1
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Findley TO, Palei AC, Cho KS, Zhao Z, Shi C, Mahajan G, Corno AF, Salazar J, McCullough L. Sex differences in metabolic adaptation in infants with cyanotic congenital heart disease. Pediatr Res 2024:10.1038/s41390-024-03291-4. [PMID: 38839995 DOI: 10.1038/s41390-024-03291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Female infants with congenital heart disease (CHD) face significantly higher postoperative mortality rates after adjusting for cardiac complexity. Sex differences in metabolic adaptation to cardiac stressors may be an early contributor to cardiac dysfunction. In adult diseases, hypoxic/ischemic cardiomyocytes undergo a cardioprotective metabolic shift from oxidative phosphorylation to glycolysis which appears to be regulated in a sexually dimorphic manner. We hypothesize sex differences in cardiac metabolism are present in cyanotic CHD and detectable as early as the infant period. METHODS RNA sequencing was performed on blood samples (cyanotic CHD cases, n = 11; controls, n = 11) and analyzed using gene set enrichment analysis (GSEA). Global plasma metabolite profiling (UPLC-MS/MS) was performed using a larger representative cohort (cyanotic CHD, n = 27; non-cyanotic CHD, n = 11; unaffected controls, n = 12). RESULTS Hallmark gene sets in glycolysis, fatty acid metabolism, and oxidative phosphorylation were significantly enriched in cyanotic CHD females compared to male counterparts, which was consistent with metabolomic differences between sexes. Minimal sex differences in metabolic pathways were observed in normoxic patients (both controls and non-cyanotic CHD cases). CONCLUSION These observations suggest underlying differences in metabolic adaptation to chronic hypoxia between males and females with cyanotic CHD. IMPACT Children with cyanotic CHD exhibit sex differences in utilization of glycolysis vs. fatty acid oxidation pathways to meet the high-energy demands of the heart in the neonatal period. Transcriptomic and metabolomic results suggest that under hypoxic conditions, males and females undergo metabolic shifts that are sexually dimorphic. These sex differences were not observed in neonates in normoxic conditions (i.e., non-cyanotic CHD and unaffected controls). The involved metabolic pathways are similar to those observed in advanced heart failure, suggesting metabolic adaptations beginning in the neonatal period may contribute to sex differences in infant survival.
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Affiliation(s)
- Tina O Findley
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston and Children's Memorial Hermann Hospital, Houston, TX, USA.
| | - Ana Carolina Palei
- Department of Surgery, University of Mississippi Medical Center, Jackson, MS, USA
| | - Kyung Serk Cho
- Center for Precision Health, School of Biomedical Informatics at the University of Texas Health Science Center Houston, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics at the University of Texas Health Science Center Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health at the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Caleb Shi
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Gouri Mahajan
- Department of Pharmacology and Toxicology/Biobank, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Jorge Salazar
- Children's Heart Institute, McGovern Medical School at the University of Texas Health Science Center at Houston and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Louise McCullough
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, USA
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2
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Salapa HE, Thibault PA, Libner CD, Ding Y, Clarke JPWE, Denomy C, Hutchinson C, Abidullah HM, Austin Hammond S, Pastushok L, Vizeacoumar FS, Levin MC. hnRNP A1 dysfunction alters RNA splicing and drives neurodegeneration in multiple sclerosis (MS). Nat Commun 2024; 15:356. [PMID: 38191621 PMCID: PMC10774274 DOI: 10.1038/s41467-023-44658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/22/2023] [Indexed: 01/10/2024] Open
Abstract
Neurodegeneration is the primary driver of disease progression in multiple sclerosis (MS) resulting in permanent disability, creating an urgent need to discover its underlying mechanisms. Herein, we establish that dysfunction of the RNA binding protein heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) results in differential of binding to RNA targets causing alternative RNA splicing, which contributes to neurodegeneration in MS and its models. Using RNAseq of MS brains, we discovered differential expression and aberrant splicing of hnRNP A1 target RNAs involved in neuronal function and RNA homeostasis. We confirmed this in vivo in experimental autoimmune encephalomyelitis employing CLIPseq specific for hnRNP A1, where hnRNP A1 differentially binds and regulates RNA, including aberrantly spliced targets identified in human samples. Additionally, dysfunctional hnRNP A1 expression in neurons caused neurite loss and identical changes in splicing, corroborating hnRNP A1 dysfunction as a cause of neurodegeneration. Collectively, these data indicate hnRNP A1 dysfunction causes altered neuronal RNA splicing, resulting in neurodegeneration in MS.
