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Wilson CA, Postlethwait JH. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. G3 (BETHESDA, MD.) 2024; 14:jkae050. [PMID: 38466753 PMCID: PMC11075544 DOI: 10.1093/g3journal/jkae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex-determination system with the major sex locus on the right arm of chromosome-4 (Chr4R) near the largest heterochromatic block in the genome, suggesting that Chr4R transcriptomics might differ from the rest of the genome. To test this hypothesis, we conducted an RNA-seq analysis of adult ZW ovaries and ZZ testes in the Nadia strain and identified 4 regions of Chr4 with different gene expression profiles. Unique in the genome, protein-coding genes in a 41.7 Mb section (Region-2) were expressed in testis but silent in ovary. The AB lab strain, which lacks sex chromosomes, verified this result, showing that testis-biased gene expression in Region-2 depends on gonad biology, not on sex-determining mechanism. RNA-seq analyses in female and male brains and livers validated reduced transcripts from Region-2 in somatic cells, but without sex specificity. Region-2 corresponds to the heterochromatic portion of Chr4R and its content of genes and repetitive elements distinguishes it from the rest of the genome. Region-2 lacks protein-coding genes with human orthologs; has zinc finger genes expressed early in zygotic genome activation; has maternal 5S rRNA genes, maternal spliceosome genes, a concentration of tRNA genes, and a distinct set of repetitive elements. The colocalization of (1) genes silenced in ovaries but not in testes that are (2) expressed in embryos briefly at the onset of zygotic genome activation; (3) maternal-specific genes for translation machinery; (4) maternal-specific spliceosome components; and (5) adjacent genes encoding miR-430, which mediates maternal transcript degradation, suggest that this is a maternal-to-zygotic-transition gene regulatory block.
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Wilson CA, Postlethwait JH. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570431. [PMID: 38106184 PMCID: PMC10723407 DOI: 10.1101/2023.12.06.570431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex determination system with the major sex locus on the right arm of chromosome-4 (Chr4R) near the largest heterochromatic block in the genome, suggesting the hypothesis that the Chr4R transcriptome might be different from the rest of the genome. We conducted an RNA-seq analysis of adult ZW ovaries and ZZ testes and identified four regions of Chr4 with different gene expression profiles. Unique in the genome, protein-coding genes in a 41.7 Mb section (Region-2) were expressed in testis but silent in ovary. The AB lab strain, which lacks sex chromosomes, verified this result, showing that testis-biased gene expression in Region-2 depends on gonad biology, not on sex-determining mechanism. RNA-seq analyses in female and male brain and liver validated few transcripts from Region-2 in somatic cells, but without sex-specificity. Region-2 corresponds to the heterochromatic portion of Chr4R and its content of genes and repetitive elements distinguishes it from the rest of the genome. In Region-2, protein-coding genes lack human orthologs; it has zinc finger genes expressed early in zygotic genome activation; it has maternal 5S rRNA genes, maternal spliceosome genes, a concentration of tRNA genes, and an distinct set of repetitive elements. The colocalization of 1) genes silenced in ovaries but not in testes that are 2) expressed in embryos briefly at the onset of zygotic genome activation; 3) maternal-specific genes for translation machinery; 4) maternal-specific spliceosome components; and 4) adjacent genes encoding miR-430, which mediates maternal transcript degradation, suggest that this is a Maternal-to-Zygotic-Transition Gene Regulatory Block.
