 1,043 cancer cells using data from the Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE). We studied the rates of DSB (Double-Strand Breaks) loci in STAD patients by employing the Non-Homogeneous Poisson Distribution (λ), based on which we identified 145 DSB-hotspots with genes affected. We further verified DNA cytosine deamination as a critical process underlying the burden of DSB in STAD. Finally, we illustrated the clinical impact of the significant biological processes. Our findings highlighted the relationship between DNA cytosine deamination and SCNA in cancer was associated with recurrent Somatic Copy Number Alterations in STAD.
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Affiliation(s)
- Yilin Shi
- The College of Letters & Science, University of Wisconsin–Madison, Madison, WI, United States
| | - Huangxuan Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Abstract
PURPOSE OF REVIEW Structural genomic variants have emerged as a relevant cause for several disorders, including intellectual disability, neuropsychiatric disorders, cancer and congenital heart disease. In this review, we will discuss the current knowledge about the involvement of structural genomic variants and, in particular, copy number variants in the development of thoracic aortic and aortic valve disease. RECENT FINDINGS There is a growing interest in the identification of structural variants in aortopathy. Copy number variants identified in thoracic aortic aneurysms and dissections, bicuspid aortic valve related aortopathy, Williams-Beuren syndrome and Turner syndrome are discussed in detail. Most recently, the first inversion disrupting FBN1 has been reported as a cause for Marfan syndrome. SUMMARY During the past 15 years, the knowledge on the role of copy number variants as a cause for aortopathy has grown significantly, which is partially due to the development of novel technologies including next-generation sequencing. Although copy number variants are now often investigated on a routine basis in diagnostic laboratories, more complex structural variants such as inversions, which require the use of whole genome sequencing, are still relatively new to the field of thoracic aortic and aortic valve disease.
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Affiliation(s)
- Josephina A.N. Meester
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Anne Hebert
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart L. Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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Aupperle-Lellbach H, Heidrich D, Kehl A, Conrad D, Brockmann M, Törner K, Beitzinger C, Müller T. KITLG Copy Number Germline Variations in Schnauzer Breeds and Their Relevance in Digital Squamous Cell Carcinoma in Black Giant Schnauzers. Vet Sci 2023; 10:147. [PMID: 36851451 PMCID: PMC9966798 DOI: 10.3390/vetsci10020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Copy number variations (CNVs) of the KITLG gene seem to be involved in the oncogenesis of digital squamous cell carcinoma (dSCC). The aims of this study were (1) to investigate KITLG CNV in giant (GS), standard (SS), and miniature (MS) schnauzers and (2) to compare KITLG CNV between black GS with and without dSCC. Blood samples from black GS (22 with and 17 without dSCC), black SS (18 with and 4 without dSSC; 5 unknown), and 50 MS (unknown dSSC status and coat colour) were analysed by digital droplet PCR. The results are that (1) most dogs had a copy number (CN) value > 4 (range 2.5-7.6) with no significant differences between GS, SS, and MS, and (2) the CN value in black GS with dSCC was significantly higher than in those without dSCC (p = 0.02). CN values > 5.8 indicate a significantly increased risk for dSCC, while CN values < 4.7 suggest a reduced risk for dSCC (grey area: 4.7-5.8). Diagnostic testing for KITLG CNV may sensitise owners to the individual risk of their black GS for dSCC. Further studies should investigate the relevance of KITLG CNV in SS and the protective effects in MS, who rarely suffer from dSCC.
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Affiliation(s)
| | | | | | - David Conrad
- LABOKLIN GmbH & Co. KG, 97688 Bad Kissingen, Germany
| | | | - Katrin Törner
- LABOKLIN GmbH & Co. KG, 97688 Bad Kissingen, Germany
| | | | - Tobias Müller
- Institut für Bioinformatik, Universität Würzburg, 97070 Würzburg, Germany
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9
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Hu H, Geng Z, Zhang S, Xu Y, Wang Q, Chen S, Zhang B, Sun K, Lu Y. Rare copy number variation analysis identifies disease-related variants in atrioventricular septal defect patients. Front Genet 2023; 14:1075349. [PMID: 36816019 PMCID: PMC9936062 DOI: 10.3389/fgene.2023.1075349] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Atrioventricular septal defect (AVSD) is a deleterious subtype of congenital heart diseases (CHD) characterized by atrioventricular canal defect. The pathogenic genetic changes of AVSD remain elusive, particularly for copy number variation (CNV), a large segment variation of the genome, which is one of the major forms of genetic variants resulting in congenital heart diseases. In the present study, we recruited 150 AVSD cases and 100 healthy subjects as controls for whole exome sequencing (WES). We identified total 4255 rare CNVs using exon Hidden Markov model (XHMM) and screened rare CNVs by eliminating common CNVs based on controls and Database of Genomic Variants (DGV). Each patient contained at least 9 CNVs, and the CNV burden was prominently presented in chromosomes 19,22,21&16. Small CNVs (<500 kb) were frequently observed. By leveraging gene-based burden test, we further identified 20 candidate AVSD-risk genes. Among them, DYRK1A, OBSCN and TTN were presented in the core disease network of CHD and highly and dynamically expressed in the heart during the development, which indicated they possessed the high potency to be AVSD-susceptible genes. These findings not only provided a roadmap for finally unveiling the genetic cause of AVSD, but also provided more resources and proofs for clinical genetics.