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Affiliation(s)
- Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Cole D Libner
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Yulian Ding
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
- Division of Biomedical Engineering, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada
| | - Joseph-Patrick W E Clarke
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Connor Denomy
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Catherine Hutchinson
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada
| | - Hashim M Abidullah
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - S Austin Hammond
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Landon Pastushok
- Advanced Diagnostics Research Laboratory, Department of Pathology and Lab Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Michael C Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7K 0M7, Canada.
- Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 0X8, Canada.
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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3
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Hu Qian S, Shi MW, Wang DY, Fear JM, Chen L, Tu YX, Liu HS, Zhang Y, Zhang SJ, Yu SS, Oliver B, Chen ZX. Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster. Brief Bioinform 2023; 24:bbad177. [PMID: 37232385 PMCID: PMC10505420 DOI: 10.1093/bib/bbad177] [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: 12/15/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
The volume of ribonucleic acid (RNA)-seq data has increased exponentially, providing numerous new insights into various biological processes. However, due to significant practical challenges, such as data heterogeneity, it is still difficult to ensure the quality of these data when integrated. Although some quality control methods have been developed, sample consistency is rarely considered and these methods are susceptible to artificial factors. Here, we developed MassiveQC, an unsupervised machine learning-based approach, to automatically download and filter large-scale high-throughput data. In addition to the read quality used in other tools, MassiveQC also uses the alignment and expression quality as model features. Meanwhile, it is user-friendly since the cutoff is generated from self-reporting and is applicable to multimodal data. To explore its value, we applied MassiveQC to Drosophila RNA-seq data and generated a comprehensive transcriptome atlas across 28 tissues from embryogenesis to adulthood. We systematically characterized fly gene expression dynamics and found that genes with high expression dynamics were likely to be evolutionarily young and expressed at late developmental stages, exhibiting high nonsynonymous substitution rates and low phenotypic severity, and they were involved in simple regulatory programs. We also discovered that human and Drosophila had strong positive correlations in gene expression in orthologous organs, revealing the great potential of the Drosophila system for studying human development and disease.
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Affiliation(s)
- Sheng Hu Qian
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng-Wei Shi
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan-Yang Wang
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Justin M Fear
- Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lu Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Xuan Tu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong-Shan Liu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan Zhang
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuai-Jie Zhang
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Shan-Shan Yu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian Oliver
- Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhen-Xia Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
- Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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4
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Feng Y, Yang M, Fan Z, Zhao W, Kim P, Zhou X. COVIDanno, COVID-19 annotation in human. Front Microbiol 2023; 14:1129103. [PMID: 37497545 PMCID: PMC10366449 DOI: 10.3389/fmicb.2023.1129103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 19 (COVID-19), has caused a global health crisis. Despite ongoing efforts to treat patients, there is no universal prevention or cure available. One of the feasible approaches will be identifying the key genes from SARS-CoV-2-infected cells. SARS-CoV-2-infected in vitro model, allows easy control of the experimental conditions, obtaining reproducible results, and monitoring of infection progression. Currently, accumulating RNA-seq data from SARS-CoV-2 in vitro models urgently needs systematic translation and interpretation. To fill this gap, we built COVIDanno, COVID-19 annotation in humans, available at http://biomedbdc.wchscu.cn/COVIDanno/. The aim of this resource is to provide a reference resource of intensive functional annotations of differentially expressed genes (DEGs) among different time points of COVID-19 infection in human in vitro models. To do this, we performed differential expression analysis for 136 individual datasets across 13 tissue types. In total, we identified 4,935 DEGs. We performed multiple bioinformatics/computational biology studies for these DEGs. Furthermore, we developed a novel tool to help users predict the status of SARS-CoV-2 infection for a given sample. COVIDanno will be a valuable resource for identifying SARS-CoV-2-related genes and understanding their potential functional roles in different time points and multiple tissue types.
