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Sudhakar DVS, Phanindranath R, Jaishankar S, Ramani A, Kalamkar KP, Kumar U, Pawar AD, Dada R, Singh R, Gupta NJ, Deenadayal M, Tolani AD, Sharma Y, Anand A, Gopalakrishnan J, Thangaraj K. Exome sequencing and functional analyses revealed CETN1 variants leads to impaired cell division and male fertility. Hum Mol Genet 2023; 32:533-542. [PMID: 36048845 DOI: 10.1093/hmg/ddac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 02/07/2023] Open
Abstract
Human spermatogenesis requires an orchestrated expression of numerous genes in various germ cell subtypes. Therefore, the genetic landscape of male infertility is highly complex. Known genetic factors alone account for at least 15% of male infertility. However, ~40% of infertile men remain undiagnosed and are classified as idiopathic infertile men. We performed exome sequencing in 47 idiopathic infertile men (discovery cohort), followed by replication study (40 variants in 33 genes) in 844 infertile men and 709 controls using Sequenom MassARRAY® based genotyping. We report 17 variants in twelve genes that comprise both previously reported (DNAH8, DNAH17, FISP2 and SPEF2) and novel candidate genes (BRDT, CETN1, CATSPERD, GMCL1, SPATA6, TSSK4, TSKS and ZNF318) for male infertility. The latter have a strong biological nexus to human spermatogenesis and their respective mouse knockouts are concordant with human phenotypes. One candidate gene CETN1, identified in this study, was sequenced in another independent cohort of 840 infertile and 689 fertile men. Further, CETN1 variants were functionally characterized using biophysical and cell biology approaches. We demonstrate that CETN1 variant- p.Met72Thr leads to multipolar cells, fragmented nuclei during mitosis leading to cell death and show significantly perturbed ciliary disassembly dynamics. Whereas CETN1-5' UTR variant; rs367716858 leads to loss of a methylation site and increased reporter gene expression in vitro. We report a total of eight novel candidate genes identified by exome sequencing, which may have diagnostic relevance and can contribute to improved diagnostic workup and clinical management of male infertility.
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Affiliation(s)
| | - Regur Phanindranath
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500007, India
| | - Shveta Jaishankar
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Anand Ramani
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf 40225, Germany
| | - Kaustubh P Kalamkar
- Institute for Neurophysiology, University of Cologne, Cologne D-50931, Germany
| | - Umesh Kumar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500007, India
| | - Asmita D Pawar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500007, India
| | - Rima Dada
- All India Institute of Medical Sciences, New Delhi, India
| | - Rajender Singh
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
| | | | | | | | - Yogendra Sharma
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500007, India.,Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, India
| | - Anuranjan Anand
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital Düsseldorf, Heinrich-Heine-Universität, Düsseldorf 40225, Germany
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500007, India.,Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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Evaluation of the association between centrosome amplification in tumor tissue of breast cancer patients and changes in the expression of CETN1 and CNTROB genes. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Structural Basis for the Functional Diversity of Centrins: A Focus on Calcium Sensing Properties and Target Recognition. Int J Mol Sci 2021; 22:ijms222212173. [PMID: 34830049 PMCID: PMC8622359 DOI: 10.3390/ijms222212173] [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: 09/27/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 11/23/2022] Open
Abstract
Centrins are a family of small, EF hand-containing proteins that are found in all eukaryotes and are often complexed with centrosome-related structures. Since their discovery, centrins have attracted increasing interest due to their multiple, diverse cellular functions. Centrins are similar to calmodulin (CaM) in size, structure and domain organization, although in contrast to CaM, the majority of centrins possess at least one calcium (Ca2+) binding site that is non-functional, thus displaying large variance in Ca2+ sensing abilities that could support their functional versatility. In this review, we summarize current knowledge on centrins from both biophysical and structural perspectives with an emphasis on centrin-target interactions. In-depth analysis of the Ca2+ sensing properties of centrins and structures of centrins complexed with target proteins can provide useful insight into the mechanisms of the different functions of centrins and how these proteins contribute to the complexity of the Ca2+ signaling cascade. Moreover, it can help to better understand the functional redundancy of centrin isoforms and centrin-binding proteins.
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Phanindranath R, Sudhakar DVS, Thangaraj K, Sharma Y. Conformational scanning of individual EF-hand motifs of calcium sensor protein centrin-1. Biochem Biophys Res Commun 2021; 570:67-73. [PMID: 34273620 DOI: 10.1016/j.bbrc.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Centrin-1, a Ca2+ sensor protein of the centrin family is a crucial player for cell division in eukaryotes and plays a key role in the microtubule organising centre. Despite being regarded as a calcium sensor with a matched structure to calmodulin/troponin C, the protein undergoes mild changes in conformation and binds Ca2+ with moderate affinity. We present an in-depth analysis of the Ca2+ sensing by individual EF-hand motifs of centrin-1 and address unsolved questions of the rationales for moderate affinity and conformational transitions of the protein. Employing the more sensitive approach of Trp scanning of individual EF-hand motif, we have undertaken an exhaustive investigation of Ca2+ binding to individual EF-hand motifs, named EF1 to EF4. All four EF-hand motifs of centrin-1 are structural as all of them bind both Ca2+ and Mg2+. EF1 and EF4 are the most flexible sites as they undergo drastic conformational changes following Ca2+ binding, whereas EF3 responds to Ca2+ minimally. On the other hand, EF2 moves towards the protein surface upon binding Ca2+. The independent filling mode of Ca2+ to EF-hand motifs and lack of intermotif communication explain the lack of cooperativity of binding, thus constraining centrin-1 to a moderate affinity binding protein. Thus, centrin-1 is distinct from other calcium sensors such as calmodulin.
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Affiliation(s)
| | | | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India; Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Yogendra Sharma
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India; Indian Institute of Science Education and Research (IISER) Berhampur, India.
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