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Affiliation(s)
- Huan Hu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zilong Geng
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuejuan Xu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qingjie Wang
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bing Zhang
- Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
| | - Kun Sun
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
| | - Yanan Lu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Bing Zhang, ; Kun Sun, ; Yanan Lu,
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10
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Santos FB, Del-Bem LE. The Evolution of tRNA Copy Number and Repertoire in Cellular Life. Genes (Basel) 2022; 14:27. [PMID: 36672768 PMCID: PMC9858662 DOI: 10.3390/genes14010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
tRNAs are universal decoders that bridge the gap between transcriptome and proteome. They can also be processed into small RNA fragments with regulatory functions. In this work, we show that tRNA copy number is largely controlled by genome size in all cellular organisms, in contrast to what is observed for protein-coding genes that stop expanding between ~20,000 and ~35,000 loci per haploid genome in eukaryotes, regardless of genome size. Our analyses indicate that after the bacteria/archaea split, the tRNA gene pool experienced the evolution of increased anticodon diversity in the archaeal lineage, along with a tRNA gene size increase and mature tRNA size decrease. The evolution and diversification of eukaryotes from archaeal ancestors involved further expansion of the tRNA anticodon repertoire, additional increase in tRNA gene size and decrease in mature tRNA length, along with an explosion of the tRNA gene copy number that emerged coupled with accelerated genome size expansion. Our findings support the notion that macroscopic eukaryotes with a high diversity of cell types, such as land plants and vertebrates, independently evolved a high diversity of tRNA anticodons along with high gene redundancy caused by the expansion of the tRNA copy number. The results presented here suggest that the evolution of tRNA genes played important roles in the early split between bacteria and archaea, and in eukaryogenesis and the later emergence of complex eukaryotes, with potential implications in protein translation and gene regulation through tRNA-derived RNA fragments.
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Affiliation(s)
- Fenícia Brito Santos
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
- Graduate Program in Bioinformatics, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
| | - Luiz-Eduardo Del-Bem
- Del-Bem Lab, Department of Botany, Institute of Biological Sciences (ICB), Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil
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11
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Zhang H, Huang Y, Yang E, Gao X, Zou P, Sun J, Tian Z, Bao M, Liao D, Ge J, Yang Q, Li X, Zhang Z, Luo P, Jiang X. Identification of a Fibroblast-Related Prognostic Model in Glioma Based on Bioinformatics Methods. Biomolecules 2022; 12:biom12111598. [PMID: 36358948 PMCID: PMC9687522 DOI: 10.3390/biom12111598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 12/03/2022] Open
Abstract
Background: Glioma is the most common primary tumor of the central nervous system with a high lethality rate. This study aims to mine fibroblast-related genes with prognostic value and construct a corresponding prognostic model. Methods: A glioma-related TCGA (The Cancer Genome Atlas) cohort and a CGGA (Chinese Glioma Genome Atlas) cohort were incorporated into this study. Variance expression profiling was executed via the “limma” R package. The “clusterProfiler” R package was applied to perform a GO (Gene Ontology) analysis. The Kaplan–Meier (K–M) curve, LASSO regression analysis, and Cox analyses were implemented to determine the prognostic genes. A fibroblast-related risk model was created and affirmed by independent cohorts. We derived enriched pathways between the fibroblast-related high- and low-risk subgroups using gene set variation analysis (GSEA). The immune infiltration cell and the stromal cell were calculated using the microenvironment cell populations-counter (MCP-counter) method, and the immunotherapy response was assessed with the SubMap algorithm. The chemotherapy sensitivity was estimated using the “pRRophetic” R package. Results: A total of 93 differentially expressed fibroblast-related genes (DEFRGs) were uncovered in glioma. Seven prognostic genes were filtered out to create a fibroblast-related gene signature in the TCGA-glioma cohort training set. We then affirmed the fibroblast-related risk model via TCGA-glioma cohort and CGGA-glioma cohort testing sets. The Cox regression analysis proved that the fibroblast-related risk score was an independent prognostic predictor in prediction of the overall survival of glioma patients. The fibroblast-related gene signature revealed by the GSEA was applicable to the immune-relevant pathways. The MCP-counter algorithm results pointed to significant distinctions in the tumor microenvironment between fibroblast-related high- and low-risk subgroups. The SubMap analysis proved that the fibroblast-related risk score could predict the clinical sensitivity of immunotherapy. The chemotherapy sensitivity analysis indicated that low-risk patients were more sensitive to multiple chemotherapeutic drugs. Conclusion: Our study identified prognostic fibroblast-related genes and generated a novel risk signature that could evaluate the prognosis of glioma and offer a theoretical basis for clinical glioma therapy.
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Affiliation(s)
- Haofuzi Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Yutao Huang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Erwan Yang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Xiangyu Gao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Peng Zou
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Jidong Sun
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Zhicheng Tian
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Mingdong Bao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Dan Liao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Junmiao Ge
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Qiuzi Yang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Xin Li
- Department of Anesthesiology, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
| | - Zhuoyuan Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
- Biochemistry and Molecular Biology, College of Life Science, Northwest University, Xi’an 710127, China
| | - Peng Luo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
- Correspondence: (P.L.); (X.J.)
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China
- Correspondence: (P.L.); (X.J.)