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Affiliation(s)
- Yuzhou Feng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Mengyuan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhiwei Fan
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
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5
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Wapeesittipan P, Joshi A. Integrated analysis of robust sex-biased gene signatures in human brain. Biol Sex Differ 2023; 14:36. [PMID: 37221602 DOI: 10.1186/s13293-023-00515-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Sexual dimorphism is highly prominent in mammals with many physiological and behavioral differences between male and female form of the species. Accordingly, the fundamental social and cultural stratification factors for humans is sex. The sex differences are thought to emerge from a combination of genetic and environmental factors. It distinguishes individuals most prominently on the reproductive traits, but also affects many of the other related traits and manifest in different disease susceptibilities and treatment responses across sexes. Sex differences in brain have raised a lot of controversy due to small and sometimes contradictory sex-specific effects. Many studies have been published to identify sex-biased genes in one or several brain regions, but the assessment of the robustness of these studies is missing. We therefore collected huge amount of publicly available transcriptomic data to first estimate whether consistent sex differences exist and further explore their likely origin and functional significance. RESULTS AND CONCLUSION In order to systematically characterise sex-specific differences across human brain regions, we collected transcription profiles for more than 16,000 samples from 46 datasets across 11 brain regions. By systematic integration of the data from multiple studies, we identified robust transcription level differences in human brain across to identify male-biased and female-biased genes in each brain region. Firstly, both male and female-biased genes were highly conserved across primates and showed a high overlap with sex-biased genes in other species. Female-biased genes were enriched for neuron-associated processes while male-biased genes were enriched for membranes and nuclear structures. Male-biased genes were enriched on the Y chromosome while female-biased genes were enriched on the X chromosome, which included X chromosome inactivation escapees explaining the origins of some sex differences. Male-biased genes were enriched for mitotic processes while female-biased genes were enriched for synaptic membrane and lumen. Finally, sex-biased genes were enriched for drug-targets and more female-biased genes were affected by adverse drug reactions than male-biased genes. In summary, by building a comprehensive resource of sex differences across human brain regions at gene expression level, we explored their likely origin and functional significance. We have also developed a web resource to make the entire analysis available for the scientific community for further exploration, available at https://joshiapps.cbu.uib.no/SRB_app/.
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Affiliation(s)
- Pattama Wapeesittipan
- Department of Clinical Sciences, Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Anagha Joshi
- Department of Clinical Sciences, Computational Biology Unit, University of Bergen, Bergen, Norway.
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6
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Constitutively Active Androgen Receptor in Hepatocellular Carcinoma. Int J Mol Sci 2022; 23:ijms232213768. [PMID: 36430245 PMCID: PMC9699340 DOI: 10.3390/ijms232213768] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 11/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the predominant type of liver cancer and a leading cause of cancer-related death globally. It is also a sexually dimorphic disease with a male predominance both in HCC and in its precursors, non-alcoholic fatty liver disease (NAFLD)/non-alcoholic steatohepatitis (NASH). The role of the androgen receptor (AR) in HCC has been well documented; however, AR-targeted therapies have failed to demonstrate efficacy in HCC. Building upon understandings of AR in prostate cancer (PCa), this review examines the role of AR in HCC, non-androgen-mediated mechanisms of induced AR expression, the existence of AR splice variants (AR-SV) in HCC and concludes by surveying current AR-targeted therapeutic approaches in PCa that show potential for efficacy in HCC in light of AR-SV expression.
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7
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Ran X, Xiao J, Cheng F, Wang T, Teng H, Sun Z. Pan-cancer analyses of synonymous mutations based on tissue-specific codon optimality. Comput Struct Biotechnol J 2022; 20:3567-3580. [PMID: 35860410 PMCID: PMC9287186 DOI: 10.1016/j.csbj.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/22/2022] [Accepted: 07/03/2022] [Indexed: 11/24/2022] Open
Abstract
Developed tissue-specific codon optimality in 29 human tissues. Applied these to analyze synonymous mutations in ∼10,000 tumor and normal samples. Synonymous mutations frequently increase optimal codons in most cancer types. Synonymous mutations frequently increase optimal codons cell cycle-related genes. Frequency of optimal codon gain relates to proliferation, DDR deficiency, and survival.
