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Cai H, Li X, Niu X, Li J, Lan X, Lei C, Huang Y, Xu H, Li M, Chen H. Copy number variations within fibroblast growth factor 13 gene influence growth traits and alternative splicing in cattle. Anim Biotechnol 2024; 35:2314104. [PMID: 38426908 DOI: 10.1080/10495398.2024.2314104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (FGF13) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (P < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (P < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in FGF13 gene, which resulted from alternative 5' splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (r = -0.525, P < 0.05). The CNVs in bovine FGF13 gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine FGF13 gene, delivering potentially useful information for future Chinese cattle breeding programs.
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Affiliation(s)
- Hanfang Cai
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xinran Niu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Jing Li
- Animal Health Supervision Institute of Biyang, Biyang, Henan, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agriculture University, Urumqi, China
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Andrawus M, David GB, Terziyska I, Sharvit L, Bergman A, Barzilai N, Raj SM, Govindaraju DR, Atzmon G. Genome integrity as a potential index of longevity in Ashkenazi Centenarian's families. GeroScience 2024; 46:4147-4162. [PMID: 38724875 PMCID: PMC11335978 DOI: 10.1007/s11357-024-01178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/24/2024] [Indexed: 06/19/2024] Open
Abstract
The aging process, or senescence, is characterized by age-specific decline in physical and physiological function, and increased frailty and genomic changes, including mutation accumulation. However, the mechanisms through which changes in genomic architecture influence human longevity have remained obscure. Copy number variants (CNVs), an abundant class of genomic variants, offer unique opportunities for understanding age-related genomic changes. Here we report the spectrum of CNVs in a cohort of 670 Ashkenazi Jewish centenarians, their progeny, and unrelated controls. The average ages of these groups were 97.4 ± 2.8, 69.2 ± 9.2, and 66.5 ± 7.0 respectively. For the first time, we compared different size classes of CNVs, from 1 kB to 100 MB in size. Using a high-resolution custom Affymetrix array, targeting 44,639 genomic regions, we identified a total of 12,166, 22,188, and 10,285 CNVs in centenarians, their progeny, and control groups, respectively. Interestingly, the offspring group showed the highest number of unique CNVs, followed by control and centenarians. While both gains and losses were found in all three groups, centenarians showed a significantly higher average number of both total gains and losses relative to their controls (p < 0.0327, 0.0182, respectively). Moreover, centenarians showed a lower total length of genomic material lost, suggesting that they may maintain superior genomic integrity over time. We also observe a significance fold increase of CNVs among the offspring, implying greater genomic integrity and a putative mechanism for longevity preservation. Genomic regions that experienced loss or gains appear to be distributed across many sites in the genome and contain genes involved in DNA transcription, cellular transport, developmental pathways, and metabolic functions. Our findings suggest that the exceptional longevity observed in centenarians may be attributed to the prolonged maintenance of functionally important genes. These genes are intrinsic to specific genomic regions as well as to the overall integrity of the genomic architecture. Additionally, a strong association between longer CNVs and differential gene expression observed in this study supports the notion that genomic integrity could positively influence longevity.
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Affiliation(s)
| | - Gil Ben David
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., 3498838, Mount Carmel, Haifa, Israel
| | | | - Lital Sharvit
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Srilakshmi M Raj
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | | | - Gil Atzmon
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel.
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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Ma Y, Shao G, Xie Y, Yang D, Li K, Tan B, Wang C, Sun P, Cao J. Multiomics Analysis of Interleukin-21 as a Potential Immunologic and Biomarker in Hepatocellular Carcinoma. J Immunother 2024; 47:266-274. [PMID: 38832536 DOI: 10.1097/cji.0000000000000526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 04/18/2024] [Indexed: 06/05/2024]
Abstract
Interleukin-21 (IL-21) is an important antitumor cytokine that contributes to the proliferation and differentiation of CD8 + T cells. It has been proven to enhance the response to immune checkpoint inhibitors (ICIs) in various solid tumors. However, its role in hepatocellular carcinoma (HCC) has not yet been clarified. In this research, we aimed to investigate the antitumor effect of IL-21 in HCC and its effect on ICI treatment. Through transcriptome sequencing analysis and immunohistochemistry validation, we found that patients with high IL-21 expression had a better prognosis. HCCs with high expression of IL-21 had higher infiltration of CD8 + T cells, increased expression of immune checkpoints, and an improved response to ICI treatment. In conclusion, IL-21 can enhance the efficacy of ICI treatment and improve the prognosis of patients by promoting the infiltration of CD8 + T cells and the expression of immune checkpoint-related genes.
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Affiliation(s)
- Yonghui Ma
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Zhang Y, Li X, Guo Q, Wang Z, Jiang Y, Yuan X, Chen G, Chang G, Bai H. Genome-wide association study reveals 2 copy number variations associated with the variation of plumage color in the white duck hybrid population. Poult Sci 2024; 103:104107. [PMID: 39094499 PMCID: PMC11342262 DOI: 10.1016/j.psj.2024.104107] [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: 05/17/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
Plumage color is an intuitive external poultry characteristic with rich manifestations and complex genetic mechanisms. In our previous study, we observed that there were more dark variations in plumage color in the F2 population derived from the hybridization of 2 white duck varieties. Therefore, based on the statistics of plumage color of 308 F2 populations, we further used the resequencing data of these individuals to detect copy number variations (CNVs) in the whole genome and conducted genome-wide association studies (GWAS) to determine the genetic basis related to plumage color traits. The CNV detection revealed 9,337 CNVs, with an average length of 15,950 bp and a total length of 142.02 MB, accounting for approximately 12.91% of the reference genome. The CNV distribution on the chromosomes was relatively uniform, and the number of CNVs on each chromosome positively correlated with the length of the chromosome. In the pure black plumage group, 2,101 CNVs were only identified, and 1,714 were specifically identified in the pure white plumage group. Ten CNVs were randomly selected for validation using quantitative real-time PCR, and 9 CNVs had the same CNV types as predicted, with an accuracy of 90%. Based on GWAS, we identified 2 CNVs potentially associated with plumage color variations, with the associated CNV regions covering 9 genes. Enrichment analysis of these 9 candidate genes showed significant enrichment of 3 pathways (ribosome biogenesis in eukaryotes, RNA transport, and protein export) and 17 gene ontology terms. Among these, VWA5A can downregulate MITF by binding to the regulatory factors SOX10. The occurrence of CNV may indirectly contribute to duck plumage color variation by affecting the regulatory factors of the switch gene MITF in the melanogenesis pathway. These findings have improved the understanding of the genetic basis of duck plumage color variation and have been beneficial for developing and using plumage color traits in subsequent poultry breeding.
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Affiliation(s)
- Yi Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaofan Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qixin Guo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoya Yuan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
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Oliveira FG, Rosa-e-Silva JC, Gomes AG, Grzesiuk JD, Vidotto T, Squire JA, Panepucci RA, Meola J, Martelli L. Identification of a rare copy number polymorphic gain at 3q12.2 with candidate genes for familial endometriosis. REVISTA BRASILEIRA DE GINECOLOGIA E OBSTETRÍCIA 2024; 46:e-rbgo12. [PMID: 38765507 PMCID: PMC11075382 DOI: 10.61622/rbgo/2024cr12] [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: 09/23/2023] [Accepted: 10/10/2023] [Indexed: 05/22/2024] Open
Abstract
Endometriosis is a complex disease that affects 10-15% of women of reproductive age. Familial studies show that relatives of affected patients have a higher risk of developing the disease, implicating a genetic role for this disorder. Little is known about the impact of germline genomic copy number variant (CNV) polymorphisms on the heredity of the disease. In this study, we describe a rare CNV identified in two sisters with familial endometriosis, which contain genes that may increase the susceptibility and progression of this disease. We investigated the presence of CNVs from the endometrium and blood of the sisters with endometriosis and normal endometrium of five women as controls without the disease using array-CGH through the Agilent 2x400K platform. We excluded common CNVs that were present in the database of genomic variation. We identified, in both sisters, a rare CNV gain affecting 113kb at band 3q12.2 involving two candidate genes: ADGRG7 and TFG. The CNV gain was validated by qPCR. ADGRG7 is located at 3q12.2 and encodes a G protein-coupled receptor influencing the NF-kappaβ pathway. TFG participates in chromosomal translocations associated with hematologic tumor and soft tissue sarcomas, and is also involved in the NF-kappa B pathway. The CNV gain in this family provides a new candidate genetic marker for future familial endometriosis studies. Additional longitudinal studies of affected families must confirm any associations between this rare CNV gain and genes involved in the NF-kappaβ pathway in predisposition to endometriosis.
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Affiliation(s)
- Flávia Gaona Oliveira
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Júlio Cesar Rosa-e-Silva
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of Gynecology and ObstetricsRibeirão PretoSPBrazilDepartment of Gynecology and Obstetrics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Alexandra Galvão Gomes
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Juliana Dourado Grzesiuk
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Thiago Vidotto
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Jeremy Andrew Squire
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Rodrigo Alexandre Panepucci
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
- Universidade de São PauloBlood CenterCenter for Cell TherapyRibeirão PretoSPBrazilCenter for Cell Therapy, Blood Center, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Juliana Meola
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of Gynecology and ObstetricsRibeirão PretoSPBrazilDepartment of Gynecology and Obstetrics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Lúcia Martelli
- Universidade de São PauloRibeirão Preto Medical SchoolDepartment of GeneticsRibeirão PretoSPBrazilDepartment of Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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Xian W, Asad M, Wu S, Bai Z, Li F, Lu J, Zu G, Brintnell E, Chen H, Mao Y, Zhou G, Liao B, Wu J, Wang E, You L. Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq analysis. Front Med 2024; 18:147-168. [PMID: 37955814 DOI: 10.1007/s11684-023-1017-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/24/2023] [Indexed: 11/14/2023]
Abstract
The association of neurogenesis and gliogenesis with glioma remains unclear. By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitive oligodendrocyte precursor cell (pri-OPC)-like and radial glia (RG)-like tumors and validated it in a public cohort and TCGA glioma. The RG-like tumors exhibited wild-type isocitrate dehydrogenase and tended to carry EGFR mutations, and the pri-OPC-like ones were prone to carrying TP53 mutations. Tumor subclones only in pri-OPC-like tumors showed substantially down-regulated MHC-I genes, suggesting their distinct immune evasion programs. Furthermore, the two subgroups appeared to extensively modulate glioma-infiltrating lymphocytes in distinct manners. Some specific genes not expressed in normal immune cells were found in glioma-infiltrating lymphocytes. For example, glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors IGLC2/IGKC were expressed in pri-OPC-like and RG-like glioma-infiltrating lymphocytes, respectively. Their expression was positively correlated with those of immune checkpoint genes (e.g., LGALS33) and poor survivals as validated by the increased expression of LGALS3 upon IGKC overexpression in Jurkat cells. This finding indicated a potential inhibitory role in tumor-infiltrating lymphocytes and could provide a new way of cancer immune evasion.
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Affiliation(s)
- Weiwei Xian
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Mohammad Asad
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Shuai Wu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zhixin Bai
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Fengjiao Li
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Junfeng Lu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Gaoyu Zu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Erin Brintnell
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Guomin Zhou
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai, 200040, China
| | - Bo Liao
- School of Mathematics and Statistics, Hainan Normal University, Haikou, 570100, China
| | - Jinsong Wu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai, 200040, China.