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12
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Liu M, Huang C, Dai R, Ren W, Li X, Wu X, Ma X, Chu M, Bao P, Guo X, Pei J, Xiong L, Yan P, Liang C. Copy Number Variations in the MICALL2 and MOGAT2 Genes Are Associated with Ashidan Yak Growth Traits. Animals (Basel) 2022; 12:ani12202779. [PMID: 36290165 PMCID: PMC9597734 DOI: 10.3390/ani12202779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/29/2022] Open
Abstract
Copy number variations (CNVs) are a result of genomic rearrangement affecting DNA regions over 1 kb in length, and can include inversions, translocations, deletions, and duplications. The molecule interacting with CasL-like protein 2 (MICALL2) gene is primarily associated with mitochondrial protein targeting and exhibits predicted stress fiber colocalization. The monoacylglycerol O-acyltransferase 2 (MOGAT2) gene encodes an enzyme responsible for catalyzing diacylglycerol synthesis from 2-monoacylglycerol and fatty acyl-CoA. For this study, blood samples were obtained from 315 yaks, and the body weight, body length, withers height, and chest girth of these animals were measured at 6, 12, 18, and 30 months of age. Genomic DNA was harvested from the collected blood samples, and CNVs in these samples were detected by qPCR. The resultant data were compared using ANOVAs, revealing significant associations between MICALL2 gene CNVs and body weight at 6 months of age (p < 0.05), body length and chest girth at 30 months of age (p < 0.05), and withers height at 18 months of age (p < 0.01) in Ashidan yaks. Similarly, MOGAT2 CNVs were significantly associated with body weight at 6 and 30 months of age (p < 0.05), and with withers height at 18 months of age (p < 0.01) in these Ashidan yaks. MICALL2 and MOGAT2 gene expression was further analyzed in yak tissue samples, revealing that MICALL2 was most highly expressed in the adipose tissue, whereas MOGAT2 was most highly expressed in the lung. These results thus confirmed the relationship between CNVs in the MICALL2 and MOGAT2 genes and Ashidan yak growth traits, providing a valuable gene locus that can be leveraged for future marker-assisted yak breeding efforts.
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Affiliation(s)
- Modian Liu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chun Huang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Wenwen Ren
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xinyi Li
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.)
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: (P.Y.); (C.L.)
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13
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Applegate CD, Schiettecatte F, Hamosh A, Amberger JS. Exploring Genes and Phenotypes Within Chromosomal Regions Using OMIM's GeneScout. Curr Protoc 2022; 2:e530. [PMID: 36130039 DOI: 10.1002/cpz1.530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Structural variation in genomes, such as copy number variants (CNVs), is under scrutiny for its contribution to phenotypic expression and evolution. Regions of homozygosity (ROH) are ripe for phenotype-gene discovery. Determining the genes and related phenotypes within genomic regions is key to studying potential functional and phenotypic consequences. Because individuals have multiple CNVs and ROHs in their genome, identifying genomic regions that are phenotypically significant is challenging. GeneScout is a web-based tool that can be used to search genomic regions to display and filter the genes and their associated phenotypes within regions of interest. Phenotypes and their associated gene(s) can then be filtered to show only the genes with phenotypes that have a particular inheritance pattern and/or specific clinical feature(s). Phenotypes can then be selected to compare the clinical synopses side-by-side in Online Mendelian Inheritance in Man (OMIM® ). Additionally, two coordinate sets can be compared to determine either the regions of overlap or the unique regions (subtraction). The resulting coordinate ranges are displayed on the results page, and the results table displays only the genes and phenotypes present within the coordinate ranges. The interactive table includes gene-specific links to external resources such as ClinVar, ClinGen validity, ClinGen dosage, and gnomAD, and a diamond symbol next to the gene name indicates a gene that spans the start or end of a coordinate range. Searches and comparisons may be performed for coordinates in assemblies GRCh37 (hg19) and GRCh38 (hg38). The results page offers the option to liftover coordinates entered in GRCh37 to GRCh38 and updates the results table to display the gene content based on assembly GRCh38. The search coordinates and results table can be downloaded in a tab-delimited or Excel file. © 2022 Wiley Periodicals LLC. Basic Protocol: Searching GeneScout.
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Affiliation(s)
- Carolyn D Applegate
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ada Hamosh
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joanna S Amberger
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
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14
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Gao Y, Zhong Z, Yang P. Genetics in Behcet's Disease: An Update Review. FRONTIERS IN OPHTHALMOLOGY 2022; 2:916887. [PMID: 38983559 PMCID: PMC11182159 DOI: 10.3389/fopht.2022.916887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 07/11/2024]
Abstract
Behcet's disease (BD) is one of the most vision-threatening clinical entities of uveitis. Although the etiopathogenesis of BD remains obscure, accumulating evidence has demonstrated that both genetic and environmental factors may contribute to the development of BD. Genome-wide association studies (GWAS) and candidate association studies have identified several genetic variants strongly associated with BD, including variants in human leukocyte antigen (HLA) -A02, -A03, -A24, -A26, -A31, -B15, -B27, -B35, -B49, -B51, -B57, -B58, -C0704, CIITA, ERAP1, MICA, IL1A-IL1B, IL10, IL12, IL23R, IL-23R/IL-12RB2, IL1RL1-IL18R1, STAT4, TFCP2L1, TRAF5, TNFAIP3, CCR1/CCR3, RIPK2, ADO-ZNF365-EGR2, KLRC4, LACC1, MEFV, IRF8, FUT2, CEBPB-PTPN1, ZMIZ1, RPS6KA4, IL10RA, SIPA1-FIBP-FOSL1, VAMP1, JRKL/CTCN5, IFNGR1 and miRNA-146a. Epigenetic modifications are also reported to play essential roles in the development of BD, including DNA methylation and histone modification. We review here the recent advances in the genetic and epigenetic factors associated with the BD pathogenesis.