Codon optimality has been demonstrated to be an important determinant of mRNA stability and expression levels in multiple model organisms and human cell lines. However, tissue-specific codon optimality has not been developed to investigate how codon optimality is usually perturbed by somatic synonymous mutations in human cancers. Here, we determined tissue-specific codon optimality in 29 human tissues based on mRNA expression data from the Genotype-Tissue Expression project. We found that optimal codons were associated with differentiation, whereas non-optimal codons were correlated with proliferation. Furthermore, codons biased toward differentiation displayed greater tissue specificity in codon optimality, and the tissue specificity of codon optimality was primarily present in amino acids with high degeneracy of the genetic code. By applying tissue-specific codon optimality to somatic synonymous mutations in 8532 tumor samples across 24 cancer types and to those in 416 normal cells across six human tissues, we found that synonymous mutations frequently increased optimal codons in tumor cells and cancer-related genes (e.g., genes involved in cell cycle). Furthermore, an elevated frequency of optimal codon gain was found to promote tumor cell proliferation in three cancer types characterized by DNA damage repair deficiency and could act as a prognostic biomarker for patients with triple-negative breast cancer. In summary, this study profiled tissue-specific codon optimality in human tissues, revealed alterations in codon optimality caused by synonymous mutations in human cancers, and highlighted the non-negligible role of optimal codon gain in tumorigenesis and therapeutics.
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Affiliation(s)
- Xia Ran
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyuan Xiao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Fang Cheng
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
| | - Huajing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
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8
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Chen S, Jin Y, Wang S, Xing S, Wu Y, Tao Y, Ma Y, Zuo S, Liu X, Hu Y, Chen H, Luo Y, Xia F, Xie C, Yin J, Wang X, Liu Z, Zhang N, Zech Xu Z, Lu ZJ, Wang P. Cancer type classification using plasma cell-free RNAs derived from human and microbes. eLife 2022; 11:75181. [PMID: 35816095 PMCID: PMC9273212 DOI: 10.7554/elife.75181] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/26/2022] [Indexed: 11/23/2022] Open
Abstract
The utility of cell-free nucleic acids in monitoring cancer has been recognized by both scientists and clinicians. In addition to human transcripts, a fraction of cell-free nucleic acids in human plasma were proven to be derived from microbes and reported to have relevance to cancer. To obtain a better understanding of plasma cell-free RNAs (cfRNAs) in cancer patients, we profiled cfRNAs in ~300 plasma samples of 5 cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer, and esophageal cancer) and healthy donors (HDs) with RNA-seq. Microbe-derived cfRNAs were consistently detected by different computational methods when potential contaminations were carefully filtered. Clinically relevant signals were identified from human and microbial reads, and enriched Kyoto Encyclopedia of Genes and Genomes pathways of downregulated human genes and higher prevalence torque teno viruses both suggest that a fraction of cancer patients were immunosuppressed. Our data support the diagnostic value of human and microbe-derived plasma cfRNAs for cancer detection, as an area under the ROC curve of approximately 0.9 for distinguishing cancer patients from HDs was achieved. Moreover, human and microbial cfRNAs both have cancer type specificity, and combining two types of features could distinguish tumors of five different primary locations with an average recall of 60.4%. Compared to using human features alone, adding microbial features improved the average recall by approximately 8%. In summary, this work provides evidence for the clinical relevance of human and microbe-derived plasma cfRNAs and their potential utilities in cancer detection as well as the determination of tumor sites.
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Affiliation(s)
- Shanwen Chen
- Division of General Surgery, Peking University First Hospital, Beijing, China.,Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yingchao Wu
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yongchen Ma
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Shuai Zuo
- Division of General Surgery, Peking University First Hospital, Beijing, China
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yichen Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Hongyan Chen
- 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
| | - Yuandeng Luo
- Institute of Hepatobiliary Surgery, The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Feng Xia
- Institute of Hepatobiliary Surgery, The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Chuanming Xie
- Institute of Hepatobiliary Surgery, The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer /Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihua Liu
- 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
| | - Ning Zhang
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, China.,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Pengyuan Wang
- Division of General Surgery, Peking University First Hospital, Beijing, China
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9
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Wang X, Hu W, Li X, Huang D, Li Q, Chan H, Zeng J, Xie C, Chen H, Liu X, Gin T, Wang MH, Cheng ASL, Kang W, To KF, Plewczynski D, Zhang Q, Chen X, Chan DCW, Ko H, Wong SH, Yu J, Chan MTV, Zhang L, Wu WKK. Single-Hit Inactivation Drove Tumor Suppressor Genes Out of the X Chromosome during Evolution. Cancer Res 2022; 82:1482-1491. [PMID: 35247889 DOI: 10.1158/0008-5472.can-21-3458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
Cancer-related genes are under intense evolutionary pressure. In this study, we conjecture that X-linked tumor suppressor genes (TSG) are not protected by the Knudson's two-hit mechanism and are therefore subject to negative selection. Accordingly, nearly all mammalian species exhibited lower TSG-to-noncancer gene ratios on their X chromosomes compared with nonmammalian species. Synteny analysis revealed that mammalian X-linked TSGs were depleted shortly after the emergence of the XY sex-determination system. A phylogeny-based model unveiled a higher X chromosome-to-autosome relocation flux for human TSGs. This was verified in other mammals by assessing the concordance/discordance of chromosomal locations of mammalian TSGs and their orthologs in Xenopus tropicalis. In humans, X-linked TSGs are younger or larger in size. Consistently, pan-cancer analysis revealed more frequent nonsynonymous somatic mutations of X-linked TSGs. These findings suggest that relocation of TSGs out of the X chromosome could confer a survival advantage by facilitating evasion of single-hit inactivation. SIGNIFICANCE This work unveils extensive trafficking of TSGs from the X chromosome to autosomes during evolution, thus identifying X-linked TSGs as a genetic Achilles' heel in tumor suppression.