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Lee S, Kim J, Ohn JH. Exploring quantitative traits-associated copy number deletions through reanalysis of UK10K consortium whole genome sequencing cohorts. BMC Genomics 2023; 24:787. [PMID: 38110883 PMCID: PMC10729411 DOI: 10.1186/s12864-023-09903-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023] Open
Abstract
OBJECTIVES We performed comprehensive association analyses of common high-confidence gnomAD-reported copy number deletions (CNDs) with 60 quantitative traits from UK10K consortium WGS data. METHODS The study made use of data generated by the UK10K Consortium. UK10K consortium WGS data consist of TwinsUK (n = 1754, middle-aged females) and ALSPAC (n = 1867, birth to adolescence) cohorts. UK10K consortium called 18,739 CNDs (hg19) with GenomeSTRiP software. After filtering out variants with minor allele frequency < 0.05 or HWE P < 1.0 × 10- 6, 1222 (TwinsUK) and 1211 (ALSPAC) CNDs remained for association analyses with 60 normalized quantitative traits. RESULTS We identified 23 genome-wide significant associations at 13 loci, among which 2 associations reached experiment-wide significance. We found that two common deletions in chromosome 4, located between WDR1 and ZNF518B (23.3 kb, dbVar ID:nssv15888957, 4:10211262-10,234,569 and 9.8 kb, dbVar ID:nssv15888975, 4:10392422-10,402,191), were associated with uric acid levels (P = 5.23 × 10- 11 and 2.29 × 10- 8, respectively). We also discovered a novel deletion spanning chromosome 18 (823 bp, dbVar ID: nssv15841628, 8:74347187-74,348,010) associated with low HDL cholesterol levels (P = 4.15 × 10- 7). Additionally, we observed two red blood cell traits-associated loci with genome-wide significance, a 13.2 kb deletion in 7q22.1 (nssv15922542) and a 3.7 kb deletion in 12q24.12 (nssv15813226), both of which were located in regions previously reported to be associated with red blood cell traits. Two deletions in 11q11 (nssv15803200 and nssv15802240), where clusters of multiple olfactory receptor genes exist, and a deletion (nssv15929560) upstream to DOCK5 were associated with childhood obesity. Finally, when defining Trait-Associated copy number Deletions (TADs) as CNDs with phenotype associations at sub-threshold significance (P < 10- 3), we identified 157 (97.5%) out of 161 TADs in non-coding regions, with a mean size of 4 kb (range: 209 - 47,942 bp). CONCLUSION We conducted a reanalysis of the UK10K Whole Genome Sequencing cohort, which led to the identification of multiple high confidence copy number deletions associated with quantitative traits. These deletions have standard dbVar IDs and replicate previous findings, as well as reveal novel loci that require further replication studies.
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Affiliation(s)
- Sejoon Lee
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, 173-82, Gumi-ro, Bundang-gu, Seongnam, Gyeonggi-do, 13620, South Korea
- Department of Pathology, Seoul National University Bundang Hospital, 173-82, Gumi-ro, Bundang-gu, Seongnam, Gyeonggi-do, 13620, South Korea
| | - Jinho Kim
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, 173-82, Gumi-ro, Bundang-gu, Seongnam, Gyeonggi-do, 13620, South Korea
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, 173-82, Gumi-ro, Bundang-gu, Seongnam, Gyeonggi-do, 13620, South Korea
| | - Jung Hun Ohn
- Precision Medicine Center, Future Innovation Research Division, Seoul National University Bundang Hospital, 173-82, Gumi-ro, Bundang-gu, Seongnam, Gyeonggi-do, 13620, South Korea.
- Department of Internal Medicine, Seoul National University Bundang Hospital, 173-82, Gumi-ro, Bundang-gu, Seongnam, Gyeonggi-do, 13620, South Korea.
- Department of Internal Medicine, College of Medicine, Seoul National University, 103, Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
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Kong Y, Liu Y, Li X, Rao M, Li D, Ruan X, Li S, Jiang Z, Zhang Q. Palmitoylation landscapes across human cancers reveal a role of palmitoylation in tumorigenesis. J Transl Med 2023; 21:826. [PMID: 37978524 PMCID: PMC10655258 DOI: 10.1186/s12967-023-04611-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Protein palmitoylation, which is catalyzed by palmitoyl-transferase and de-palmitoyl-transferase, plays a crucial role in various biological processes. However, the landscape and dynamics of protein palmitoylation in human cancers are not well understood. METHODS We utilized 23 palmitoyl-acyltransferases and seven de-palmitoyl-acyltransferases as palmitoylation-related genes for protein palmitoylation analysis. Multiple publicly available datasets were employed to conduct pan-cancer analysis, examining the transcriptome, genomic alterations, clinical outcomes, and correlation with c-Myc (Myc) for palmitoylation-related genes. Real-time quantitative PCR and immunoblotting were performed to assess the expression of palmitoylation-related genes and global protein palmitoylation levels in cancer cells treated with Myc depletion or small molecule inhibitors. Protein docking and drug sensitivity analyses were employed to predict small molecules that target palmitoylation-related genes. RESULTS We identified associations between palmitoylation and cancer subtype, stage, and patient survival. We discovered that abnormal DNA methylation and oncogenic Myc-driven transcriptional regulation synergistically contribute to the dysregulation of palmitoylation-related genes. This dysregulation of palmitoylation was closely correlated with immune infiltration in the tumor microenvironment and the response to immunotherapy. Importantly, dysregulated palmitoylation was found to modulate canonical cancer-related pathways, thus influencing tumorigenesis. To support our findings, we performed a proof-of-concept experiment showing that depletion of Myc led to reduced expression of most palmitoylation-related genes, resulting in decreased global protein palmitoylation levels. Through mass spectrometry and enrichment analyses, we also identified palmitoyl-acyltransferases ZDHHC7 and ZDHHC23 as significant contributors to mTOR signaling, DNA repair, and immune pathways, highlighting their potential roles in tumorigenesis. Additionally, our study explored the potential of three small molecular (BI-2531, etoposide, and piperlongumine) to modulate palmitoylation by targeting the expression or activity of palmitoylation-related genes or enzymes. CONCLUSIONS Overall, our findings underscore the critical role of dysregulated palmitoylation in tumorigenesis and the response to immunotherapy, mediated through classical cancer-related pathways and immune cell infiltration. Additionally, we propose that the aforementioned three small molecule hold promise as potential therapeutics for modulating palmitoylation, thereby offering novel avenues for cancer therapy.
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Affiliation(s)
- Yue Kong
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China
| | - Yugeng Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xianzhe Li
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Menglan Rao
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Dawei Li
- Zhumadian Central Hospital, Huanghuai University, Zhumadian, 463000, China
| | - Xiaolan Ruan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, 510632, China
| | - Shanglin Li
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China
| | - Zhenyou Jiang
- Department of Microbiology and Immunology, Basic Medicine College, Jinan University, No.601, West Huangpu Avenue, Guangzhou, 510632, Guangdong, China.
- Key Laboratory of Ministry of Education for Viral Pathogenesis and Infection Prevention and Control, Jinan University, Guangzhou, 510632, China.
| | - Qiang Zhang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, China.
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9
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Arias KD, Gutiérrez JP, Fernández I, Álvarez I, Goyache F. Copy Number Variation Regions Differing in Segregation Patterns Span Different Sets of Genes. Animals (Basel) 2023; 13:2351. [PMID: 37508128 PMCID: PMC10376189 DOI: 10.3390/ani13142351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Copy number variations regions (CNVRs) can be classified either as segregating, when found in both parents, and offspring, or non-segregating. A total of 65 segregating and 31 non-segregating CNVRs identified in at least 10 individuals within a dense pedigree of the Gochu Asturcelta pig breed was subjected to enrichment and functional annotation analyses to ascertain their functional independence and importance. Enrichment analyses allowed us to annotate 1018 and 351 candidate genes within the bounds of the segregating and non-segregating CNVRs, respectively. The information retrieved suggested that the candidate genes spanned by segregating and non-segregating CNVRs were functionally independent. Functional annotation analyses allowed us to identify nine different significantly enriched functional annotation clusters (ACs) in segregating CNVR candidate genes mainly involved in immunity and regulation of the cell cycle. Up to five significantly enriched ACs, mainly involved in reproduction and meat quality, were identified in non-segregating CNVRs. The current analysis fits with previous reports suggesting that segregating CNVRs would explain performance at the population level, whereas non-segregating CNVRs could explain between-individuals differences in performance.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, 33394 Gijón, Spain
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10
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Ye B, Tang X, Liao S, Ding K. A comparison of algorithms for identifying copy number variants in family-based whole-exome sequencing data and its implications in inheritance pattern analysis. Gene 2023; 861:147237. [PMID: 36731620 DOI: 10.1016/j.gene.2023.147237] [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: 08/17/2022] [Revised: 12/27/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
There remain challenges in accurately identifying constitutional or germline copy number variants (gCNVs) based on whole-exome sequencing data that have implications for genetic diagnosis for 'rare undiagnosed disease' in the clinical setting. Although multiple algorithms have been proposed, a systematic comparison of these algorithms for calling gCNVs and analyzing inherited pattern have yet to be fully conducted. Therefore, we empirically compared seven exome-based algorithms, including XHMM, CLAMMS, CODEX2, ExomeDepth, DECoN, CN.MOPS, and GATK gCNV, for calling gCNVs in 151 individuals from 44 pedigrees, together with the gold standard of genotyping-derived gCNVs in the same cohort for the performance assessment. These algorithms demonstrated varied powers in identifying gCNVs, although the distribution of gCNVs size was similar. The number of shared gCNVs across these algorithms was limited (e.g., only four gCNVs shared among seven algorithms); however, several algorithms showed varying degrees of consistency (e.g., 1,843 gCNVs shared between DECoN and ExomeDepth). CLAMMS and CODEX2 outperformed the remaining algorithms according to a relatively higher F-score (i.e., 0.145 and 0.152, respectively). In addition, these algorithms exhibited different Mendelian inconsistencies of gCNVs and significant challenges remained in inheritance pattern analysis. In conclusion, selecting good algorithms may have important implications in gCNVs-based inheritance pattern analysis for family-based studies.
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Affiliation(s)
- Bo Ye
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xia Tang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, PR China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, Henan Province 450003, PR China.
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, Henan Province 450003, PR China; Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55905, United States.
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11
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Sun T, Pei S, Liu Y, Hanif Q, Xu H, Chen N, Lei C, Yue X. Whole genome sequencing of simmental cattle for SNP and CNV discovery. BMC Genomics 2023; 24:179. [PMID: 37020271 PMCID: PMC10077681 DOI: 10.1186/s12864-023-09248-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUD The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity. RESULTS In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility. CONCLUSIONS In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.
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Affiliation(s)
- Ting Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Shengwei Pei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Yangkai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
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12
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Shen S, Chen J, Li H, Jiang Y, Wei Y, Zhang R, Zhao Y, Chen F. Large-scale integration of the non-coding RNAs with DNA methylation in human cancers. Cell Rep 2023; 42:112261. [PMID: 36924495 DOI: 10.1016/j.celrep.2023.112261] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Characterizing influences of DNA methylation (DNAm) on non-coding RNAs (ncRNAs) is important to understand the mechanisms of gene regulation and cancer outcome. In our study, we describe the results of ncRNA quantitative trait methylation sites (ncQTM) analyses on 8,545 samples from The Cancer Genome Atlas (TCGA), 763 samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC), and 516 samples from Genotype-Tissue Expression (GTEx) to identify the significant associations between DNAm sites and ncRNAs (miRNA, long non-coding RNA [lncRNA], small nuclear RNA [snRNA], small nucleolar RNA [snoRNA], and rRNA) across 32 cancer types. With more than 22 billion tests, we identify 302,764 cis-ncQTMs (6.28% of all tested) and 79,841,728 trans-ncQTMs (1.15% of all tested). Most DNAm sites (70.6% on average) are in trans association, while only 25.2% DNAm sites are in cis association. Further, we develop a subtype named ncmcluster based on cancer-specific ncRNAs thatis associated with tumor microenvironment, clinical outcome, and biological pathways. To comprehensively describe the ncQTM patterns, we developed a database named Pancan-ncQTM (http://bigdata.njmu.edu.cn/Pancan-ncQTM/).
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Affiliation(s)
- Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
| | - Jiajin Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongru Li
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yunke Jiang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yongyue Wei
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Key Laboratory of Biomedical Big Data of Nanjing Medical University, Nanjing 211166, China.