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Affiliation(s)
| | | | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, and Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
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15
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Liang J, Wang Y, Cai L, Liu J, Yan J, Chen X, Wu X, Chen Q. Comparative Genomic Analysis Reveals Genetic Variations in Multiple Primary Esophageal Squamous Cell Carcinoma of Chinese Population. Front Oncol 2022; 12:868301. [PMID: 35515115 PMCID: PMC9065449 DOI: 10.3389/fonc.2022.868301] [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: 02/02/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common and lethal malignant tumors. The incidence of malignant transformation of esophageal mucosa increases greatly due to long-term exposure to factors such as smoking, drinking, and poor eating habits. Furthermore, multiple primary tumors could occur synchronously or asynchronously in the upper aerodigestive tract, especially in the esophagus, adding difficulty to the treatment of ESCC. Genetic mutations are important during the malignant transformation from normal mucosa to esophageal cancer, but the underlying mechanism has not been fully elucidated. In this study, we used whole-exome sequencing (WES) to profile genetic variations in physiologically normal mucosa (PNM) and ESCC tumors, as well as PNM of non-ESCC subjects. We found significant differences in mutation frequencies of NOTCH1 and NOTCH2, copy number variations (CNVs) at both gene and chromosomal arm levels, and cancer-related HIPPO, WNT, and NRF2 signaling pathways between ESCC tumors and normal mucosa. Our analysis of both primary tumors and paired PNM in bifocal ESCC revealed three different primary tumor evolution modes, and the most common mode exhibited a complete genomic divergence in all the samples from the same patient. Furthermore, the mutation frequency of TP53 was significantly higher in ESCC cases than that in non-ESCC cases. Overall, our results provide important evidence for further elucidating the mechanisms of genetic mutations underlying the cause of ESCC.
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Affiliation(s)
- Jinxiao Liang
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Yinjie Wang
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Lei Cai
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Jinshi Liu
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Junrong Yan
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xin Chen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Xiaoying Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qixun Chen
- Department of Oncological Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China
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16
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Abi-Raad R, Prasad ML, Adeniran AJ, Cai G. Copy number variations identified in thyroid FNA specimens are associated with Hürthle cell cytomorphology. Cancer Cytopathol 2022; 130:415-422. [PMID: 35332982 DOI: 10.1002/cncy.22569] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The fine-needle aspiration (FNA) diagnosis of thyroid Hürthle cell neoplasms (HCNs) remains challenging. This study explored a possible association of copy number variations (CNVs) with Hürthle cell lesions of the thyroid. METHODS Thyroid FNA cases that were diagnosed as follicular lesion of undetermined significance (FLUS) or follicular neoplasm (FN)/HCN for which the ThyroSeq version 3 genomic classifier test was performed were retrieved. RESULTS A total of 324 thyroid FNA cases (228 FLUS cases, 46 HCN cases, and 50 FN cases) were included in the study. FLUS cases were further classified as Hürthle cell type (follicular lesion of undetermined significance-Hürthle cell type [FLUS-HCT]; 20 cases) or non-Hürthle cell type (follicular lesion of undetermined significance-non-Hürthle cell type [FLUS-NHCT]; 208 cases). HCN and FLUS-HCT cases showed a higher prevalence of CNVs (23 of 66 [35%]) in comparison with those classified as FN or FLUS-NHCT (14 of 258 [5%]; P < .001). A total of 105 patients had histopathologic follow-up. Cases with CNVs were more likely to be neoplastic (18 of 26 [69%]) and associated with Hürthle cell changes (14 of 26 [54%]) in comparison with cases without any molecular alterations (neoplastic, 8 of 24 [33%]; Hürthle cell changes, 2 of 24 [8%]; P < .05). In HCN/FLUS-HCT cases with CNVs (n = 14), Hürthle cell changes (13 of 14 [93%]) and neoplasms (9 of 14 [64%]) were more likely to be seen on surgical follow-up in comparison with the 17 cases without CNVs (Hürthle cell changes, 6 of 17 [35%]; neoplastic, 3 of 17 [18%]; P < .05). CONCLUSIONS CNVs identified in thyroid FNA cases are associated with Hürthle cell morphology and are suggestive of a neoplasm with Hürthle cell features in thyroid FNAs classified as FLUS-HCT/HCN. This finding may be helpful in triaging patients who would benefit from surgical management.
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Affiliation(s)
- Rita Abi-Raad
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Manju L Prasad
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Adebowale J Adeniran
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Guoping Cai
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
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17
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Raos D, Abramović I, Tomić M, Vrtarić A, Kuliš T, Ćorić M, Ulamec M, Katušić Bojanac A, Ježek D, Sinčić N. CNV Hotspots in Testicular Seminoma Tissue and Seminal Plasma. Cancers (Basel) 2021; 14:189. [PMID: 35008352 PMCID: PMC8750740 DOI: 10.3390/cancers14010189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 12/22/2022] Open
Abstract
Seminoma (SE) is the most frequent type of testicular tumour, affecting predominantly young men. Early detection and diagnosis of SE could significantly improve life quality and reproductive health after diagnosis and treatment. Copy number variation (CNV) has already been associated with various cancers as well as SE. In this study, we selected four genes (MAGEC2, NANOG, RASSF1A, and KITLG) for CNV analysis in genomic DNA (gDNA), which are located on chromosomes susceptible to gains, and whose aberrant expression was already detected in SE. Furthermore, CNV was analysed in cell-free DNA (cfDNA) from seminal plasma. Analysis was performed by droplet digital polymerase chain reaction (ddPCR) on gDNA from SE and nonmalignant testicular tissue. Seminal plasma cfDNA from SE patients before and after surgery was analysed, as well as from healthy volunteers. The CNV hotspot in gDNA from SE tissue was detected for the first time in all analysed genes, and for two genes, NANOG and KITLG it was reflected in cfDNA from seminal plasma. Although clinical value is yet to be determined, presented data emphasize a potential use of CNV as a potential SE biomarker from a liquid biopsy.