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Affiliation(s)
- Xiansong Wang
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,CUHK Shenzhen Research Institute, Shenzhen, Guangdong, People's Republic of China
| | - Wei Hu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, People's Republic of China
| | - Xiangchun Li
- Public Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Dan Huang
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Qing Li
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Hung Chan
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Judeng Zeng
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Chuan Xie
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Huarong Chen
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Xiaodong Liu
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Tony Gin
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Maggie Haitian Wang
- CUHK Shenzhen Research Institute, Shenzhen, Guangdong, People's Republic of China.,Division of Biostatistics, Center for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | | | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Dariusz Plewczynski
- Center of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Qingpeng Zhang
- School of Data Science, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Xiaoting Chen
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Danny Cheuk Wing Chan
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Gerald Choa Neuroscience Center, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Ho Ko
- Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Gerald Choa Neuroscience Center, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Margaret K. L. Cheung Research Center for Management of Parkinsonism, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Sunny Hei Wong
- CUHK Shenzhen Research Institute, Shenzhen, Guangdong, People's Republic of China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Jun Yu
- CUHK Shenzhen Research Institute, Shenzhen, Guangdong, People's Republic of China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Matthew Tak Vai Chan
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,CUHK Shenzhen Research Institute, Shenzhen, Guangdong, People's Republic of China.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Lin Zhang
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,CUHK Shenzhen Research Institute, Shenzhen, Guangdong, People's Republic of China.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - William Ka Kei Wu
- Department of Anesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,CUHK Shenzhen Research Institute, Shenzhen, Guangdong, People's Republic of China.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, People's Republic of China.,State Key Laboratory of Digestive Diseases, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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10
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Shireman JM, Ammanuel S, Eickhoff JC, Dey M. Sexual dimorphism of the immune system predicts clinical outcomes in glioblastoma immunotherapy: A systematic review and meta-analysis. Neurooncol Adv 2022; 4:vdac082. [PMID: 35821678 PMCID: PMC9268746 DOI: 10.1093/noajnl/vdac082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Biological differences based on sex have been documented throughout the scientific literature. Glioblastoma (GBM), the most common primary malignant brain tumor in adults, has a male sex incidence bias, however, no clinical trial data examining differential effects of treatment between sexes currently exists. Method We analyzed genomic data, as well as clinical trials, to delineate the effect of sex on the immune system and GBM outcome following immunotherapy. Results We found that in general females possess enriched immunological signatures on gene set enrichment analysis, which also stratified patient survival when delineated by sex. Female GBM patients treated with immunotherapy had a statistically significant survival advantage at the 1-year compared to males (relative risk [RR] = 1.15; P = .0241). This effect was even more pronounced in vaccine-based immunotherapy (RR = 1.29; P = .0158). Conclusions Our study shows a meaningful difference in the immunobiology between males and females that also influences the overall response to immunotherapy in the setting of GBM.