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
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13
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Kim HS, Park H, Wang H, Kim T, Ki JS. Saxitoxins-producing potential of the marine dinoflagellate Alexandrium affine and its environmental implications revealed by toxins and transcriptome profiling. MARINE ENVIRONMENTAL RESEARCH 2023; 185:105874. [PMID: 36689843 DOI: 10.1016/j.marenvres.2023.105874] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/08/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The marine dinoflagellate Alexandrium occurs widely in coastal waters, and some of them can produce saxitoxins (STXs) that cause paralytic shellfish poisoning (PSP). Alexandrium affine is a harmful algal bloom (HAB)-forming species off the coast of Asia; however, its ability to produce STXs has been controversial. In the present study, we detected STXs in A. affine Alex02 isolated from the southern coast of Korea. The total STXs equivalent (STXs eq) and profiles of Alex02 varied depending on the tested environmental conditions, including the temperature and nitrate concentrations. STXs toxicity levels of A. affine Alex02 (<0.8 STXs eq fmol cell-1) were significantly lower than those of toxic A. catenella Alex03 and A. pacificum Alex05. On a genetic basis, we identified all the STX biosynthesis sxt genes, except sxtX in A. affine, via large-scale transcriptome analysis. Interestingly, the two proteins, sxtA4 and sxtG, were similar in sequence and domain structure to those of other toxic dinoflagellates and cyanobacteria; however, their transcript levels were extremely low. Our results suggest that A. affine has the potential to produce STXs, while its toxicity is much lower or negligible, which is unlikely to cause PSP incidents in marine environments.
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Affiliation(s)
- Han-Sol Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Hyunjun Park
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Hui Wang
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Taehee Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea.
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14
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Wang ZJ, Dai ZZ, Hu MZ, Liu JN, Liang H, Shen MM, Zhu SJ, Sheng HJ, Gao J, Huang AL, Tang KF. Upregulation of TUBG1 expression promotes hepatocellular carcinoma development. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2023; 40:96. [PMID: 36792863 DOI: 10.1007/s12032-023-01966-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
Tubulin γ-1 (TUBG1) is a highly conserved component of the centrosome and its deregulation is involved in the development of several types of cancer. However, the role of TUBG1 in hepatocellular carcinoma (HCC) remains unclear. In this study, we found that TUBG1 was upregulated in human HCC cells and tissues and that TUBG1 upregulation was associated with promoter hypomethylation in HCC tissues. TUBG1 knockdown suppressed the proliferation, invasion, and migration of HCC cells. While TUBG1 expression was positively correlated with CD4 + memory T lymphocyte infiltration, it was negatively correlated with CD4 + regulatory T-cell infiltration in human HCC tissues. Furthermore, TUBG1 expression was positively correlated with the expression of genes involved in cell division. Noticeably, high expression of TUBG1 was associated with poor prognosis in patients with HCC. Overall, our findings revealed that TUBG1 promotes hepatocarcinogenesis by increasing proliferation, invasion, and migration of HCC cells and may regulate T lymphocyte infiltration. The current findings provide important insights into TUBG1 regulation in HCC, which could provide new therapeutic targets for hepatocarcinoma which has a very high incidence and mortality rate worldwide.
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Affiliation(s)
- Zi-Jian Wang
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China.,The First Clinical College, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Zhi-Zheng Dai
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Mei-Zhen Hu
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jun-Nan Liu
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hang Liang
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Mei-Mei Shen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Shu-Juan Zhu
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hua-Jun Sheng
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Jian Gao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Kai-Fu Tang
- Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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15
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Peripolli E, Stafuzza NB, Machado MA, do Carmo Panetto JC, do Egito AA, Baldi F, da Silva MVGB. Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re-sequencing data. Anim Genet 2023; 54:254-270. [PMID: 36740987 DOI: 10.1111/age.13298] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/13/2021] [Accepted: 01/13/2023] [Indexed: 02/07/2023]
Abstract
Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective pressures and phenotype variation. A comprehensive genome-wide assessment of copy number variations (CNVs) based on whole-genome re-sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS-UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75-2.07-fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA-DQB, BOLA-DQA5, CD1A, β-defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over-represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy-related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.
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Affiliation(s)
- Elisa Peripolli
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | | | | | | | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
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16
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Chang HC, Lee YJ, Javed S, Haque M, Chang YT, Lin YC, Oram C, Huang WH. rAAV-CRISPRa therapy corrects Rai1 haploinsufficiency and rescues selective disease features in Smith-Magenis syndrome mice. J Biol Chem 2022; 299:102728. [PMID: 36410433 PMCID: PMC9762195 DOI: 10.1016/j.jbc.2022.102728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/20/2022] Open
Abstract
Haploinsufficiency in retinoic acid induced 1 (RAI1) causes Smith-Magenis syndrome (SMS), a severe neurodevelopmental disorder characterized by neurocognitive deficits and obesity. Currently, curative treatments for SMS do not exist. Here, we take a recombinant adeno-associated virus (rAAV)-clustered regularly interspaced short palindromic repeats activation (CRISPRa) approach to increase expression of the remaining intact Rai1 allele. Building upon our previous work that found the paraventricular nucleus of hypothalamus plays a central role in SMS pathogenesis, we performed paraventricular nucleus of hypothalamus-specific rAAV-CRISPRa therapy by increasing endogenous Rai1 expression in SMS (Rai1±) mice. We found that rAAV-CRISPRa therapy rescues excessive repetitive behavior, delays the onset of obesity, and partially reduces hyperphagia in SMS mice. Our work provides evidence that rAAV-CRISPRa therapy during early adolescence can boost the expression of healthy Rai1 allele and modify disease progression in a mouse model of Smith-Magenis syndrome.
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Affiliation(s)
- Hao-Cheng Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu-Ju Lee
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Sehrish Javed
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Minza Haque
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Ya-Ting Chang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yu Cheng Lin
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Cameron Oram
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Wei-Hsiang Huang
- Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, McGill University, Québec, Canada,Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montréal, Québec, Canada,For correspondence: Wei-Hsiang Huang
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17
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Li X, Dong H, Chen L, Wang Y, Hao Z, Zhang Y, Jiao Y, Zhao Z, Peng X, Zhan X. Identification of N7-methylguanosine related subtypes and construction of prognostic model in gastric cancer. Front Immunol 2022; 13:984149. [PMID: 36300121 PMCID: PMC9589367 DOI: 10.3389/fimmu.2022.984149] [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: 07/01/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022] Open
Abstract
Background N7-methylguanosine (m7G), one of the most common post-transcriptional modifications, can be present in tRNA, mRNA, and miRNA to mediate the progression of various tumors. However, the possible role of m7G in gastric cancer (GC) is still unknown. Materials and Methods In this study, SNVs (single nucleotide variations), CNVs (copy number variations), and methylation of m7G-related genes (m7GRGs) were analyzed. The relationship between them and the expression of m7GRGs and prognosis of GC patients was explored. Based on 13 prognostic-related m7GRGs, 567 GC samples were classified into three subtypes using the ConsensusClusterPlus package. we compared survival status, clinical traits, immune cell infiltration, immune checkpoints, tumor microenvironment (TME), tumor immune dysfunction and exclusion (TIDE), and potential biological pathways among the three subtypes. Then, patients were again grouped into different genetic subtypes based on the DEGs among the three subtypes. In addition, a prognostic m7GRG_Score was constructed using five risk genes applicable to patients of any age, gender and stage. We also assessed tumor mutational burden (TMB), microsatellite instability (MSI), cancer stem cell (CSC) index, sensitivity of antineoplastic drugs, efficacy of anti-PD-1 and anti-CTLA4 immunotherapy between high and low m7GRG_Score groups. Finally, we established a nomogram based on m7GRG_Score and tumor stage to enhance the clinical application of the model. miRNAs and lncRNAs that could regulate expression of risk genes were searched. Results SNVs, CNVs, and methylation of m7GRGs were associated with m7GRGs expression. However, they did not significantly affect the survival of GC patients. Our results also confirmed that patients in subtypes B and C and low m7GRG_Score groups had longer survival time, better clinical stage, more immune cell infiltration, fewer immune escape and dysfunction compared to subtype A and high m7GRG_Score groups. A low m7GRG_score was featured with increased microsatellite instability-high (MSI-H), TMB, and efficacy of immunotherapy. Conclusion The m7GRG_Score model may become a beneficial tool for predicting prognosis and guiding personalized treatment in GC patients. These findings will improve our knowledge of m7G in GC and provide new methods for more effective treatment strategies.
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Affiliation(s)
- Xiaoxiao Li
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Hao Dong
- Department of Gastrointestinal Nutrition and Hernia Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Ling Chen
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yujie Wang
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Zhibin Hao
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yingyi Zhang
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yuan Jiao
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Zhiyue Zhao
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaobo Peng
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
- *Correspondence: Xiaobo Peng, ; Xianbao Zhan,
| | - Xianbao Zhan
- Department of Oncology, Changhai Hospital, Naval Military Medical University, Shanghai, China
- *Correspondence: Xiaobo Peng, ; Xianbao Zhan,
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18
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Kerick M, Acosta-Herrera M, Simeón-Aznar CP, Callejas JL, Assassi S, Proudman SM, Nikpour M, Hunzelmann N, Moroncini G, de Vries-Bouwstra JK, Orozco G, Barton A, Herrick AL, Terao C, Allanore Y, Fonseca C, Alarcón-Riquelme ME, Radstake TRDJ, Beretta L, Denton CP, Mayes MD, Martin J. Complement component C4 structural variation and quantitative traits contribute to sex-biased vulnerability in systemic sclerosis. NPJ Genom Med 2022; 7:57. [PMID: 36198672 PMCID: PMC9534873 DOI: 10.1038/s41525-022-00327-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Copy number (CN) polymorphisms of complement C4 play distinct roles in many conditions, including immune-mediated diseases. We investigated the association of C4 CN with systemic sclerosis (SSc) risk. Imputed total C4, C4A, C4B, and HERV-K CN were analyzed in 26,633 individuals and validated in an independent cohort. Our results showed that higher C4 CN confers protection to SSc, and deviations from CN parity of C4A and C4B augmented risk. The protection contributed per copy of C4A and C4B differed by sex. Stronger protection was afforded by C4A in men and by C4B in women. C4 CN correlated well with its gene expression and serum protein levels, and less C4 was detected for both in SSc patients. Conditioned analysis suggests that C4 genetics strongly contributes to the SSc association within the major histocompatibility complex locus and highlights classical alleles and amino acid variants of HLA-DRB1 and HLA-DPB1 as C4-independent signals.
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Affiliation(s)
- Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain.
| | | | | | - Shervin Assassi
- Department of Rheumatology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susanna M Proudman
- Rheumatology Unit, Royal Adelaide Hospital and University of Adelaide, Adelaide, SA, Australia
| | - Mandana Nikpour
- The University of Melbourne at St. Vincent's Hospital, Melbourne, VIC, Australia
| | | | - Gianluca Moroncini
- Department of Clinical and Molecular Science, Università Politecnica delle Marche e Ospedali Riuniti, Ancona, Italy
| | | | - Gisela Orozco
- Center for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Center, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Anne Barton
- Center for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Center, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Ariane L Herrick
- Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Northern care Alliance NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yannick Allanore
- Department of Rheumatology A, Hospital Cochin, Paris, Île-de-France, France
| | - Carmen Fonseca
- Center for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Marta Eugenia Alarcón-Riquelme
- Center for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Timothy R D J Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Christopher P Denton
- Center for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Maureen D Mayes
- Department of Rheumatology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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19
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Caloto R, Lorenzo-Martín LF, Quesada V, Carracedo A, Bustelo XR. CiberAMP: An R Package to Identify Differential mRNA Expression Linked to Somatic Copy Number Variations in Cancer Datasets. BIOLOGY 2022; 11:biology11101411. [PMID: 36290315 PMCID: PMC9598370 DOI: 10.3390/biology11101411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 11/27/2022]
Abstract
Simple Summary The ability to establish accurate correlations between the number of copies of genes and the expression levels of their encoded transcripts remains a challenge despite the extensive progress made in the understanding of the genome of cancer cells. Here, we describe a new algorithm that does so by integrating both genomics and transcriptomics data from the Cancer Genome Atlas. In addition to explaining the step-by-step basis of this new method, we provide examples of how this new algorithm can help identify functionally meaningful gene copy alterations that are recurrently detected in cancer patients. Abstract Somatic copy number variations (SCNVs) are genetic alterations frequently found in cancer cells. These genetic alterations can lead to concomitant perturbations in the expression of the genes included in them and, as a result, promote a selective advantage to cancer cells. However, this is not always the case. Due to this, it is important to develop in silico tools to facilitate the accurate identification and functional cataloging of gene expression changes associated with SCNVs from pan-cancer data. Here, we present a new R-coded tool, designated as CiberAMP, which utilizes genomic and transcriptomic data contained in the Cancer Genome Atlas (TCGA) to identify such events. It also includes information on the genomic context in which such SCNVs take place. By doing so, CiberAMP provides clues about the potential functional relevance of each of the SCNV-associated gene expression changes found in the interrogated tumor samples. The main features and advantages of this new algorithm are illustrated using glioblastoma data from the TCGA database.