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Affiliation(s)
- Dora Raos
- Department of Medical Biology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (D.R.); (I.A.); (M.Ć.); (A.K.B.)
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (M.U.)
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Irena Abramović
- Department of Medical Biology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (D.R.); (I.A.); (M.Ć.); (A.K.B.)
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (M.U.)
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Miroslav Tomić
- Department of Urology, University Clinical Hospital Centre “Sestre Milosrdnice”, 10000 Zagreb, Croatia;
| | - Alen Vrtarić
- Department of Clinical Chemistry, University Clinical Hospital Centre “Sestre Milosrdnice”, 10000 Zagreb, Croatia;
| | - Tomislav Kuliš
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (M.U.)
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Urology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Marijana Ćorić
- Department of Medical Biology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (D.R.); (I.A.); (M.Ć.); (A.K.B.)
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Pathology and Cytology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Monika Ulamec
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (M.U.)
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Ljudevit Jurak Clinical Department of Pathology and Cytology, University Clinical Hospital Centre “Sestre Milosrdnice”, 10000 Zagreb, Croatia
- Department of Pathology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Ana Katušić Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (D.R.); (I.A.); (M.Ć.); (A.K.B.)
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Davor Ježek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Histology and Embryology, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Nino Sinčić
- Department of Medical Biology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (D.R.); (I.A.); (M.Ć.); (A.K.B.)
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (T.K.); (M.U.)
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
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18
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Liao R, Chen X, Cao Q, Wang Y, Miao Z, Lei X, Jiang Q, Chen J, Wu X, Li X, Li J, Dong C. HIST1H1B Promotes Basal-Like Breast Cancer Progression by Modulating CSF2 Expression. Front Oncol 2021; 11:780094. [PMID: 34746019 PMCID: PMC8570124 DOI: 10.3389/fonc.2021.780094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/05/2021] [Indexed: 01/09/2023] Open
Abstract
Background Basal-like breast cancer (BLBC) is associated with a poor clinical outcome; however, the mechanism of BLBC aggressiveness is still unclear. It has been shown that a linker histone functions as either a positive or negative regulator of gene expression in tumors. Here, we aimed to investigate the possible involvement and mechanism of HIST1H1B in BLBC progression. Experimental design We analyzed multiple gene expression datasets to determine the relevance of HIST1H1B expression with BLBC. We employed quantitative real-time PCR, transwell assay, colony formation assay, and mammosphere assay to dissect the molecular events associated with the expression of HIST1H1B in human breast cancer. We studied the association of HIST1H1B with CSF2 by ChIP assay. Using tumorigenesis assays, we determine the effect of HIST1H1B expression on tumorigenicity of BLBC cells. Results Here, we show that the linker histone HIST1H1B is dramatically elevated in BLBC due to HIST1H1B copy number amplification and promoter hypomethylation. HIST1H1B upregulates colony-stimulating factor 2 (CSF2) expression by binding the CSF2 promoter. HIST1H1B expression promotes, whereas knockdown of HIST1H1B expression suppresses tumorigenicity. In breast cancer patients, HIST1H1B expression is positively correlated with large tumor size, high grade, metastasis and poor survival. Conclusion HIST1H1B contributes to basal-like breast cancer progression by modulating CSF2 expression, indicating a potential prognostic marker and therapeutic target for this disease.
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Affiliation(s)
- Ruocen Liao
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xingyu Chen
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianhua Cao
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifan Wang
- Cancer Institute of Integrative Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Zhaorui Miao
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xingyu Lei
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianjin Jiang
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Chen
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuebiao Wu
- Department of Pathophysiology, Gannan Medical University, Gannan, China
| | - Xiaoli Li
- R&D Department of Hangzhou, Abcam Plc, Hangzhou, China
| | - Jun Li
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chenfang Dong
- Department of Pathology and Pathophysiology, and Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Key Laboratory for Disease Proteomics, Zhejiang University School of Medicine, Hangzhou, China
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19
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Yang X, Fang L, Zhang C. CNV Analysis of the Correlation between Preoperative Lymph Node Metastasis and Prognosis of Early Tongue Cancer. J Cancer 2021; 12:6135-6144. [PMID: 34539886 PMCID: PMC8425219 DOI: 10.7150/jca.60447] [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: 03/15/2021] [Accepted: 08/07/2021] [Indexed: 11/17/2022] Open
Abstract
Objective: To investigate the relationship between preoperative concealed lymph node metastasis (LNM) and prognosis in patients with early tongue cancer. Methods: According to preoperative lymph node dissection, 41 patients with tongue cancer were divided into the LNM group (n=19) and the non-LNM group (n=22). Analysis of single nucleotide variation (SNV), tumor mutation burden (TMB), mutant allele tumor heterogeneity (MATH), aneuploidy and copy number variation (CNV) was performed to identify differentially expressed genes (DEGs) related to LNM. While KEGG analysis was conducted to reveal the CNV differentially expressed genes and main enriched pathways, the correlation between pathways and genes was analyzed by hierarchical clustering. The clinical information of LNM and data on overall survival (OS) rate were obtained from The Cancer Genome Atlas (TCGA), and survival analysis was performed based on combined LNM information. Results: We observed significant correlations for the mTOR signaling pathway, Hippo signaling pathway and Wnt signaling pathway with the LNM group, while leukocyte transendothelial migration and cytokine-cytokine receptor interaction were markedly correlated with the non-LNM group. Moreover, TNFRSF10C was identified as the main DEG in the leukocyte transendothelial migration pathway. TCGA-based validation revealed that the disease-free survival (DFS) of the non-LNM group was significantly higher than that of the LNM group (P<0.005) when TNFRSF10C CNV was set to a log2 ratio>-0.163. Conclusion: The differential expression of TNFRSF10C in leukocyte transendothelial migration, an immune-related pathway, is associated with LNM and DFS. The TNFRSF10C CNV log2 ratio could potentially serve as an indicator of good prognosis for tongue cancer patients with non-LNM after neck dissection.