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Affiliation(s)
- Jack M Shireman
- Department of Neurosurgery, University of Wisconsin School of Medicine and Public Health, UW Carbone Cancer Center, Madison, Wisconsin, USA
| | - Simon Ammanuel
- Department of Neurosurgery, University of Wisconsin School of Medicine and Public Health, UW Carbone Cancer Center, Madison, Wisconsin, USA
| | - Jens C Eickhoff
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Mahua Dey
- Department of Neurosurgery, University of Wisconsin School of Medicine and Public Health, UW Carbone Cancer Center, Madison, Wisconsin, USA
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11
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Liu W, Yu J, Wang YF, Shan QQ, Wang YX. Selection of suitable internal controls for gene expression normalization in rats with spinal cord injury. Neural Regen Res 2021; 17:1387-1392. [PMID: 34782586 PMCID: PMC8643046 DOI: 10.4103/1673-5374.327350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
There is a lack of systematic research on the expression of internal control genes used for gene expression normalization in real-time reverse transcription polymerase chain reaction in spinal cord injury research. In this study, we used rat models of spinal cord hemisection to analyze the expression stability of 13 commonly applied reference genes: Actb, Ankrd27, CypA, Gapdh, Hprt1, Mrpl10, Pgk1, Rictor, Rn18s, Tbp, Ubc, Ubxn11, and Ywhaz. Our results show that the expression of Ankrd27, Ubc, and Tbp were stable after spinal cord injury, while Actb was the most unstable internal control gene. Ankrd27, Ubc, Tbp, and Actb were consequently used to investigate the effects of internal control genes with differing stabilities on the normalization of target gene expression. Target gene expression levels and changes over time were similar when Ankrd27, Ubc, and Tbp were used as internal controls but different when Actb was used as an internal control. We recommend that Ankrd27, Ubc, and Tbp are used as internal control genes for real-time reverse transcription polymerase chain reaction in spinal cord injury research. This study was approved by the Administration Committee of Experimental Animals, Jiangsu Province, China (approval No. 20180304-008) on March 4, 2018.
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Affiliation(s)
- Wei Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
| | - Jie Yu
- Department of Nursing, The Affiliated Hospital of Nantong University; Department of Clinical Medicine, Medical School of Nantong University, Nantong, Jiangsu Province, China
| | - Yi-Fan Wang
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, Jiangsu Province, China
| | - Qian-Qian Shan
- Department of Radiotherapy and Oncology, The Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Ya-Xian Wang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, National Medical Products Administration (NMPA) Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, Jiangsu Province, China
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12
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Faranda AP, Shihan MH, Wang Y, Duncan MK. The effect of sex on the mouse lens transcriptome. Exp Eye Res 2021; 209:108676. [PMID: 34146586 DOI: 10.1016/j.exer.2021.108676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 02/08/2023]
Abstract
The transcriptome of mammalian tissues differs between males and females, and these differences can change across the lifespan, likely regulating known sexual dimorphisms in disease prevalence and severity. Cataract, the most prevalent disease of the ocular lens, occurs at similar rates in young individuals, but its incidence is elevated in older women compared to men of the same age. However, the influence of sex on the lens transcriptome was unknown. RNAseq based transcriptomic profiling of young adult C57BL/6J mouse lens epithelial and fiber cells revealed that few genes are differentially expressed between the sexes. In contrast, lens cells from aged (24 month old) male and female C57BL/6J mice differentially expressed many genes, including several whose expression is lens preferred. Like cataracts, posterior capsular opacification (PCO), a major sequela of cataract surgery, may also be more prevalent in women. Lens epithelial cells isolated from mouse eyes 24 h after lens fiber cell removal exhibited numerous transcriptomic differences between the sexes, including genes implicated in complement cascades and extracellular matrix regulation, and these differences are much more pronounced in aged mice than in young mice. These results provide an unbiased basis for future studies on how sex affects the lens response to aging, cataract development, and cataract surgery.
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Affiliation(s)
- Adam P Faranda
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA
| | - Mahbubul H Shihan
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA
| | - Yan Wang
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA
| | - Melinda K Duncan
- Department of Biological Sciences University of Delaware, Newark, DE, 19716, USA.