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Affiliation(s)
- Rubén Caloto
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer de Salamanca, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - L. Francisco Lorenzo-Martín
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer de Salamanca, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Víctor Quesada
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Arkaitz Carracedo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
- Center for Cooperative Research in Biosciences (CIC-bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Traslational Prostate Cancer Research Lab, CIC-bioGUNE, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - Xosé R. Bustelo
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Instituto de Biología Molecular y Celular del Cáncer de Salamanca, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, 37007 Salamanca, Spain
- Correspondence:
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20
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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21
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Song Y, Fang Q, Mi Y. Prognostic significance of copy number variation in B-cell acute lymphoblastic leukemia. Front Oncol 2022; 12:981036. [PMID: 35992882 PMCID: PMC9386345 DOI: 10.3389/fonc.2022.981036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Copy number variations (CNVs) are widespread in both pediatric and adult cases of B-cell acute lymphoblastic leukemia (B-ALL); however, their clinical significance remains unclear. This review primarily discusses the most prevalent CNVs in B-ALL to elucidate their clinical value and further personalized management of this population. The discovery of the molecular mechanism of gene deletion and the development of targeted drugs will further enhance the clinical prognosis of B-ALL.
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Affiliation(s)
| | - Qiuyun Fang
- *Correspondence: Qiuyun Fang, ; Yingchang Mi,
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22
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Alhazmi S, Alzahrani M, Farsi R, Alharbi M, Algothmi K, Alburae N, Ganash M, Azhari S, Basingab F, Almuhammadi A, Alqosaibi A, Alkhatabi H, Elaimi A, Jan M, Aldhalaan HM, Alrafiah A, Alrofaidi A. Multiple Recurrent Copy Number Variations (CNVs) in Chromosome 22 Including 22q11.2 Associated with Autism Spectrum Disorder. Pharmgenomics Pers Med 2022; 15:705-720. [PMID: 35898556 PMCID: PMC9309317 DOI: 10.2147/pgpm.s366826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a developmental disorder that can cause substantial social, communication, and behavioral challenges. Genetic factors play a significant role in ASD, where the risk of ASD has been increased for unclear reasons. Twin studies have shown important evidence of both genetic and environmental contributions in ASD, where the level of contribution of these factors has not been proven yet. It has been suggested that copy number variation (CNV) duplication and the deletion of many genes in chromosome 22 (Ch22) may have a strong association with ASD. This study screened the CNVs in Ch22 in autistic Saudi children and assessed the candidate gene in the CNVs region of Ch22 that is most associated with ASD. Methods This study included 15 autistic Saudi children as well as 4 healthy children as controls; DNA was extracted from samples and analyzed using array comparative genomic hybridization (aCGH) and DNA sequencing. Results The aCGH detected (in only 6 autistic samples) deletion and duplication in many regions of Ch22, including some critical genes. Moreover, DNA sequencing determined a genetic mutation in the TBX1 gene sequence in autistic samples. This study, carried out using aCGH, found that six autistic patients had CNVs in Ch22, and DNA sequencing revealed mutations in the TBX1 gene in autistic samples but none in the control. Conclusion CNV deletion and the duplication of the TBX1 gene could be related to ASD; therefore, this gene needs more analysis in terms of expression levels.
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Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Farsi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khloud Algothmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Heba Alkhatabi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Jan
- College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hesham M Aldhalaan
- Center for Autism Research at King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Aziza Alrafiah
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Correspondence: Aziza Alrafiah, Department of Medical Laboratory Science, King Abdulaziz University, P.O Box 80200, Jeddah, 21589, Saudi Arabia, Tel +966 126401000 Ext. 23495, Fax +966 126401000 Ext. 21686, Email
| | - Aisha Alrofaidi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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23
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Fonova EA, Tolmacheva EN, Kashevarova AA, Sazhenova EA, Nikitina TV, Lopatkina ME, Vasilyeva OY, Zarubin AА, Aleksandrova TN, Yuriev SY, Skryabin NA, Stepanov VA, Lebedev IN. Skewed X-Chromosome Inactivation as a Possible Marker of X-Linked CNV in Women with Pregnancy Loss. Cytogenet Genome Res 2022; 162:97-108. [PMID: 35636401 DOI: 10.1159/000524342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
Skewed X-chromosome inactivation (sXCI) can be a marker of lethal genetic variants on the X chromosome in a woman since sXCI modifies the pathological phenotype. The aim of this study was to search for CNVs in women with miscarriages and sXCI. XCI was assayed using the classical method based on the amplification of highly polymorphic exon 1 of the androgen receptor (AR) gene. The XCI status was analysed in 313 women with pregnancy loss and in 87 spontaneously aborted embryos with 46,XX karyotype, as well as in control groups of 135 women without pregnancy loss and 64 embryos with 46,XX karyotype from induced abortions in women who terminated a normal pregnancy. The frequency of sXCI differed significantly between women with miscarriages and women without pregnancy losses (6.3% and 2.2%, respectively; p = 0.019). To exclude primary causes of sXCI, sequencing of the XIST and XACT genes was performed. The XIST and XACT gene sequencing revealed no known pathogenic variants that could lead to sXCI. Molecular karyotyping was performed using aCGH, followed by verification of X-linked CNVs by RT-PCR and MLPA. Microdeletions at Xp11.23 and Xq24 as well as gains of Xq28 were detected in women with sXCI and pregnancy loss.
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Affiliation(s)
- Elizaveta A Fonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Elena A Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Tatyana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Maria E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Aleksei А Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Tatyana N Aleksandrova
- Department of Obstetrics and Gynecology, Siberian State Medical University, Tomsk, Russian Federation
| | - Sergey Yu Yuriev
- Department of Obstetrics and Gynecology, Siberian State Medical University, Tomsk, Russian Federation
| | - Nikolay A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Vadim A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
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24
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Ahn B, Jeon H, Cho HS, Nagasundarapandian S, Park C. Sequence polymorphisms of PR39 cathelicidins and extensive copy variations in commercial pig breeds. Gene 2022; 822:146323. [PMID: 35181502 DOI: 10.1016/j.gene.2022.146323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/09/2022] [Accepted: 02/11/2022] [Indexed: 02/06/2023]
Abstract
Copy number polymorphisms (CNPs) of antimicrobial peptides (AMPs) in livestock can influence the innate immune response of individuals. We conducted a high-resolution analysis of the genomic variations of porcine cathelicidin PR39 using cloned PR39 amplicons corresponding to the 5' untranslated region (UTR) to 3' UTR from four individuals of three different pig breeds. We identified 15 different sequences corresponding to 9 different coding domain sequences (CDSs), encoding 7 different protein sequences consisting of 3 functional and 4 non-functional forms. Subsequently, we developed a PR39 CNP typing method using real-time polymerase chain reaction (PCR) and analyzed the PR39 copy numbers from 44 pigs of six breeds. Significant variations in PR39 copies ranging from 2 to 10 copies, with a mean copy number of 5, were observed among all commercial breeds, except the wild boar. Among the different breeds, the PR39 copy number was highest (10) in Korean native pigs. Gene expression analysis showed that PR39 expression was correlated with the copy number. Moreover, the comparative analysis of the cathelicidin cluster-containing region among eight mammalian species showed the complete evolutionary conservation of the region, except for differences in the degree of cathelicidin expansion in each species. Therefore, characterization of CNPs in AMP genes could aid in improving the genetic potential of innate immune responses in livestock animals.
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Affiliation(s)
- Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hye-Sun Cho
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | | | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea.
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25
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Hernández-Gómez C, Hernández-Lemus E, Espinal-Enríquez J. The Role of Copy Number Variants in Gene Co-Expression Patterns for Luminal B Breast Tumors. Front Genet 2022; 13:806607. [PMID: 35432489 PMCID: PMC9010943 DOI: 10.3389/fgene.2022.806607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/03/2022] [Indexed: 12/20/2022] Open
Abstract
Gene co-expression networks have become a usual approach to integrate the vast amounts of information coming from gene expression studies in cancer cohorts. The reprogramming of the gene regulatory control and the molecular pathways depending on such control are central to the characterization of the disease, aiming to unveil the consequences for cancer prognosis and therapeutics. There is, however, a multitude of factors which have been associated with anomalous control of gene expression in cancer. In the particular case of co-expression patterns, we have previously documented a phenomenon of loss of long distance co-expression in several cancer types, including breast cancer. Of the many potential factors that may contribute to this phenomenology, copy number variants (CNVs) have been often discussed. However, no systematic assessment of the role that CNVs may play in shaping gene co-expression patterns in breast cancer has been performed to date. For this reason we have decided to develop such analysis. In this study, we focus on using probabilistic modeling techniques to evaluate to what extent CNVs affect the phenomenon of long/short range co-expression in Luminal B breast tumors. We analyzed the co-expression patterns in chromosome 8, since it is known to be affected by amplifications/deletions during cancer development. We found that the CNVs pattern in chromosome 8 of Luminal B network does not alter the co-expression patterns significantly, which means that the co-expression program in this cancer phenotype is not determined by CNV structure. Additionally, we found that region 8q24.3 is highly dense in interactions, as well as region p21.3. The most connected genes in this network belong to those cytobands and are associated with several manifestations of cancer in different tissues. Interestingly, among the most connected genes, we found MAF1 and POLR3D, which may constitute an axis of regulation of gene transcription, in particular for non-coding RNA species. We believe that by advancing on our knowledge of the molecular mechanisms behind gene regulation in cancer, we will be better equipped, not only to understand tumor biology, but also to broaden the scope of diagnostic, prognostic and therapeutic interventions to ultimately benefit oncologic patients.
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Affiliation(s)
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Jesús Espinal-Enríquez, ; Enrique Hernández-Lemus,
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Jesús Espinal-Enríquez, ; Enrique Hernández-Lemus,
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26
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Merkle FT, Ghosh S, Genovese G, Handsaker RE, Kashin S, Meyer D, Karczewski KJ, O'Dushlaine C, Pato C, Pato M, MacArthur DG, McCarroll SA, Eggan K. Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. Cell Stem Cell 2022; 29:472-486.e7. [PMID: 35176222 PMCID: PMC8900618 DOI: 10.1016/j.stem.2022.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 02/02/2023]
Abstract
Despite their widespread use in research, there has not yet been a systematic genomic analysis of human embryonic stem cell (hESC) lines at a single-nucleotide resolution. We therefore performed whole-genome sequencing (WGS) of 143 hESC lines and annotated their single-nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer-scale structural and single-nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESC genomes and human blood-derived genomes at similar frequencies. Moreover, WGS allowed us to identify SNVs associated with cancer and other diseases that could alter cellular phenotypes and compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection.