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Tornheim JA, Madugundu AK, Paradkar M, Fukutani KF, Queiroz ATL, Gupte N, Gupte AN, Kinikar A, Kulkarni V, Balasubramanian U, Sreenivasamurthy S, Raja R, Pradhan N, Shivakumar SVBY, Valvi C, Hanna LE, Andrade BB, Mave V, Pandey A, Gupta A. Transcriptomic Profiles of Confirmed Pediatric Tuberculosis Patients and Household Contacts Identifies Active Tuberculosis, Infection, and Treatment Response Among Indian Children. J Infect Dis 2021; 221:1647-1658. [PMID: 31796955 DOI: 10.1093/infdis/jiz639] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/03/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Gene expression profiling is emerging as a tool for tuberculosis diagnosis and treatment response monitoring, but limited data specific to Indian children and incident tuberculosis infection (TBI) exist. METHODS Sixteen pediatric Indian tuberculosis cases were age- and sex-matched to 32 tuberculosis-exposed controls (13 developed incident TBI without subsequent active tuberculosis). Longitudinal samples were collected for ribonucleic acid sequencing. Differential expression analysis generated gene lists that identify tuberculosis diagnosis and tuberculosis treatment response. Data were compared with published gene lists. Population-specific risk score thresholds were calculated. RESULTS Seventy-one genes identified tuberculosis diagnosis and 25 treatment response. Within-group expression was partially explained by age, sex, and incident TBI. Transient changes in gene expression were identified after both infection and treatment. Application of 27 published gene lists to our data found variable performance for tuberculosis diagnosis (sensitivity 0.38-1.00, specificity 0.48-0.93) and treatment response (sensitivity 0.70-0.80, specificity 0.40-0.80). Our gene lists found similarly variable performance when applied to published datasets for diagnosis (sensitivity 0.56-0.85, specificity 0.50-0.85) and treatment response (sensitivity 0.49- 0.86, specificity 0.50-0.84). CONCLUSIONS Gene expression profiles among Indian children with confirmed tuberculosis were distinct from adult-derived gene lists, highlighting the importance of including distinct populations in differential gene expression models.
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Affiliation(s)
- Jeffrey A Tornheim
- Center for Clinical Global Health Education, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anil K Madugundu
- Institute of Bioinformatics, Bangalore, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India.,Department of Laboratory Medicine and Pathology and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mandar Paradkar
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Kiyoshi F Fukutani
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil.,Faculdade de Tecnologia e Ciências (FTC), Salvador, Brazil
| | - Artur T L Queiroz
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil
| | - Nikhil Gupte
- Center for Clinical Global Health Education, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Akshay N Gupte
- Center for Clinical Global Health Education, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Aarti Kinikar
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Vandana Kulkarni
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Usha Balasubramanian
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Sreelakshmi Sreenivasamurthy
- Institute of Bioinformatics, Bangalore, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Remya Raja
- Institute of Bioinformatics, Bangalore, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Neeta Pradhan
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | | | - Chhaya Valvi
- Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | | | - Bruno B Andrade
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil.,Multinational Organization Network Sponsoring Translational and Epidemiological Research (MONSTER) Initiative, Salvador, Brazil.,Faculdade de Tecnologia e Ciências (FTC), Salvador, Brazil.,Universidade Salvador (UNIFACS), Laureate Universities, Salvador, Brazil.,Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Brazil
| | - Vidya Mave
- Center for Clinical Global Health Education, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, Maharashtra, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, Bangalore, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Department of Laboratory Medicine and Pathology and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amita Gupta
- Center for Clinical Global Health Education, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Xiao N, Mansukhani NA, Mendes de Oliveira DF, Kibbe MR. Association of Author Gender With Sex Bias in Surgical Research. JAMA Surg 2019; 153:663-670. [PMID: 29590329 DOI: 10.1001/jamasurg.2018.0040] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Importance Previous studies demonstrate sex bias in surgical research. Female participants and investigators are underrepresented in surgical scientific research. Objectives To describe the distribution of male and female authors in 5 general-interest surgery journals, assess the association of author gender with sex bias, and explore whether investigators benefit from performing sex-inclusion research. Design, Setting, and Participants For this bibliometric analysis, data were abstracted from 1921 original, peer-reviewed articles published from January 1, 2011, through December 31, 2012, in Annals of Surgery, American Journal of Surgery, JAMA Surgery, The Journal of Surgical Research, and Surgery. Excluded articles pertained to a sex-specific disease or did not report the number of study participants. An additional 119 articles contained gender-ambiguous author names and were omitted. Data were analyzed from April to June 2017. Main Outcomes and Measures Male and female first and senior authors, number of female and male participants in each study, surgical specialty, and number of citations received per article. Results Of the 3604 authors of 1802 articles included in this study, 2791 first and senior authors (77.4%) were male and 813 (22.6%) were female. The prevalence of male and female authors was consistent across all 5 journals and among clinical and basic science research. Articles by female authors included a higher median number of female study participants compared with their male counterparts (27.5 vs 16.0; P = .01), but sex matched the inclusion of participants less frequently (36% vs 45%; P = .001). No sex-based differences occurred between male and female authors in reporting, statistical analysis, and discussion of the data or in the number of citations received. Compared with studies that did not report, analyze, or discuss data by sex, studies that performed sex-specific data reporting yielded a mean of 2.8 more citations (95% CI, 1.2-4.4; P = .001); those that performed statistical analysis, a mean of 3.5 more citations (95% CI, 1.8-5.1; P = .001); and those that discussed the data, a mean of 2.6 more citations (95% CI, 0.7-4.5; P = .001). Articles with a higher percentage of sex matching of participants also received more citations, with an increase of 1 citation per 4.8% (95% CI, 2.0%-7.7%; P = .001) increase in percentage of sex matching. Conclusions and Relevance Sex bias in surgical research is prevalent among male and female authors; however, female authors included proportionally more female participants in their studies compared with male authors. Notably, studies that addressed sex bias were rewarded by the scientific community with increased citations of their published work.