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Affiliation(s)
- Xi Yang
- Department of Oral & MaxillofacialeHead & Neck Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China
| | - Lu Fang
- Genecast Biotechnology Co., Ltd, Wuxi 214104, China
| | - Chenping Zhang
- Department of Oral & MaxillofacialeHead & Neck Oncology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China
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20
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Jin C, Liu X, Zheng W, Su L, Liu Y, Guo X, Gu X, Li H, Xu B, Wang G, Yu J, Zhang Q, Bao D, Wan S, Xu F, Lai X, Liu J, Xing J. Characterization of fragment sizes, copy number aberrations and 4-mer end motifs in cell-free DNA of hepatocellular carcinoma for enhanced liquid biopsy-based cancer detection. Mol Oncol 2021; 15:2377-2389. [PMID: 34133846 PMCID: PMC8410516 DOI: 10.1002/1878-0261.13041] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/24/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Circulating cell‐free DNA (cfDNA) fragmentomics, which encompasses the measurement of cfDNA length and short nucleotide motifs at the ends of cfDNA molecules, is an emerging field for cancer diagnosis. The utilization of cfDNA fragmentomics for the diagnosis of patients with hepatocellular carcinoma (HCC) caused by hepatitis B virus (HBV) is currently limited. In this study, we utilized whole‐genome sequencing data of cfDNA in samples from patients with HCC (n = 197) and HBV (n = 187) to analyze the association of fragment size selection (< 150 bp) with tumor fraction (TF), copy number variation (CNV) alterations and the change in the proportion of 4‐mer end motifs in HCC and HBV samples. Our analyses identified five typical CNV markers (i.e. loss in chr1p, chr4q and chr8p, and gain in chr1q and chr8q) in cfDNA with a cumulatively positive rate of ˜ 95% in HCC samples. Size selection (< 150 bp) significantly enhanced TF and CNV signals in HCC samples. Additionally, three 4‐mer end motifs (CCCA, CCTG and CCAG) were identified as preferred end motifs in HCC samples. We identified 139 end motifs significantly associated with fragment size that showed similar patterns of associations between patients with HCC and HBV, suggesting that end motifs might be inherently coupled with fragment size by a ubiquitous mechanism. Here we conclude that CNV markers, fragment size selection and end‐motif pattern in cfDNA have potential for effective detection of patients with HCC.
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Affiliation(s)
- Chao Jin
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaonan Liu
- Ambulatory Surgery Center of Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wenyuan Zheng
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Liping Su
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Yang Liu
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xu Guo
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiaoming Gu
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Hongping Li
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Bo Xu
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Gang Wang
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Jiyan Yu
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Qiong Zhang
- Research and Development Division, Oriomics Biotech, Hangzhou, China
| | - Dengke Bao
- Laboratory of Cancer Biomarkers and Liquid Biopsy, School of Pharmacy, Henan University, Kaifeng, China
| | - Shaogui Wan
- Center for Molecular Pathology, First Affiliated Hospital, Gannan Medical University, Ganzhou, China
| | - Fei Xu
- Department of Hepatology, The Fifth People's Hospital of Ganzhou, China
| | - Xiaohuan Lai
- Department of Hepatology, The Fifth People's Hospital of Ganzhou, China
| | - Jiayun Liu
- Department of Clinical Laboratory, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
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21
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AlShibli A, Mathkour H. Fuzzy methods for the detection of copy number variations in comparative genomic hybridization arrays. Saudi J Biol Sci 2020; 27:3647-3654. [PMID: 33304176 PMCID: PMC7714972 DOI: 10.1016/j.sjbs.2020.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 11/19/2022] Open
Abstract
Genomic copy number variations (CNVs) are considered as a significant source of genetic diversity and widely involved in gene expression and regulatory mechanism, genetic disorders and disease risk, susceptibility to certain diseases and conditions, and resistance to medical drugs. Many studies have targeted the identification, profiling, analysis, and associations of genetic CNVs. We propose herein two new fuzzy methods, taht is, one based on the fuzzy inference from the pre-processed input, and another based on fuzzy C-means clustering. Our solutions present a higher true positive rate and a lower false negative with no false positive, efficient performance and consumption of least resources.