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Affiliation(s)
- Florian T Merkle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome - MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Sulagna Ghosh
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Colm O'Dushlaine
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Michele Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA; Department of Psychiatry, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Daniel G MacArthur
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Zhao LF, Qi FY, Zhang JG, Pang JR, Ren HM, Shen DD, Zhao LJ, Qi L, Liu HM, Zheng YC. Identification of the upstream regulators of KDM5B in gastric cancer. Life Sci 2022; 298:120458. [DOI: 10.1016/j.lfs.2022.120458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/19/2022] [Accepted: 03/01/2022] [Indexed: 02/03/2023]
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The Psychoemotional Stress-Induced Changes in the Abundance of SatIII (1q12) and Telomere Repeats, but Not Ribosomal DNA, in Human Leukocytes. Genes (Basel) 2022; 13:genes13020343. [PMID: 35205387 PMCID: PMC8872136 DOI: 10.3390/genes13020343] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/01/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION. As shown earlier, copy number variations (CNV) in the human satellite III (1q12) fragment (f-SatIII) and the telomere repeat (TR) reflects the cell’s response to oxidative stress. The contents of f-SatIII and TR in schizophrenic (SZ) patients were found to be lower than in healthy controls (HC) in previous studies. The major question of this study was: ‘What are the f-SatIII and TR CNV dynamic changes in human leukocytes, depending on psychoemotional stress?’ MATERIALS AND METHODS. We chose a model of psychoemotional stress experienced by second-year medical students during their exams. Blood samples were taken in stressful conditions (exams) and in a control non-stressful period. Biotinylated probes were used for f-SatIII, rDNA, and TR quantitation in leukocyte DNA by non-radioactive quantitative hybridization in SZ patients (n = 97), HC (n = 97), and medical students (n = 17, n = 42). A flow cytometry analysis was used for the oxidative stress marker (NOX4, 8-oxodG, and γH2AX) detection in the lymphocytes of the three groups. RESULTS. Oxidative stress markers increased significantly in the students’ lymphocytes during psychoemotional stress. The TR and f-SatIII, but not the rDNA, contents significantly changed in the DNA isolated from human blood leukocytes. After a restoration period (post-examinational vacations), the f-SatIII content decreased, and the TR content increased. Changes in the blood cells of students during examinational stress were similar to those in SZ patients during an exacerbation of the disease. CONCLUSIONS. Psychoemotional stress in students during exams triggers a universal mechanism of oxidative stress. The oxidative stress causes significant changes in the f-SatIII and TR contents, while the ribosomal repeat content remains stable. A hypothesis is proposed to explain the quantitative polymorphisms of f-SatIII and TR contents under transient (e.g., students’ exams) or chronic (in SZ patients) stress. The changes in the f-SatIII and TR copy numbers are non-specific events, irrespective of the source of stress. Thus, our findings suggest that the psychoemotional stress, common in SZ patients and healthy students during exams, but not in a schizophrenia-specific event, was responsible for the changes in the repeat contents that we observed earlier in SZ patients.
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Tang R, Li Y, Han F, Li Z, Lin X, Sun H, Zhang X, Jiang Q, Nie H, Li Y. A CTCF-Binding Element and Histone Deacetylation Cooperatively Maintain Chromatin Loops, Linking to Long-Range Gene Regulation in Cancer Genomes. Front Oncol 2022; 11:821495. [PMID: 35127534 PMCID: PMC8813737 DOI: 10.3389/fonc.2021.821495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022] Open
Abstract
Background Genes spanning long chromosomal domains are coordinately regulated in human genome, which contribute to global gene dysregulation and carcinogenesis in cancer. It has been noticed that epigenetic modification and chromatin architecture may participate in the regulation process. However, the regulation patterns and functional elements of long-range gene regulation are unclear. Methods Based on the clinical transcriptome data from different tumor sets, a novel expressional correlation analysis pipeline was performed to classify the co-regulated regions and subsets of intercorrelated regions. The GLAM2 program was used to predict conserved DNA elements that enriched in regions. Two conserved elements were selected to delete in Ishikawa and HeLa cells by CRISPR-Cas9. SAHA treatment and HDAC knockdown were used to change the histone acetylation status. Using qPCR, MTT, and scratch healing assay, we evaluate the effect on gene expression and cancer cell phenotype. By DNA pull-down and ChIP, the element-binding proteins were testified. 3C and 3D-FISH were performed to depict the alteration in chromatin architecture. Results In multiple cancer genomes, we classified subsets of coordinately regulated regions (sub-CRRs) that possibly shared the same regulatory mechanisms and exhibited similar expression patterns. A new conserved DNA element (CRE30) was enriched in sub-CRRs and associated with cancer patient survival. CRE30 could restrict gene regulation in sub-CRRs and affect cancer cell phenotypes. DNA pull-down showed that multiple proteins including CTCF were recruited on the CRE30 locus, and ChIP assay confirmed the CTCF-binding signals. Subsequent results uncovered that as an essential element, CRE30 maintained chromatin loops and mediated a compact chromatin architecture. Moreover, we found that blocking global histone deacetylation induced chromatin loop disruption and CTCF dropping in the region containing CRE30, linked to promoted gene regulation. Additionally, similar effects were observed with CRE30 deletion in another locus of chromosome 8. Conclusions Our research clarified a new functional element that recruits CTCF and collaborates with histone deacetylation to maintain high-order chromatin organizations, linking to long-range gene regulation in cancer genomes. The findings highlight a close relationship among conserved DNA element, epigenetic modification, and chromatin architecture in long-range gene regulation process.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Huan Nie
- *Correspondence: Yu Li, ; Huan Nie,
| | - Yu Li
- *Correspondence: Yu Li, ; Huan Nie,
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Contribution of schizophrenia polygenic burden to longitudinal phenotypic variance in 22q11.2 deletion syndrome. Mol Psychiatry 2022; 27:4191-4200. [PMID: 35768638 PMCID: PMC9718680 DOI: 10.1038/s41380-022-01674-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 02/07/2023]
Abstract
While the recurrent 22q11.2 deletion is one of the strongest genetic risk factors for schizophrenia (SCZ), variability of its associated neuropsychiatric endophenotypes reflects its incomplete penetrance for psychosis development. To assess whether this phenotypic variability is linked to common variants associated with SCZ, we studied the association between SCZ polygenic risk score (PRS) and longitudinally acquired phenotypic information of the Swiss 22q11.2DS cohort (n = 97, 50% females, mean age 17.7 yr, mean visit interval 3.8 yr). The SCZ PRS with the best predictive performance was ascertained in the Estonian Biobank (n = 201,146) with LDpred. The infinitesimal SCZ PRS model showed the strongest capacity in discriminating SCZ cases from controls with one SD difference in SCZ PRS corresponding to an odds ratio (OR) of 1.73 (95% CI 1.57-1.90, P = 1.47 × 10-29). In 22q11.2 patients, random-effects ordinal regression modelling using longitudinal data showed SCZ PRS to have the strongest effect on social anhedonia (OR = 2.09, P = 0.0002), and occupational functioning (OR = 1.82, P = 0.0003) within the negative symptoms course, and dysphoric mood (OR = 2.00, P = 0.002) and stress intolerance (OR = 1.76, P = 0.0002) within the general symptoms course. Genetic liability for SCZ was additionally associated with full scale cognitive decline (β = -0.25, P = 0.02) and with longitudinal volumetric reduction of the right and left hippocampi (β = -0.28, P = 0.005; β = -0.23, P = 0.02, respectively). Our results indicate that the polygenic contribution to SCZ acts upon the threshold-lowering first hit (i.e., the deletion). It modifies the endophenotypes of 22q11.2DS and augments the derailment of developmental trajectories of negative and general symptoms, cognition, and hippocampal volume.
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Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zou Z, Zhuang J, Xia L, Li Y, Yin J, Mu Y. DCD-chip designed for the digital and ultraprecise quantification of copy number variation. Analyst 2022; 147:4371-4378. [DOI: 10.1039/d2an00982j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The progress of CNV detection in DCD-chip.
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Affiliation(s)
- Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, P. R. China
- College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Jianjian Zhuang
- Department of Clinical pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, P. R. China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, P. R. China
- College of Life Sciences, Zhejiang University, Hangzhou, P. R. China
| | - Ying Li
- Department of Public Health, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Juxin Yin
- School of information and Electrical Engineering, Zhejiang University City College, Hangzhou, Zhejiang Province, P. R. China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, P. R. China
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Zhong W, Wang D, Yao B, Chen X, Wang Z, Qu H, Ma B, Ye L, Qiu J. Integrative analysis of prognostic long non-coding RNAs with copy number variation in bladder cancer. J Zhejiang Univ Sci B 2021; 22:664-681. [PMID: 34414701 DOI: 10.1631/jzus.b2000494] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs), which can affect the role of long non-coding RNAs (lncRNAs), are important genetic changes seen in some malignant tumors. We analyzed lncRNAs with CNV to explore the relationship between lncRNAs and prognosis in bladder cancer (BLCA). Messenger RNA (mRNA) expression levels, DNA methylation, and DNA copy number data of 408 BLCA patients were subjected to integrative bioinformatics analysis. Cluster analysis was performed to obtain different subtypes and differently expressed lncRNAs and coding genes. Weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression gene and lncRNA modules. CNV-associated lncRNA data and their influence on cancer prognosis were assessed with Kaplan-Meier survival curve. Multi-omics integration analysis revealed five prognostic lncRNAs with CNV, namely NR2F1-AS1, LINC01138, THUMPD3-AS1, LOC101928489,and TMEM147-AS1,and a risk-score signature related to overall survival in BLCA was identified. Moreover, validated results in another independent Gene Expression Omnibus (GEO) dataset, GSE31684, were consistent with these results. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway, focal adhesion pathway, and Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling pathway were enriched in a high-risk score pattern, suggesting that imbalance in these pathways is closely related to tumor development. We revealed the prognosis-related lncRNAs by analyzing the expression profiles of lncRNAs and CNVs, which can be used as prognostic biomarkers for BLCA.
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Affiliation(s)
- Wenwen Zhong
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Dejuan Wang
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Bing Yao
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Xiaoxia Chen
- Department of Medical Record Management Section, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Zhongyang Wang
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Hu Qu
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Bo Ma
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Lei Ye
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Jianguang Qiu
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China.
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Metwally M, Bayoumi A, Khan A, Adams LA, Aller R, García-Monzón C, Arias-Loste MT, Bugianesi E, Miele L, Anna A, Latchoumanin O, Han S, Alenizi S, Sharkawy RE, Elattar A, Gallego-Durán R, Fischer J, Berg T, Liddle C, Romero-Gomez M, George J, Eslam M. Copy number variation and expression of exportin-4 associates with severity of fibrosis in metabolic associated fatty liver disease. EBioMedicine 2021; 70:103521. [PMID: 34388518 PMCID: PMC8365315 DOI: 10.1016/j.ebiom.2021.103521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/11/2023] Open
Abstract
Background Liver fibrosis risk is a heritable trait, the outcome of which is the net deposition of extracellular matrix by hepatic stellate cell-derived myofibroblasts. Whereas nucleotide sequence variations have been extensively studied in liver fibrosis, the role of copy number variations (CNV) in which genes exist in abnormal numbers of copies (mostly due to duplication or deletion) has had limited exploration. Methods The impact of the XPO4 CNV on histological liver damage was examined in a cohort comprised 646 Caucasian patients with biopsy-proven MAFLD and 170 healthy controls. XPO4 expression was modulated and function was examined in human and animal models. Findings Here we demonstrate in a cohort of 816 subjects, 646 with biopsy-proven metabolic associated liver disease (MAFLD) and 170 controls, that duplication in the exportin 4 (XPO4) CNV is associated with the severity of liver fibrosis. Functionally, this occurs via reduced expression of hepatic XPO4 that maintains sustained activation of SMAD3/SMAD4 and promotes TGF-β1-mediated HSC activation and fibrosis. This effect was mediated through termination of nuclear SMAD3 signalling. XPO4 demonstrated preferential binding to SMAD3 compared to other SMADs and led to reduced SMAD3-mediated responses as shown by attenuation of TGFβ1 induced SMAD transcriptional activity, reductions in the recruitment of SMAD3 to target gene promoters following TGF-β1, as well as attenuation of SMAD3 phosphorylation and disturbed SMAD3/SMAD4 complex formation. Interpretation We conclude that a CNV in XPO4 is a critical mediator of fibrosis severity and can be exploited as a therapeutic target for liver fibrosis. Funding ME and JG are supported by the Robert W. Storr Bequest to the Sydney Medical Foundation, University of Sydney; a National Health and Medical Research Council of Australia (NHMRC) Program Grant (APP1053206) and Project and ideas grants (APP2001692, APP1107178 and APP1108422). AB is supported by an Australian Government Research Training Program (RTP) scholarship. EB is supported by Horizon 2020 under grant 634413 for the project EPoS.
