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Novel Mutations of TSPY1 Gene Associate Spermatogenic Failure Among Men

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Abstract

Etiology of male infertility is intriguing owing to complex genetic regulation of human spermatogenesis and ethnic variations in genetic architecture of human populations. The present study characterizes the role of Y chromosome specific spermatogenic regulator testis-specific protein Y-encoded 1 (TSPY1) gene mutation in spermatogenic failure. This case-control study includes 163 cases of spermatogenic failure and 175 age-matched fertile men as controls. We found five novel base substitutions, namely, MT162695, MN879413, MN889982, MN889983, MN719943, two deletions MN734578 and MN734579, three novel insertions MN719941, MN719942 and MN719944 through Sanger’s dideoxy sequencing of TSPY1 gene reading frame. All these mutations exhibited strong association with male infertility. In silico analyses suggest prospective disruption in splice sites and alteration in different isoforms of TSPY1 transcripts and amino acid sequence in TSPY1 protein. The study provides novel evidence in favour of implication of TSPY1 gene in male fertility. The outcome sheds light to get insight into the issue of idiopathic male infertility in Bengali population.

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Data Availability

The datasets generated and analyzed during the current study are included in this article.

Code Availability

The original version of software programs is used for statistical modelling. Additionally, some free version software were used to conduct association studies.

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Acknowledgements

We are thankful to all the participating volunteers who gave their consents to use tissue samples. We are thankful to all the clinician medical staffs for their active cooperation in sample collection. The departmental instrumental facilities were supported by UGC-UPE II, DST-FIST, DST-PURSE program at the University of Calcutta. Pranab Paladhi is thankful to ICMR India, for providing him fellowship.

Funding

The study was supported financially by the grants from Indian Council for Medical Research, Grant Number: 5/10/FR/10/2015-RCH.

Author information

Authors and Affiliations

  1. Cytogenetics and Genomics Research Unit, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700019, India

    Pranab Paladhi, Saurav Dutta, Samudra Pal & Sujay Ghosh

  2. Institute of Reproductive Medicine (IRM), HB-36/A/3 1st Cross Rd Bidhannagar, Sector III, Bidhannagar, Kolkata, West Bengal, 700106, India

    Gunja Bose, Ratna Chattopadhyay & Baidyanath Chakravarty

  3. Department of Zoology, Bijoy Krishna Girls’ College (Affiliated to University of Calcutta), Howrah, West Bengal, India

    Papiya Ghosh

  4. Genome - The Fertility Centre, 61-E, Sarat Bose Road, Kolkata, West Bengal, 700025, India

    Indranil Saha

Authors
  1. Pranab Paladhi
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  4. Gunja Bose
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Contributions

SG conceptualized the project, designed the experiments and wrote the paper. PP performed the major experiments, analyzed data, reported the novel variants and wrote the paper. PG, SD and SP helped in experiments and data analysis. BC, RC, IS and GB recruited infertile as well as control individuals, confirmed diagnosis of the infertile patients and recorded epidemiological data. All authors approved the last version.

Corresponding author

Correspondence to Sujay Ghosh.

Ethics declarations

Ethics Approval

The study was conducted following the declaration of Helsinki and rules outlined by the Indian Council of Medical Research. Ethical approval was obtained by the ethics review board constituted by the University of Calcutta.

Consent to Participate

All the families consented to participate in the study.

Consent for Publication

All the families consented for publication of data based on their donated tissue and information.

Conflict of Interest

The authors declare no competing interests.

Web Resources

https://mutalyzer.nl/

http://biomodel.uah.es/en/lab/cybertory/analysis/trans.htm

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides

https://www.ncbi.nlm.nih.gov/orffinder/

https://web.expasy.org/translate/

http://genetics.bwh.harvard.edu/pph2/

https://www.regulationspotter.org/

http://provean.jcvi.org/index.php

https://sift.bii.a-star.edu.sg/

http://www.umd.be/HSF/

http://www.introni.it/splicing.html

https://gnomad.broadinstitute.org/variant/Y-9306347-G-A?dataset=gnomad_r2_1

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Supplementary Information

Below is the link to the electronic supplementary material.

43032_2021_839_MOESM1_ESM.pdf

Supplementary Information 1 Outcome of in silico analyses by Polyphen-2 program shows the effect of mutations MT162695 (NC_000024.10:g.9467148G>C), MN879413 (NC_000024.10:g.9467392C>T), MN889982 (NC_000024.10:g.9467443G>T) and MN719943 (NC_000024.10:g.9468104A>C) on TSPY1 transcript and protein (PDF 536 kb)

43032_2021_839_MOESM2_ESM.pdf

Supplementary Information 2 Outcome of in silico analyses by RegulationSpotter-program shows the effect of mutations MT162695 (NC_000024.10:g.9467148G>C), MN879413 (NC_000024.10:g.9467392C>T), MN889982 (NC_000024.10:g.9467443G>T), MN889983 (NC_000024.10:g.9467643G>A), MN719943 (NC_000024.10:g.9468104A>C) and rs566754601 (NC_000024.10:g.9468738G>A) on TSPY1 transcript and protein. (PDF 396 kb)

43032_2021_839_MOESM3_ESM.pdf

Supplementary Information 3 Outcome of in silico analyses by PROVEAN program shows the effect of mutations MT162695 (NC_000024.10:g.9467148G>C), MN879413 (NC_000024.10:g.9467392C>T), MN889982 (NC_000024.10:g.9467443G>T) and MN719943 (NC_000024.10:g.9468104A>C) on TSPY1 transcript and protein. (PDF 395 kb)

43032_2021_839_MOESM4_ESM.pdf

Supplementary Information 4 Outcome of in silico analyses by SIFT program shows the effect of mutations MT162695 (NC_000024.10:g.9467148G>C), MN879413 (NC_000024.10:g.9467392C>T), MN889982 (NC_000024.10:g.9467443G>T), MN719943 (NC_000024.10:g.9468104A>C), MN719944 (NC_000024.10:g.9468815_9468816insA) and MN734578 (NC_000024.10:g.9468830del) on TSPY1 transcript and protein. (PDF 575 kb)

43032_2021_839_MOESM5_ESM.pdf

Supplementary Information 5 Outcome of in silico analyses by Human-Splicing Finder program shows the effect of mutations MT162695(NC_000024.10:g.9467148G>C), MN879413(NC_000024.10:g.9467392C>T), MN889982(NC_000024.10:g.9467443G>T), MN889983(NC_000024.10:g.9467643G>A), MN719943(NC_000024.10:g.9468104A>C), MN734579(NC_000024.10:g.9468207del), MN719941(NC_000024.10:g.9468698_9468699insT), MN719942(NC_000024.10:g.9468711_9468712insG), rs566754601 (NC_000024.10:g.9468738G>A), MN719944(NC_000024.10:g.9468815_9468816insA) and MN734578(NC_000024.10:g.9468830del) on TSPY1 transcript and protein. (PDF 3316 kb)

Supplementary Information 6 Outcome of the Mutalyzer program. (PDF 910 kb)

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Paladhi, P., Dutta, S., Pal, S. et al. Novel Mutations of TSPY1 Gene Associate Spermatogenic Failure Among Men. Reprod. Sci. 29, 1241–1261 (2022). https://doi.org/10.1007/s43032-021-00839-1

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