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Affiliation(s)
- Ahmad AlShibli
- Department of computer science, College of computer and information sciences, King Saud University, Riyadh, Saudi Arabia
- Corresponding author at: P.O. Box 230734, Riyadh, Saudi Arabia.
| | - Hassan Mathkour
- Department of computer science, College of computer and information sciences, King Saud University, Riyadh, Saudi Arabia
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22
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Hu W, Su Y, Fei X, Wang X, Zhang G, Su C, Du T, Yang T, Wang G, Tang Z, Zhang J. Ubiquitin specific peptidase 19 is a prognostic biomarker and affect the proliferation and migration of clear cell renal cell carcinoma. Oncol Rep 2020; 43:1964-1974. [PMID: 32236633 PMCID: PMC7160536 DOI: 10.3892/or.2020.7565] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/14/2020] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin specific peptidase 19 (USP19) is a member of the USP family and exhibits diverse roles in various biological processes, such as cell differentiation, cell cycle progression and apoptosis. There is limited knowledge regarding the role and impact of USP19 in cancer, particularly clear cell renal cell carcinoma (ccRCC). To examine the function of USP19 in ccRCC, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases were examined to determine USP19 mRNA expression levels. USP19 mRNA levels were significantly lower in ccRCC tissues than in normal tissues. USP19 downregulation was associated with ccRCC progression and poor prognostic outcomes in TCGA cohort. Furthermore, the functional involvement of USP19 in ccRCC was examined using Cell Counting Kit-8, soft agar, Transwell and wound healing assays in vitro following overexpression or knockdown of USP19 in the Caki-1 cell line. USP19 overexpression inhibited ccRCC proliferation and migration, whereas USP19 knockdown promoted ccRCC proliferation and migration in vitro. Consistent with these results, it was further demonstrated that USP19 downregulation promoted tumor growth in vivo in a xenograft model. Mechanistically, it was found that USP19 exerted its inhibitory effect on ccRCC proliferation and migration by suppressing the activation of ERK. Collectively, the present findings identified a role for USP19 as a tumor suppressor in ccRCC and demonstrated that USP19 is a potential prognostic biomarker that could be applied in ccRCC therapy.
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Affiliation(s)
- Wenbing Hu
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Yanfang Su
- Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430000, P.R. China
| | - Xinxiong Fei
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Xudong Wang
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Guanglin Zhang
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Chunyan Su
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Tianxing Du
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Tao Yang
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Gangsheng Wang
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Ze Tang
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
| | - Jierong Zhang
- Department of Oncology, Huangshi Central Hospital of Edong Healthcare, Affiliated Hospital of Hubei Polytechnic University, Huangshi, Hubei 435000, P.R. China
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23
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Ramkumar B, Dharaskar SP, Mounika G, Paithankar K, Sreedhar AS. Mitochondrial chaperone, TRAP1 as a potential pharmacological target to combat cancer metabolism. Mitochondrion 2019; 50:42-50. [PMID: 31669620 DOI: 10.1016/j.mito.2019.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/17/2022]
Abstract
The stress response forms the most ancient defense system in living cells. Heat shock proteins (Hsps) are highly conserved across species and play major roles in mounting the stress response. The emerging information now suggests that Hsp90 family of chaperones display additional cellular roles contributing to diseases like cancer. For this reason, pharmacological targeting of Hsp90 has emerged as a novel antitumor strategy. However, its mitochondrial homologue TRAP1 has not been implicated in cancer with conclusive mechanistic insights. Since understanding the mutational spectrum of cancer cells indicates the outcome of the disease as well as treatment response, we examined mutational spectrum of TRAP1. Our in silico analyses of TRAP1 SNPs and CNVs correlated with the aggressive cancer phenotypes, and are found to be predominant over Hsp90 itself. The increased CNVs have been correlated with increased expression of TRAP1 in metastatic cancer cells, increased ATP production, and decreased oxygen consumption rate of mitochondria. Examining TRAP1 knockdown as well as over expression in metastatic cancer cells furthered our understanding that TRAP1 likely to facilitate the altered energy metabolism in the functional compromise of mitochondrial OXPHOS. Interestingly, the increased ATP levels in the TRAP1 background are found to be independent of glucose oxidation. Our results suggest TRAP1 role in triggering the alternate energy metabolism in cancer cells. Since targeting tumor metabolism is considered as an alternate strategy to combat cancer, we propose pharmacological targeting of TRAP1 to target alternate energy metabolism.
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Affiliation(s)
- Balaji Ramkumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India
| | - Shrikant P Dharaskar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India; Academy of Scientific & Innovation Research, Government of India, India
| | - Guntipally Mounika
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India
| | - Khanderao Paithankar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India
| | - Amere Subbarao Sreedhar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, Telangana, India.
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24
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A Shallow Convolutional Learning Network for Classification of Cancers Based on Copy Number Variations. SENSORS 2019; 19:s19194207. [PMID: 31569801 PMCID: PMC6806227 DOI: 10.3390/s19194207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/29/2022]
Abstract
Genomic copy number variations (CNVs) are among the most important structural variations. They are linked to several diseases and cancer types. Cancer is a leading cause of death worldwide. Several studies were conducted to investigate the causes of cancer and its association with genomic changes to enhance its management and improve the treatment opportunities. Classification of cancer types based on the CNVs falls in this category of research. We reviewed the recent, most successful methods that used machine learning algorithms to solve this problem and obtained a dataset that was tested by some of these methods for evaluation and comparison purposes. We propose three deep learning techniques to classify cancer types based on CNVs: a six-layer convolutional net (CNN6), residual six-layer convolutional net (ResCNN6), and transfer learning of pretrained VGG16 net. The results of the experiments performed on the data of six cancer types demonstrated a high accuracy of 86% for ResCNN6 followed by 85% for CNN6 and 77% for VGG16. The results revealed a lower prediction accuracy for one of the classes (uterine corpus endometrial carcinoma (UCEC)). Repeating the experiments after excluding this class reveals improvements in the accuracies: 91% for CNN6 and 92% for Res CNN6. We observed that UCEC and ovarian serous carcinoma (OV) share a considerable subset of their features, which causes a struggle for learning in the classifiers. We repeated the experiment again by balancing the six classes through oversampling of the training dataset and the result was an enhancement in both overall and UCEC classification accuracies.