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13
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Sex-specific responses to cold in a very cold-tolerant, northern Drosophila species. Heredity (Edinb) 2021; 126:695-705. [PMID: 33510465 PMCID: PMC8182794 DOI: 10.1038/s41437-020-00398-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 01/30/2023] Open
Abstract
Organisms can plastically alter resource allocation in response to changing environmental factors. For example, in harsh conditions, organisms are expected to shift investment from reproduction toward survival; however, the factors and mechanisms that govern the magnitude of such shifts are relatively poorly studied. Here we compared the impact of cold on males and females of the highly cold-tolerant species Drosophila montana at the phenotypic and transcriptomic levels. Although both sexes showed similar changes in cold tolerance and gene expression in response to cold treatment, indicating that the majority of changes are concordant between the sexes, we identified a clear reduction in sexually dimorphic gene expression, suggesting that preparing for the colder season involves reducing investment in sex-specific traits. This reduction was larger in males than females, as expected if male sexual traits are more condition-dependent than female traits, as predicted by theory. Gene expression changes were primarily associated with shifts in metabolic profile, which likely play a role in increasing cold tolerance. Finally, we found that the expression of immune genes was reduced following cold treatment, suggesting that reduced investment in costly immune function may be important in helping flies survive colder periods.
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14
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Chen XI, Mei Y, Chen M, Jing D, He Y, Liu F, He K, Li F. InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6122465. [PMID: 33507270 PMCID: PMC7904046 DOI: 10.1093/database/baab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022]
Abstract
Sex determination and the regulation of sexual dimorphism are among the most fascinating topics in modern biology. As the most species-rich group of sexually reproducing organisms on Earth, insects have multiple sex determination systems. Though sex chromosomes and sex-biased genes are well-studied in dozens of insects, their gene sequences are scattered in various databases. Moreover, a shortage of annotation hinders the deep mining of these data. Here, we collected the chromosome-level sex chromosome data of 49 insect species, including 34 X chromosomes, 15 Z chromosomes, 5 W chromosomes and 2 Y chromosomes. We also obtained Y-linked contigs of four insects species—Anopheles gambiae, Drosophila innubila, Drosophila yakuba and Tribolium castaneum. The unannotated chromosome-level sex chromosomes were annotated using a standard pipeline, yielding a total of 123 030 protein-coding genes, 2 159 427 repeat sequences, 894 miRNAs, 1574 rRNAs, 5105 tRNAs, 395 snoRNAs (small nucleolar RNA), 54 snRNAs (small nuclear RNA) and 5959 other ncRNAs (non-coding RNA). In addition, 36 781 sex-biased genes were identified by analyzing 62 RNA-seq (RNA sequencing) datasets. Together with 5707 sex-biased genes from the Drosophila genus collected from the Sex-Associated Gene Database, we obtained a total of 42 488 sex-biased genes from 13 insect species. All these data were deposited into InSexBase, a new user-friendly database of insect sex chromosomes and sex-biased genes. Database URL:http://www.insect-genome.com/Sexdb/.
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Affiliation(s)
- X I Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yang Mei
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Mengyao Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Dong Jing
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yumin He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Feiling Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Kang He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Fei Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
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15
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Li H, Hou J, Chen Z, Zeng J, Ni Y, Li Y, Xiao X, Zhou Y, Zhang N, Long D, Liu H, Yang L, Bai X, Li Q, Li T, Che D, Li L, Wang X, Zhang P, Liao M. FifBase: a comprehensive fertility-associated indicators factor database for domestic animals. Brief Bioinform 2021; 22:6120284. [PMID: 33497436 DOI: 10.1093/bib/bbaa432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/13/2020] [Accepted: 12/23/2020] [Indexed: 11/15/2022] Open
Abstract
Fertility refers to the ability of animals to maintain reproductive function and give birth to offspring, which is an important indicator to measure the productivity of animals. Fertility is affected by many factors, among which environmental factors may also play key roles. During the past years, substantial research studies have been conducted to detect the factors related to fecundity, including genetic factors and environmental factors. However, the identified genes associated with fertility from countless previous studies are randomly dispersed in the literature, whereas some other novel fertility-related genes are needed to detect from omics-based datasets. Here, we constructed a fertility index factor database FifBase based on manually curated published literature and RNA-Seq datasets. During the construction of the literature group, we obtained 3301 articles related to fecundity for 13 species from PubMed, involving 2823 genes, which are related to 75 fecundity indicators or 47 environmental factors. Eventually, 1558 genes associated with fertility were filtered in 10 species, of which 1088 and 470 were from RNA-Seq datasets and text mining data, respectively, involving 2910 fertility-gene pairs and 58 fertility-environmental factors. All these data were cataloged into FifBase (http://www.nwsuaflmz.com/FifBase/), where the fertility-related factor information, including gene annotation and environmental factors, can be browsed, retrieved and downloaded with the user-friendly interface.