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Affiliation(s)
- Mayada Metwally
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Ali Bayoumi
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Anis Khan
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Leon A Adams
- Medical School, Sir Charles Gairdner Hospital Unit, University of Western Australia, Nedlands, WA, Australia
| | - Rocio Aller
- Center of Investigation of Endocrinology and Nutrition, School of Medicine, and Unit of Investigation, Hospital Clinico Universitario de Valladolid, Valladolid, Spain
| | - Carmelo García-Monzón
- Liver Research Unit, Instituto de Investigacion Sanitaria Princesa, University Hospital Santa Cristina, CIBERehd, Madrid, Spain
| | - María Teresa Arias-Loste
- Gastroenterology and Hepatology Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain
| | - Elisabetta Bugianesi
- Division of Gastroenterology, Department of Medical Science, University of Turin, Turin, Italy
| | - Luca Miele
- Department of Internal Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Alisi Anna
- Research Unit of Molecular Genetics of Complex Phenotypes, IRCCS "Bambino Gesù" Children's Hospital, Rome, Italy
| | - Olivier Latchoumanin
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Shuanglin Han
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Shafi Alenizi
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Rasha El Sharkawy
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Afaf Elattar
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Rocio Gallego-Durán
- Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, Sevilla, Spain
| | - Janett Fischer
- Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Thomas Berg
- Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Manuel Romero-Gomez
- Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, Sevilla, Spain
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
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Hu W, Li M, Zhang Q, Liu C, Wang X, Li J, Qiu S, Li L. Establishment of a novel CNV-related prognostic signature predicting prognosis in patients with breast cancer. J Ovarian Res 2021; 14:103. [PMID: 34364397 PMCID: PMC8349487 DOI: 10.1186/s13048-021-00823-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/10/2021] [Indexed: 01/17/2023] Open
Abstract
Background Copy number variation (CNVs) is a key factor in breast cancer development. This study determined prognostic molecular characteristics to predict breast cancer through performing a comprehensive analysis of copy number and gene expression data. Methods Breast cancer expression profiles, CNV and complete information from The Cancer Genome Atlas (TCGA) dataset were collected. Gene Expression Omnibus (GEO) chip data sets (GSE20685 and GSE31448) containing breast cancer samples were used as external validation sets. Univariate survival COX analysis, multivariate survival COX analysis, least absolute shrinkage and selection operator (LASSO), Chi square, Kaplan-Meier (KM) survival curve and receiver operating characteristic (ROC) analysis were applied to build a gene signature model and assess its performance. Results A total of 649 CNV related-differentially expressed gene obtained from TCGA-breast cancer dataset were related to several cancer pathways and functions. A prognostic gene sets with 9 genes were developed to stratify patients into high-risk and low-risk groups, and its prognostic performance was verified in two independent patient cohorts (n = 327, 246). The result uncovered that 9-gene signature could independently predict breast cancer prognosis. Lower mutation of PIK3CA and higher mutation of TP53 and CDH1 were found in samples with high-risk score compared with samples with low-risk score. Patients in the high-risk group showed higher immune score, malignant clinical features than those in the low-risk group. The 9-gene signature developed in this study achieved a higher AUC. Conclusion The current research established a 5-CNV gene signature to evaluate prognosis of breast cancer patients, which may innovate clinical application of prognostic assessment. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00823-y.
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Affiliation(s)
- Wei Hu
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China
| | - Mingyue Li
- Department of Rehabilitation Medicine, The Third Affilated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Qi Zhang
- Blood Transfusion Department, Zibo Central Hospital, Zibo, 255036, China
| | - Chuan Liu
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China
| | - Xinmei Wang
- Department of Pathology, ZiBo Central Hospital, Zibo, 255036, China
| | - Jing Li
- Department of Pathology, ZiBo Central Hospital, Zibo, 255036, China.
| | - Shusheng Qiu
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China.
| | - Liang Li
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China.
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Chattopadhyay A, Teoh ZH, Wu CY, Juang JMJ, Lai LC, Tsai MH, Wu CH, Lu TP, Chuang EY. CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6321046. [PMID: 34259866 PMCID: PMC8278790 DOI: 10.1093/database/baab044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 11/14/2022]
Abstract
Human copy number variations (CNVs) and copy number alterations (CNAs) are DNA segments (>1000 base pairs) of duplications or deletions with respect to the reference genome, potentially causing genomic imbalance leading to diseases such as cancer. CNVs further cause genetic diversity in healthy populations and are predominant drivers of gene/genome evolution. Initiatives have been taken by the research community to establish large-scale databases to comprehensively characterize CNVs in humans. Exome Aggregation Consortium (ExAC) is one such endeavor that catalogs CNVs, of nearly 60 000 healthy individuals across five demographic clusters. Furthermore, large projects such as the Catalogue of Somatic Mutations in Cancer (COSMIC) and the Cancer Cell Line Encyclopedia (CCLE) combine CNA data from cancer-affected individuals and large panels of human cancer cell lines, respectively. However, we lack a structured and comprehensive CNV/CNA resource including both healthy individuals and cancer patients across large populations. CNVIntegrate is the first web-based system that hosts CNV and CNA data from both healthy populations and cancer patients, respectively, and concomitantly provides statistical comparisons between copy number frequencies of multiple ethnic populations. It further includes, for the first time, well-cataloged CNV and CNA data from Taiwanese healthy individuals and Taiwan Breast Cancer data, respectively, along with imported resources from ExAC, COSMIC and CCLE. CNVIntegrate offers a CNV/CNA-data hub for structured information retrieval for clinicians and scientists towards important drug discoveries and precision treatments. Database URL: http://cnvintegrate.cgm.ntu.edu.tw/.
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Affiliation(s)
- Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Zi Han Teoh
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Yun Wu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Jyh-Ming Jimmy Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 10008, Taiwan.,College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Graduate Institute of Physiology, National Taiwan University, Taipei 10051, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Chia-Hsin Wu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Master Program for Biomedical Engineering, China Medical University, Taichung 40402, Taiwan
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Yilmaz F, Null M, Astling D, Yu HC, Cole J, Santorico SA, Hallgrimsson B, Manyama M, Spritz RA, Hendricks AE, Shaikh TH. Genome-wide copy number variations in a large cohort of bantu African children. BMC Med Genomics 2021; 14:129. [PMID: 34001112 PMCID: PMC8130444 DOI: 10.1186/s12920-021-00978-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) account for a substantial proportion of inter-individual genomic variation. However, a majority of genomic variation studies have focused on single-nucleotide variations (SNVs), with limited genome-wide analysis of CNVs in large cohorts, especially in populations that are under-represented in genetic studies including people of African descent. METHODS We carried out a genome-wide copy number analysis in > 3400 healthy Bantu Africans from Tanzania. Signal intensity data from high density (> 2.5 million probes) genotyping arrays were used for CNV calling with three algorithms including PennCNV, DNAcopy and VanillaICE. Stringent quality metrics and filtering criteria were applied to obtain high confidence CNVs. RESULTS We identified over 400,000 CNVs larger than 1 kilobase (kb), for an average of 120 CNVs (SE = 2.57) per individual. We detected 866 large CNVs (≥ 300 kb), some of which overlapped genomic regions previously associated with multiple congenital anomaly syndromes, including Prader-Willi/Angelman syndrome (Type1) and 22q11.2 deletion syndrome. Furthermore, several of the common CNVs seen in our cohort (≥ 5%) overlap genes previously associated with developmental disorders. CONCLUSIONS These findings may help refine the phenotypic outcomes and penetrance of variations affecting genes and genomic regions previously implicated in diseases. Our study provides one of the largest datasets of CNVs from individuals of African ancestry, enabling improved clinical evaluation and disease association of CNVs observed in research and clinical studies in African populations.
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Affiliation(s)
- Feyza Yilmaz
- Integrative and Systems Biology Program, University of Colorado Denver, Denver, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
| | - Megan Null
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, USA
| | - David Astling
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA
| | - Hung-Chun Yu
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
| | - Joanne Cole
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
| | - Stephanie A Santorico
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
- Biostatistics and Informatics, Colorado School of Public Health, Aurora, USA
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, Cumming School of Medicine and Alberta, Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Mange Manyama
- Anatomy in Radiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Richard A Spritz
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
| | - Audrey E Hendricks
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
- Biostatistics and Informatics, Colorado School of Public Health, Aurora, USA
| | - Tamim H Shaikh
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA.
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA.
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38
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Ayuso P, García-Martín E, Cornejo-García JA, Agúndez JAG, Ladero JM. Genetic Variants of Alcohol Metabolizing Enzymes and Alcohol-Related Liver Cirrhosis Risk. J Pers Med 2021; 11:jpm11050409. [PMID: 34068303 PMCID: PMC8153263 DOI: 10.3390/jpm11050409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 11/25/2022] Open
Abstract
Alcohol-related liver disease (ARLD) is a major public health issue caused by excessive alcohol consumption. ARLD encompasses a wide range of chronic liver lesions, alcohol-related liver cirrhosis being the most severe and harmful state. Variations in the genes encoding the enzymes, which play an active role in ethanol metabolism, might influence alcohol exposure and hence be considered as risk factors of developing cirrhosis. We conducted a case-control study in which 164 alcohol-related liver cirrhosis patients and 272 healthy controls were genotyped for the following functional single nucleotide variations (SNVs): ADH1B gene, rs1229984, rs1041969, rs6413413, and rs2066702; ADH1C gene, rs35385902, rs283413, rs34195308, rs1693482, and rs35719513; CYP2E1 gene, rs3813867. Furthermore, copy number variations (CNVs) for ADH1A, ADH1B, ADH1C, and CYP2E1 genes were analyzed. A significant protective association with the risk of developing alcohol-related liver cirrhosis was observed between the mutant alleles of SNVs ADH1B rs1229984 (Pc value = 0.037) and ADH1C rs283413 (Pc value = 0.037). We identified CNVs in all genes studied, ADH1A gene deletions being more common in alcohol-related liver cirrhosis patients than in control subjects, although the association lost statistical significance after multivariate analyses. Our findings support that susceptibility to alcohol-related liver cirrhosis is related to variations in alcohol metabolism genes.
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Affiliation(s)
- Pedro Ayuso
- ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, UEx, 10003 Cáceres, Spain; (E.G.-M.); (J.A.G.A.)
- Correspondence:
| | - Elena García-Martín
- ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, UEx, 10003 Cáceres, Spain; (E.G.-M.); (J.A.G.A.)
| | - José A. Cornejo-García
- ARADyAL, Instituto de Salud Carlos III Research Laboratory, IBIMA, Regional University Hospital of Málaga, UMA, 29010 Málaga, Spain;
| | - José A. G. Agúndez
- ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, UEx, 10003 Cáceres, Spain; (E.G.-M.); (J.A.G.A.)
| | - José María Ladero
- Service of Gastroenterology (Liver Unit), Hospital Clínico San Carlos, Universidad Complutense Medical School, 28040 Madrid, Spain;
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Liu Y, Ye X, Zhan X, Yu CY, Zhang J, Huang K. TPQCI: A topology potential-based method to quantify functional influence of copy number variations. Methods 2021; 192:46-56. [PMID: 33894380 DOI: 10.1016/j.ymeth.2021.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Copy number variation (CNV) is a major type of chromosomal structural variation that play important roles in many diseases including cancers. Due to genome instability, a large number of CNV events can be detected in diseases such as cancer. Therefore, it is important to identify the functionally important CNVs in diseases, which currently still poses a challenge in genomics. One of the critical steps to solve the problem is to define the influence of CNV. In this paper, we provide a topology potential based method, TPQCI, to quantify this kind of influence by integrating statistics, gene regulatory associations, and biological function information. We used this metric to detect functionally enriched genes on genomic segments with CNV in breast cancer and multiple myeloma and discovered biological functions influenced by CNV. Our results demonstrate that, by using our proposed TPQCI metric, we can detect disease-specific genes that are influenced by CNVs. Source codes of TPQCI are provided in Github (https://github.com/usos/TPQCI).