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Affiliation(s)
- Nicholas Xiao
- Department of Surgery, Northwestern University, Chicago, Illinois
| | | | | | - Melina R Kibbe
- Department of Surgery, Northwestern University, Chicago, Illinois.,Department of Surgery and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill.,Editor
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Mansukhani NA, Yoon DY, Teter KA, Stubbs VC, Helenowski IB, Woodruff TK, Kibbe MR. Determining If Sex Bias Exists in Human Surgical Clinical Research. JAMA Surg 2017; 151:1022-1030. [PMID: 27551816 DOI: 10.1001/jamasurg.2016.2032] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Importance Sex is a variable that is poorly controlled for in clinical research. Objectives To determine if sex bias exists in human surgical clinical research, to determine if data are reported and analyzed using sex as an independent variable, and to identify specialties in which the greatest and least sex biases exist. Design, Setting, and Participants For this bibliometric analysis, data were abstracted from 1303 original peer-reviewed articles published from January 1, 2011, through December 31, 2012, in 5 surgery journals. Main Outcomes and Measures Study type, location, number and sex of participants, degree of sex matching of included participants, and inclusion of sex-based reporting, statistical analysis, and discussion of data. Results Of 2347 articles reviewed, 1668 (71.1%) included human participants. After excluding 365 articles, 1303 remained: 17 (1.3%) included males only, 41 (3.1%) included females only, 1020 (78.3%) included males and females, and 225 (17.3%) did not document the sex of the participants. Although female participants represent more than 50% (n = 57 688 606) of the total number (115 377 213) included, considerable variability existed with the number of male (46 111 818), female (58 805 665), and unspecified (10 459 730) participants included among the journals, between US domestic and international studies, and between single vs multicenter studies. For articles included in the study, 38.1% (497 of 1303) reported these data by sex, 33.2% (432 of 1303) analyzed these data by sex, and 22.9% (299 of 1303) included a discussion of sex-based results. Sex matching of the included participants in the research overall was poor, with 45.2% (589 of 1303) of the studies matching the inclusion of both sexes by 50%. During analysis of the different surgical specialties, a wide variation in sex-based inclusion, matching, and data reporting existed, with colorectal surgery having the best matching of male and female participants and cardiac surgery having the worst. Conclusions and Relevance Sex bias exists in human surgical clinical research. Few studies included men and women equally, less than one-third performed data analysis by sex, and there was wide variation in inclusion and matching of the sexes among the specialties and the journals reviewed. Because clinical research is the foundation for evidence-based medicine, it is imperative that this disparity be addressed so that therapies benefit both sexes.
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Affiliation(s)
| | - Dustin Y Yoon
- Department of Surgery, Northwestern University, Chicago, Illinois
| | | | - Vanessa C Stubbs
- Department of Surgery, Northwestern University, Chicago, Illinois
| | | | - Teresa K Woodruff
- Department of Obstetrics and Gynecology, Northwestern University, Chicago, Illinois3Women's Health Research Institute, Northwestern University, Chicago, Illinois
| | - Melina R Kibbe
- Department of Surgery, Northwestern University, Chicago, Illinois3Women's Health Research Institute, Northwestern University, Chicago, Illinois4Editor, JAMA Surgery5now with Department of Surgery, University of North Carolina at Chapel Hill
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