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25
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Lin CZ, Qi BR, Hu JS, Huang YD, Huang XQ. Chromosome 15q13 microduplication in a fetus with cardiac rhabdomyoma: a case report. Mol Cytogenet 2019; 12:24. [PMID: 31149030 PMCID: PMC6537215 DOI: 10.1186/s13039-019-0437-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 05/17/2019] [Indexed: 01/10/2023] Open
Abstract
Background Copy number variation (CNV) is a complex genomic rearrangement that has been linked to a large number of human diseases. Chromosome 15q13 microduplication is a rare form of CNV, which has been proved to be associated with multiple human disorders; however, the association between chromosome 15q13 microduplication and cardiac disorders has not been fully understood. Case presentation A fetus with fetal cardiac developmental defects was detected by Color Doppler ultrasound imaging; however, further chromosomal G-banding revealed no abnormal karyotype. Then, chromosomal microarray analysis (CMA) was performed and revealed a 1.8 Mb-duplication of the chromosome 15q13.2q13.3 region containing 7 genes (TRPM1, KLF13, OTUD7A, CHRNA7, FAN1, MIR211 and RAHGAP11A). Cardiac ultrasound follow-up displayed significant enlargement of the space-occupying lesion in the fetal heart with extension of the gestational age, and the space-occupying lesion was finally pathologically diagnosed as cardiac rhabdomyoma. Next-generation sequencing revealed no mutations in the TSC1 or TSC2 gene in the fetus, the mother or the father. Conclusions This is the first report to demonstrate the potential association between chromosome 15q13 microduplication and fetal cardiac rhabdomyoma. It is recommended that CMA be employed in fetuses with abnormal cardiac development diagnosed by routine cardiac color Doppler ultrasound imaging for early detection of congenital genetic abnormality, which may provide valuable information for prenatal diagnostic consultation and the decision on pregnancy termination.
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Affiliation(s)
- Chen-Zhao Lin
- 1Department of Obstetrics and Gynecology, Affiliated Fuzhou First Hospital of Fujian Medical University, No. 190 Dadao Road, Taijiang District, Fuzhou, Fujian Province 350009 People's Republic of China
| | - Bi-Ru Qi
- 1Department of Obstetrics and Gynecology, Affiliated Fuzhou First Hospital of Fujian Medical University, No. 190 Dadao Road, Taijiang District, Fuzhou, Fujian Province 350009 People's Republic of China
| | - Jian-Su Hu
- 2Department of Ultrasound, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, 350009 Fujian Province People's Republic of China
| | - Yu-Dian Huang
- 3Department of Pathology, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, 350009 Fujian Province People's Republic of China
| | - Xiu-Qiong Huang
- 4Department of Laboratory Medicine, Affiliated Fuzhou First Hospital of Fujian Medical University, Fuzhou, 350009 Fujian Province People's Republic of China
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26
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Liu J, Liu Z, Liu Q, Li L, Fan X, Wen T, An G. CLEC3B is downregulated and inhibits proliferation in clear cell renal cell carcinoma. Oncol Rep 2018; 40:2023-2035. [PMID: 30066941 PMCID: PMC6111577 DOI: 10.3892/or.2018.6590] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/19/2018] [Indexed: 12/15/2022] Open
Abstract
Dysregulation of C-Type Lectin Domain Family 3 Member B (CLEC3B) in serum or tumor tissues has been reported in patients with various cancer types. However, the expression and function of CLEC3B in clear cell renal cell carcinoma (ccRCC) remain unknown. To examine the function of CLEC3B in ccRCC, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were examined to determine the expression of CLEC3B at the transcriptional level and it was demonstrated that CLEC3B mRNA was significantly downregulated in ccRCC compared with normal tissues (P<0.0001 and P=0.0392 in TCGA and GEO databases, respectively). The downregulation of CLEC3B was further validated at the protein level in 78.9% of ccRCCs by immunohistochemistry. To investigate the potential genetic mechanism for CLEC3B downregulation in ccRCC, copy number analysis was performed by profiling the copy number variation data from the TCGA project and it was revealed that the copy number loss of CLEC3B was prevalent in up to 88.1% of patients with ccRCC. CLEC3B genetic deletion was coupled with the well-known genetic loss of the von Hippel-Lindau tumor suppressor, which is a characteristic oncogenic event during ccRCC carcinogenesis. The downregulation of CLEC3B was associated with tumor progression and predicted unfavorable prognostic outcomes in the TCGA cohort. Real-time cell analyzer system technology revealed that CLEC3B inhibited the proliferation of ccRCC cell lines in vitro and that the mitogen-activated protein kinase pathway may contribute to this process. CLEC3B demonstrated substantial positive associations with proliferation inhibitors, but inverse associations with proliferation inducers and markers in two large ccRCC cohorts, suggesting that CLEC3B was able to identify ccRCCs with a lower proliferation capacity. In conclusion, the results of the present study propose that CLEC3B is a promising target for therapeutic intervention in ccRCC.
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Affiliation(s)
- Jian Liu
- Medical Research Center, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Zhe Liu
- Department of Oncology, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Qun Liu
- Department of Obstetrics and Gynecology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, P.R. China
| | - Lina Li
- Medical Research Center, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xiaona Fan
- Medical Research Center, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Tao Wen
- Medical Research Center, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Guangyu An
- Department of Oncology, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
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