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Affiliation(s)
- Yusong Liu
- Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China; Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Xiufen Ye
- Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, Heilongjiang 150001, China
| | - Xiaohui Zhan
- Indiana University School of Medicine, Indianapolis, IN 46202, USA; National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518037, China; Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Christina Y Yu
- Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Jie Zhang
- Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kun Huang
- Indiana University School of Medicine, Indianapolis, IN 46202, USA; Regenstrief Institute, Indianapolis, IN 46202, USA.
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40
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Liu Q, Xu J, Zhu Y, Mo Y, Yao XF, Wang R, Ku W, Huang Z, Xia S, Tong J, Huang C, Su Y, Lin W, Peng K, Liu CM, Xiao L. The Copy Number Variation of OsMTD1 Regulates Rice Plant Architecture. FRONTIERS IN PLANT SCIENCE 2021; 11:620282. [PMID: 33643334 PMCID: PMC7905320 DOI: 10.3389/fpls.2020.620282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
Copy number variation (CNV) may have phenotypic effects by altering the expression level of the gene(s) or regulatory element(s) contained. It is believed that CNVs play pivotal roles in controlling plant architecture and other traits in plant. However, the effects of CNV contributing to special traits remain largely unknown. Here we report a CNV involved in rice architecture by modulating tiller number and leaf angle. In the genome of Oryza sativa ssp. japonica cv. Nipponbare, we found a locus Loc_Os08g34249 is derived from a 13,002-bp tandem duplication in the nearby region of OsMTD1, a gene regulating tillering in rice. Further survey of 230 rice cultivars showed that the duplication occurred in only 13 japonica rice cultivars. Phenotypic investigation indicated that this CNV region may contribute to tiller number. Moreover, we revealed that OsMTD1 not only influences rice tiller number and leaf angle, but also represses pri-miR156f transcription in the CNV region. Intriguingly, this CNV performs function through both the dosage and position effects on OsMTD1 and pri-miR156f. Thus, our work identified a CNV and revealed a molecular regulatory basis for its effects on plant architecture, implying this CNV may possess importance and application potential in molecular breeding in rice.
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Affiliation(s)
- Qing Liu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jinke Xu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yunhua Zhu
- Hengyang Medical College, University of South China, Hengyang, China
| | - Yuxing Mo
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Xue-Feng Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Wenzhen Ku
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chao Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yi Su
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Wanhuang Lin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Keqin Peng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
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41
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Liu R, Shi P, Wang Z, Yuan C, Cui H. Molecular Mechanisms of MYCN Dysregulation in Cancers. Front Oncol 2021; 10:625332. [PMID: 33614505 PMCID: PMC7886978 DOI: 10.3389/fonc.2020.625332] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
MYCN, a member of MYC proto-oncogene family, encodes a basic helix-loop-helix transcription factor N-MYC. Abnormal expression of N-MYC is correlated with high-risk cancers and poor prognosis. Initially identified as an amplified oncogene in neuroblastoma in 1983, the oncogenic effect of N-MYC is expanded to multiple neuronal and nonneuronal tumors. Direct targeting N-MYC remains challenge due to its "undruggable" features. Therefore, alternative therapeutic approaches for targeting MYCN-driven tumors have been focused on the disruption of transcription, translation, protein stability as well as synthetic lethality of MYCN. In this review, we summarize the latest advances in understanding the molecular mechanisms of MYCN dysregulation in cancers.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Pengfei Shi
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Zhongze Wang
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Chaoyu Yuan
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
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42
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Abdelwahed M, Maaloul I, Benoit V, Hilbert P, Hachicha M, Kamoun H, Keskes-Ammar L, Belguith N. Copy-number variation of the NPHP1 gene in patients with juvenile Nephronophthisis. Acta Clin Belg 2021; 76:16-24. [PMID: 31402777 DOI: 10.1080/17843286.2019.1655231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective: Juvenile nephronophthisis (NPHP) is an autosomal recessive cystic disease of the kidney. It represents the most frequent genetic cause of chronic renal failure in children. Methods: we investigated clinical and molecular features in two children with Juvenile nephronophthisis using firstly Multiplex ligation-dependent probe amplification (MLPA) and secondly multiplex PCR. Results: we report a homozygous NPHP1 deletion in two children. Conclusion: NPHP1 deletion analysis using diagnostic methods (e.g. MLPA, Multiplex PCR) should always be considered in patients with nephronophthisis, especially from consanguineous families. Our results provide insights into genotype-phenotype correlations in juvenile nephronophthisis that can be utilized in genetic counseling.
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Affiliation(s)
- Mayssa Abdelwahed
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Ines Maaloul
- Pediatric Department of Hedi Chaker Hospital, Sfax, Tunisia
| | - Valerie Benoit
- Center of Human Genetics, Institute of Pathology and Genetics, Biopark Charleroi Brussels, Gosselies, Belgium
| | - Pascale Hilbert
- Center of Human Genetics, Institute of Pathology and Genetics, Biopark Charleroi Brussels, Gosselies, Belgium
| | | | - Hassen Kamoun
- Medical Genetics Department of Hedi Chaker Hospital, Sfax, Tunisia
| | - Leila Keskes-Ammar
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Neila Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine, University of Sfax, Sfax, Tunisia
- Medical Genetics Department of Hedi Chaker Hospital, Sfax, Tunisia
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43
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Yang L, Wu S, Ma C, Song S, Jin F, Niu Y, Tong WM. RNA m 6A Methylation Regulators Subclassify Luminal Subtype in Breast Cancer. Front Oncol 2021; 10:611191. [PMID: 33585234 PMCID: PMC7878528 DOI: 10.3389/fonc.2020.611191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
RNA N6-methyladenosine (m6A) methylation is the most prevalent epitranscriptomic modification in mammals, with a complex and fine-tuning regulatory system. Recent studies have illuminated the potential of m6A regulators in clinical applications including diagnosis, therapeutics, and prognosis. Based on six datasets of breast cancer in The Cancer Genome Atlas (TCGA) database and two additional proteomic datasets, we provide a comprehensive view of all the known m6A regulators in their gene expression, copy number variations (CNVs), DNA methylation status, and protein levels in breast tumors and their association with prognosis. Among four breast cancer subtypes, basal-like subtype exhibits distinct expression and genomic alteration in m6A regulators from other subtypes. Accordingly, four representative regulators (IGF2BP2, IGF2BP3, YTHDC2, and RBM15) are identified as basal-like subtype-featured genes. Notably, luminal A/B samples are subclassified into two clusters based on the methylation status of those four genes. In line with its similarity to basal-like subtype, cluster1 shows upregulation in immune-related genes and cell adhesion molecules, as well as an increased number of tumor-infiltrating lymphocytes. Besides, cluster1 has worse disease-free and progression-free survival, especially among patients diagnosed with stage II and luminal B subtype. Together, this study highlights the potential functions of m6A regulators in the occurrence and malignancy progression of breast cancer. Given the heterogeneity within luminal subtype and high risk of recurrence and metastasis in a portion of patients, the prognostic stratification of luminal A/B subtypes utilizing basal-featured m6A regulators may help to improve the accuracy of diagnosis and therapeutics of breast cancer.
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Affiliation(s)
- Lin Yang
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuangling Wu
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Chunhui Ma
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuhui Song
- China National Center for Bioinformation, Beijing, China.,National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Feng Jin
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.,School of Basic Medicine, Peking Union Medical College, Beijing, China.,Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
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44
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Berton MP, de Antunes Lemos MV, Seleguim Chud TC, Bonvino Stafuzza N, Kluska S, Amorim ST, Silva Ferlin Lopes L, Cravo Pereira AS, Bickhart D, Liu G, Galvão de Albuquerque L, Baldi F. Genome-wide association study between copy number variation regions and carcass- and meat-quality traits in Nellore cattle. ANIMAL PRODUCTION SCIENCE 2021. [DOI: 10.1071/an20275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Context
Indicine breeds are the main source of beef products in tropical and subtropical regions. However, genetic improvement for carcass- and meat-quality traits in zebu cattle have been limited and genomics studies concerning structural variations that influence these traits are essential.
Aim
The aim of this study was to perform a genome-wide association study between copy number variation regions (CNVRs) and carcass- and meat quality-traits in Nellore cattle.
Methods
In total, 3794 animals, males and females included, were genotyped using a 777962 single-nucleotide polymorphism platform of BovineHD BeadChip (777k; Illumina Inc.). Of these, 1751 Nellore bulls were slaughtered at 24 months of age for further carcass beef analysis. The following traits were studied: beef tenderness, marbling, rib-eye area, backfat thickness and meat colour (lightness, redness and yellowness). The CNV detection was conducted through PennCNV software. The association analyses were performed using CNVRuler software.
Key results
Several identified genomic regions were linked to quantitative trait loci associated with fat deposition (FABP7) and lipid metabolism (PPARA; PLA2 family; BCHE), extracellular matrix (INS; COL10A1), contraction (SLC34A3; TRDN) and muscle development (CAPZP). The gene-enrichment analyses highlighted biological mechanisms directly related to the metabolism and synthesis of lipids and fatty acids.
Conclusions
The large number of potential candidate genes identified within the CNVRs, as well as the functions and pathways identified, should help better elucidate the genetic mechanisms involved in the expression of beef and carcass traits in Nellore cattle. Several CNVRs harboured genes that might have a functional impact to improve the beef and carcass traits.
Implications
The results obtained contribute to upgrade the sensorial and organoleptic attributes of Nellore cattle and make feasible the genetic improvement of carcass- and meat-quality traits.
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45
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Li J, Fan Z, Shen F, Pendleton AL, Song Y, Xing J, Yue B, Kidd JM, Li J. Genomic Copy Number Variation Study of Nine Macaca Species Provides New Insights into Their Genetic Divergence, Adaptation, and Biomedical Application. Genome Biol Evol 2020; 12:2211-2230. [PMID: 32970804 PMCID: PMC7846157 DOI: 10.1093/gbe/evaa200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) can promote phenotypic diversification and adaptive evolution. However, the genomic architecture of CNVs among Macaca species remains scarcely reported, and the roles of CNVs in adaptation and evolution of macaques have not been well addressed. Here, we identified and characterized 1,479 genome-wide hetero-specific CNVs across nine Macaca species with bioinformatic methods, along with 26 CNV-dense regions and dozens of lineage-specific CNVs. The genes intersecting CNVs were overrepresented in nutritional metabolism, xenobiotics/drug metabolism, and immune-related pathways. Population-level transcriptome data showed that nearly 46% of CNV genes were differentially expressed across populations and also mainly consisted of metabolic and immune-related genes, which implied the role of CNVs in environmental adaptation of Macaca. Several CNVs overlapping drug metabolism genes were verified with genomic quantitative polymerase chain reaction, suggesting that these macaques may have different drug metabolism features. The CNV-dense regions, including 15 first reported here, represent unstable genomic segments in macaques where biological innovation may evolve. Twelve gains and 40 losses specific to the Barbary macaque contain genes with essential roles in energy homeostasis and immunity defense, inferring the genetic basis of its unique distribution in North Africa. Our study not only elucidated the genetic diversity across Macaca species from the perspective of structural variation but also provided suggestive evidence for the role of CNVs in adaptation and genome evolution. Additionally, our findings provide new insights into the application of diverse macaques to drug study.
