Dynamics of the gene regulatory landscape in human spermatogenesis
File(s)
Author(s)
Bhaskaran, Jahnavi
Type
Thesis
Abstract
Spermatogenesis is a complex process in which cells undergo extensive changes, including the division of their genetic material and the exchange of histones with protamines, to ultimately produce mature haploid sperm. Little is known about the gene regulatory mechanisms driving spermatogenesis. Errors in this process can lead to infertility, which affects 10-15% of couples worldwide. Approximately half of these are cases of male factor infertility (Organization et al., 2023; Agarwal et al., 2021). However, only ∼30% of male infertility cases have a known cause (Tüttelmann et al., 2018).
In this thesis, we aim to better understand the process of human spermatogenesis. For this, we have used testis biopsies of men with healthy sperm production to generate single nucleus multiome data capturing gene expression and chromatin accessibility measurements from the same cell. We have obtained more than 19,000 high quality nuclei from three patients, representing all the expected germline stages as well as supporting somatic cell types. By providing a direct association between the two captured modalities, multiome analysis reveals novel regulators of lineage-specific genes in addition to identifying rare cell populations. Using this technique, I have identified eight new subpopulations of spermatogonia, including an intermediate state whose gene expression resembles undifferentiated spermatogonia but whose transcription factor motif accessibility resembles differentiating spermatogonia. I have also captured two separate branches of undifferentiated spermatogonia during commitment to differentiation. Each branch displays a distinct pattern of niche communication, including signalling interactions that are misregulated in infertility. Additionally, I have utilized the multiome data to computationally separate haploid cells into X- and Y-spermatids...
In this thesis, we aim to better understand the process of human spermatogenesis. For this, we have used testis biopsies of men with healthy sperm production to generate single nucleus multiome data capturing gene expression and chromatin accessibility measurements from the same cell. We have obtained more than 19,000 high quality nuclei from three patients, representing all the expected germline stages as well as supporting somatic cell types. By providing a direct association between the two captured modalities, multiome analysis reveals novel regulators of lineage-specific genes in addition to identifying rare cell populations. Using this technique, I have identified eight new subpopulations of spermatogonia, including an intermediate state whose gene expression resembles undifferentiated spermatogonia but whose transcription factor motif accessibility resembles differentiating spermatogonia. I have also captured two separate branches of undifferentiated spermatogonia during commitment to differentiation. Each branch displays a distinct pattern of niche communication, including signalling interactions that are misregulated in infertility. Additionally, I have utilized the multiome data to computationally separate haploid cells into X- and Y-spermatids...
Version
Open Access
Date Issued
2023-08-14
Date Awarded
01/11/2023
License URL
Advisor
Vaquerizas, Juanma
Publisher Department
Institute of Clinical Sciences
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)