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Affiliation(s)
- Hao Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Junyao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ziyu Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingyu Zeng
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Ni
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Yayu Li
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Xia Xiao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaqi Zhou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ning Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Deyu Long
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongfei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Luyu Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyue Bai
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qun Li
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Tongtong Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Dongxue Che
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Leijie Li
- Department of Bioinformatics and Biostatistics, SJTU Yale Joint Center Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaodan Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Peng Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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16
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Schöneberg T, Liebscher I. Mutations in G Protein-Coupled Receptors: Mechanisms, Pathophysiology and Potential Therapeutic Approaches. Pharmacol Rev 2020; 73:89-119. [PMID: 33219147 DOI: 10.1124/pharmrev.120.000011] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There are approximately 800 annotated G protein-coupled receptor (GPCR) genes, making these membrane receptors members of the most abundant gene family in the human genome. Besides being involved in manifold physiologic functions and serving as important pharmacotherapeutic targets, mutations in 55 GPCR genes cause about 66 inherited monogenic diseases in humans. Alterations of nine GPCR genes are causatively involved in inherited digenic diseases. In addition to classic gain- and loss-of-function variants, other aspects, such as biased signaling, trans-signaling, ectopic expression, allele variants of GPCRs, pseudogenes, gene fusion, and gene dosage, contribute to the repertoire of GPCR dysfunctions. However, the spectrum of alterations and GPCR involvement is probably much larger because an additional 91 GPCR genes contain homozygous or hemizygous loss-of-function mutations in human individuals with currently unidentified phenotypes. This review highlights the complexity of genomic alteration of GPCR genes as well as their functional consequences and discusses derived therapeutic approaches. SIGNIFICANCE STATEMENT: With the advent of new transgenic and sequencing technologies, the number of monogenic diseases related to G protein-coupled receptor (GPCR) mutants has significantly increased, and our understanding of the functional impact of certain kinds of mutations has substantially improved. Besides the classical gain- and loss-of-function alterations, additional aspects, such as biased signaling, trans-signaling, ectopic expression, allele variants of GPCRs, uniparental disomy, pseudogenes, gene fusion, and gene dosage, need to be elaborated in light of GPCR dysfunctions and possible therapeutic strategies.
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Affiliation(s)
- Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig, Germany
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17
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Way GP, Zietz M, Rubinetti V, Himmelstein DS, Greene CS. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biol 2020; 21:109. [PMID: 32393369 PMCID: PMC7212571 DOI: 10.1186/s13059-020-02021-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 04/16/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Unsupervised compression algorithms applied to gene expression data extract latent or hidden signals representing technical and biological sources of variation. However, these algorithms require a user to select a biologically appropriate latent space dimensionality. In practice, most researchers fit a single algorithm and latent dimensionality. We sought to determine the extent by which selecting only one fit limits the biological features captured in the latent representations and, consequently, limits what can be discovered with subsequent analyses. RESULTS We compress gene expression data from three large datasets consisting of adult normal tissue, adult cancer tissue, and pediatric cancer tissue. We train many different models across a large range of latent space dimensionalities and observe various performance differences. We identify more curated pathway gene sets significantly associated with individual dimensions in denoising autoencoder and variational autoencoder models trained using an intermediate number of latent dimensionalities. Combining compressed features across algorithms and dimensionalities captures the most pathway-associated representations. When trained with different latent dimensionalities, models learn strongly associated and generalizable biological representations including sex, neuroblastoma MYCN amplification, and cell types. Stronger signals, such as tumor type, are best captured in models trained at lower dimensionalities, while more subtle signals such as pathway activity are best identified in models trained with more latent dimensionalities. CONCLUSIONS There is no single best latent dimensionality or compression algorithm for analyzing gene expression data. Instead, using features derived from different compression models across multiple latent space dimensionalities enhances biological representations.
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Affiliation(s)
- Gregory P Way
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, 10-131 SCTR 34th and Civic Center Blvd, Philadelphia, PA, 19104, USA
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Zietz
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, 10-131 SCTR 34th and Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Vincent Rubinetti
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, 10-131 SCTR 34th and Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Daniel S Himmelstein
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, 10-131 SCTR 34th and Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, 10-131 SCTR 34th and Civic Center Blvd, Philadelphia, PA, 19104, USA.
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, 19102, USA.
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