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Affiliation(s)
- Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhenxin Fan
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Feichen Shen
- Department of Human Genetics, Medical School, University of Michigan
| | | | - Yang Song
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jeffrey M Kidd
- Department of Human Genetics, Medical School, University of Michigan
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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46
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Wang G, Guo S, Zhang W, Li Z, Xu J, Li D, Wang Y, Zhan Q. A Comprehensive Analysis of Alterations in DNA Damage Repair Pathways Reveals a Potential Way to Enhance the Radio-Sensitivity of Esophageal Squamous Cell Cancer. Front Oncol 2020; 10:575711. [PMID: 33178606 PMCID: PMC7596747 DOI: 10.3389/fonc.2020.575711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Esophageal squamous cell cancer (ESCC) is a common malignancy with a poor 5-year overall survival in China. Altered DNA damage repair (DDR) pathways are associated with a predisposition to cancer and contribute to therapeutic response and resistance in cancers. However, alterations of DDR pathway genes in ESCC are still largely unknown. In this study, we employed genome sequencing data of 192 samples, comparative genomic hybridization data of 123 cases, and gene expression microarray data of 119 patients to firstly perform a comprehensive analysis of the gene alterations of 7 DDR pathways in ESCC. Gene mutations and copy number variations (CNVs) were observed in all 7 DDR pathways, and especially, CNVs were the dominant alteration types. Compared with other pathways, two DNA double-strand break (DSB) repair pathways homologous recombination (HR) and non-homologous end joining (NHEJ), carried significant gene mutations and CNVs especially gene amplifications. Most genes including RAD54B, NBS1, RAD51B, and PRKDC were significantly amplified and over-expressed in ESCC. Amplification and high expression of DSB repair pathway genes were associated with poorer overall survival. Gene set variation analysis further showed that DSB repair pathways were up-regulated in ESCC. Besides, we firstly demonstrated that combination of mirin and NU7441, two inhibitors for HR and NHEJ respectively, with ionizing radiation treatment significantly enhanced DSBs, reduced clonogenic cell survival, inhibited cell proliferation, and promoted cell apoptosis in ESCC cells with DSB pathway gene amplification. These findings suggest that DSB repair pathways were significantly altered in ESCC and inhibiting DSB repair pathways might enhance the radio-sensitivity of ESCC with DSB repair up-regulation.
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Affiliation(s)
- Guangchao Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shichao Guo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhangfu Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiancheng Xu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dan Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
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47
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Zhang S, Wu S, Wan Y, Ye Y, Zhang Y, Ma Z, Guo Q, Zhang H, Xu L. Development of MR-based preoperative nomograms predicting DNA copy number subtype in lower grade gliomas with prognostic implication. Eur Radiol 2020; 31:2094-2105. [PMID: 33025175 DOI: 10.1007/s00330-020-07350-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 08/22/2020] [Accepted: 09/24/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVES We aimed to determine the value of MR-based preoperative nomograms in predicting DNA copy number (CN) subtype in lower grade glioma (LGG) patients. METHODS The overall survival (OS) data were analyzed. MRI data of 170 subjects were retrospectively analyzed. The correlation was explored by univariate and multivariate regression analysis. RESULTS CN2 subtype was associated with shortest median OS (CN2 subtype vs. others: 46.8 vs. 221.7 months, p < 0.05). The time-dependent receiver operating characteristic for the CN2 subtype was 0.80 (95% CI: 0.74-0.85) for survival at 1 year, 0.80 (95% CI: 0.75-0.85) for survival at 2 years, and 0.77 (95% CI: 0.73-0.83) for survival at 3 years. On multivariate analysis, hemorrhage (OR: 0.118; p < 0.001; 95% CI: 0.037-0.376), poorly defined margin (OR: 4.592; p < 0.001; 95% CI: 1.965-10.730), extranodular growth (OR: 0.247; p = 0.006; 95% CI: 0.091-0.671), and volume ≥ 60 cm3 (OR: 4.734.256; p < 0.001; 95% CI: 2.051-10.924) were associated with CN1 subtype (AUC: 0.781). Proportion CE tumor (OR: 5.905; p = 0.007; 95% CI: 1.622-21.493), extranodular growth (OR: 9.047; p = 0.001; 95% CI: 2.349-34.846), width ≥ median (OR: 0.231; p = 0.049; 95% CI: 0.054-0.998), and depth ≥ median (OR: 0.192; p = 0.023; 95% CI: 0.046-0.799) were associated with CN2 subtype (AUC: 0.854). Necrosis/cystic (OR: 6.128; p = 0.007; 95% CI: 1.635-22.968), hemorrhage (OR: 5.752; p = 0.002; 95% CI: 1.953-16.942), poorly defined margin (OR: 0.164; p < 0.001; 95% CI: 0.063-0.427), and volume ≥ median (OR: 4.422; p < 0.001; 95% CI: 1.925-10.160) were associated with CN3 subtype (AUC: 0.808). All three nomograms showed good discrimination and calibration. Decision curve analysis supported that all nomograms were clinically useful. The average accuracy of the tenfold cross-validation was 0.680 (CN1), 0.794 (CN2), and 0.894 (CN3), respectively. CONCLUSIONS The shortest OS was observed in patients with CN2 subtype. This preliminary radiogenomics analysis revealed that the MR-based preoperative nomograms provide individualized prediction of DNA copy number subtype in LGG patients. KEY POINTS • This preliminary radiogenomics analysis of LGG revealed that the MR-based preoperative nomograms provide individualized prediction of DNA copy number subtype in LGG patients. • The AUC for the ROC curve was 0.781 for CN1 subtype, 0.854 for CN2 subtype, and 0.808 for CN3 subtype. Decision curve analysis supported that all nomograms were clinically useful. • The sensitivity was 0.779 (CN1), 0.731 (CN2), and 0.851 (CN3), respectively. The specificity was 0.664 (CN1), 0.872 (CN2), and 0.625 (CN3), respectively. And the accuracy was 0.717 (CN1), 0.849 (CN2), and 0.692 (CN3), respectively.
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Affiliation(s)
- Siwei Zhang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Shanshan Wu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Yun Wan
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Yongsong Ye
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Ying Zhang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Zelan Ma
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Quanlan Guo
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Hongdan Zhang
- Guangdong General Hospital, Guangzhou, People's Republic of China
| | - Li Xu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine & Guangdong Provincial Hospital of Chinese Medicine, 111 Da De Lu, Guangzhou, 510120, Guangdong Province, People's Republic of China.
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He QE, Tong YF, Ye Z, Gao LX, Zhang YZ, Wang L, Song K. A multiple genomic data fused SF2 prediction model, signature identification, and gene regulatory network inference for personalized radiotherapy. Technol Cancer Res Treat 2020; 19:1533033820909112. [PMID: 32329416 PMCID: PMC7225787 DOI: 10.1177/1533033820909112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Radiotherapy is one of the most important cancer treatments, but its response varies greatly among individual patients. Therefore, the prediction of radiosensitivity, identification of potential signature genes, and inference of their regulatory networks are important for clinical and oncological reasons. Here, we proposed a novel multiple genomic fused partial least squares deep regression method to simultaneously analyze multi-genomic data. Using 60 National Cancer Institute cell lines as examples, we aimed to identify signature genes by optimizing the radiosensitivity prediction model and uncovering regulatory relationships. A total of 113 signature genes were selected from more than 20,000 genes. The root mean square error of the model was only 0.0025, which was much lower than previously published results, suggesting that our method can predict radiosensitivity with the highest accuracy. Additionally, our regulatory network analysis identified 24 highly important ‘hub’ genes. The data analysis workflow we propose provides a unified and computational framework to harness the full potential of large-scale integrated cancer genomic data for integrative signature discovery. Furthermore, the regression model, signature genes, and their regulatory network should provide a reliable quantitative reference for optimizing personalized treatment options, and may aid our understanding of cancer progress mechanisms.
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Affiliation(s)
- Qi-En He
- School of Chemical Engineering and Technology, Tianjin University, 300350 Tianjin, China
| | - Yi-Fan Tong
- School of Chemical Engineering and Technology, Tianjin University, 300350 Tianjin, China
| | - Zhou Ye
- Department of Hematology and Oncology, Karamay Central Hospital of Xinjiang, 834000 Xinjiang, Uygur Autonomous Region, China
| | - Li-Xia Gao
- Department of Hematology and Oncology, Karamay Central Hospital of Xinjiang, 834000 Xinjiang, Uygur Autonomous Region, China
| | - Yi-Zhi Zhang
- Department of Hematology and Oncology, Karamay Central Hospital of Xinjiang, 834000 Xinjiang, Uygur Autonomous Region, China
| | - Ling Wang
- The First Affiliated Hospital Oncology of Dalian Medical University, 116011 Liaoning, China
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, 300350 Tianjin, China
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49
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Aghaei H, Farhadi E, Akhtari M, Shahba S, Mostafaei S, Jamshidi A, Poursani S, Mahmoudi M, Nicknam MH. Copy number variation of IL17RA gene and its association with the ankylosing spondylitis risk in Iranian patients: a case-control study. BMC MEDICAL GENETICS 2020; 21:147. [PMID: 32650733 PMCID: PMC7350761 DOI: 10.1186/s12881-020-01078-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
Background Ankylosing spondylitis (AS) is considered as a subtype of spondyloarthritis (SpA) that mainly leads to fatigue, stiffness, spinal ankylosis, and impaired physical functions with reduced quality of life. Interleukin (IL)-17A provokes additional inflammatory mediators and recruits immune cells to the inflamed site. IL17 expression increased in various inflammatory disorders including psoriasis, rheumatoid arthritis, multiple sclerosis, crohn’s disease, and ankylosing spondylitis. The current study aimed to evaluate the association of IL17RA copy number changes with the susceptibility to AS and their correlation to IL17RA expression in Iranian population. Methods IL17RA copy number genotyping assessments were carried out in 455 AS patients and 450 healthy controls, using custom TaqMan CNV assays. TaqMan primers and probe were located in Chr.22:17109553 based on pre-designed IL17RA Copy Number Assay ID, Hs02339506_cn. mRNA expression of IL17RA was also measured by SYBR Green real-time polymerase chain reaction (PCR). Results A IL17RA copy number loss (< 2) was associated with AS compared to 2 copies as reference (OR:2.18, 95% CI: (1.38–3.44), P-value < 0.001) and increased the risk of AS. IL17RA mRNA expression showed a significant increase in peripheral blood mononuclear cells (PBMCs) of all AS individuals than controls. The mRNA expression level of 2 copies was significantly higher in AS patients. Conclusions Our findings revealed that a low copy number of IL17RA might confer a susceptibility risk to AS. However, it is probably not directly involved in the regulation of IL17RA mRNA expression. Epigenetic mechanisms like DNA methylation, post-transcriptional, and -translational modifications that regulate the expression of the genes may contribute in upregulation of IL17RA mRNA expression in the loss of gene copy number condition.
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Affiliation(s)
- Hamideh Aghaei
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Farhadi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Akhtari
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Shahba
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shayan Mostafaei
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shiva Poursani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran. .,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Hossein Nicknam
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. .,Molecular Immunology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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50
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Liu L, Wang G, Wang L, Yu C, Li M, Song S, Hao L, Ma L, Zhang Z. Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biol Direct 2020; 15:10. [PMID: 32539851 PMCID: PMC7294636 DOI: 10.1186/s13062-020-00264-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/04/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Glioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies have led to massive multi-omics datasets, there lacks of comprehensive integration of glioma datasets for uncovering candidate biomarker genes. RESULTS In this study, we collected a large-scale assemble of multi-omics multi-cohort datasets from worldwide public resources, involving a total of 16,939 samples across 19 independent studies. Through comprehensive molecular profiling across different datasets, we revealed that PRKCG (Protein Kinase C Gamma), a brain-specific gene detectable in cerebrospinal fluid, is closely associated with glioma. Specifically, it presents lower expression and higher methylation in glioma samples compared with normal samples. PRKCG expression/methylation change from high to low is indicative of glioma progression from low-grade to high-grade and high RNA expression is suggestive of good survival. Importantly, PRKCG in combination with MGMT is effective to predict survival outcomes in a more precise manner. CONCLUSIONS PRKCG bears the great potential for glioma diagnosis, prognosis and therapy, and PRKCG-like genes may represent a set of important genes associated with different molecular mechanisms in glioma tumorigenesis. Our study indicates the importance of computational integrative multi-omics data analysis and represents a data-driven scheme toward precision tumor subtyping and accurate personalized healthcare.
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Affiliation(s)
- Lin Liu
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangyu Wang
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
- Present Address: The Methodist Hospital Research Institute, 6670 Bertner Ave, Houston, TX, 77030, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Chunlei Yu
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengwei Li
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuhui Song
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Lili Hao
- China National Center for Bioinformation, Beijing, 100101, China
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Lina Ma
- China National Center for Bioinformation, Beijing, 100101, China.
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing, 100101, China.
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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