Biology subjects

Albert, E. A.

Publications and source records attributed to Albert, E. A..

4 recordsLinked to original sources

bioRxiv2024

Systematic search for new HLA alleles in 4195 human 30x WGS samples

HLA (Human Leukocyte Antigens) is a highly polymorphic locus in the human genome which also has a high clinical significance. New alleles of HLA genes are constantly being discovered but mostly through the efforts of laboratories which primarily focus on HLA typing and are using field-specific experimental and data processing techniques, like enrichment of HLA region in high-throughput sequencing data. Nevertheless, a vast amount of whole genome sequencing (WGS) data was accumulated over the past years and continues to expand rapidly. Therefore it is an appealing possibility to identify new HLA alleles and refine the information on known alleles from already available WGS data. Currently there are many tools designed for HLA typing, e.g. assigning known alleles, from non HLA enriched WGS data, but none of them specifically tailored towards identification and immediate thorough description of new HLA alleles. Here we are presenting a pipeline HLAchecker, which is specifically designed to identify potentially new HLA alleles based on discrepancies between predicted HLA types, made by any other dedicated tool, and underlying raw 30x WGS data. HLAchecker reports structured in a way which simplifies further validation of potentially new HLA alleles and streamlines submission of alleles to appropriate databases. We validated this tool on 4195 30x WGS samples typed by HLA-HD, discovered 17 potentially new HLA alleles with substitutions in exonic regions and validated five randomly chosen alleles by Sanger sequencing.

bioinformatics↗

bioRxiv2023

Knockout of cyclin dependent kinases 8 and 19 leads to depletion of cyclin C and suppresses spermatogenesis and male fertility in mice

Paralogs CDK8 and CDK19 are regulatory kinases associated with the transcriptional Mediator complex. We have e generated mice with the systemic inducible Cdk8 knockout on the background of Cdk19 constitutive knockout. Cdk8/19 double knockout (iDKO) males, but not single Cdk8 and Cdk19 KO, had an atrophic reproductive system and were infertile. The iDKO males lacked postmeiotic spermatids and spermatocytes after meiosis I pachytene. Testosterone levels were decreased whereas the amounts of the luteinizing hormone were unchanged. Single cell RNA sequencing showed marked differences in the expression of steroidogenic genes (such as Cyp17a1, Star and Fads) in Leydig cells concomitant with alterations in Sertoli cells and spermatocytes likely associated with impaired synthesis of steroids. Star and Fads were also downregulated in cultivated Leydig cells after iDKO. The treatment of primary Leydig cells culture with a CDK8/19 inhibitor did not induce the same changes in gene expression as iDKO, and prolonged treatment of mice with a CDK8/19 inhibitor did not affect the size of testes. iDKO, in contrast to single knockouts or treatment with a CDK8/19 kinase inhibitor, led to depletion of cyclin C (CcnC), the binding partner of CDK8/19 that has been implicated in CDK8/19-independent functions. This suggests that the observed phenotype was likely mediated through kinase-independent activities of CDK8/19, such as CcnC stabilization.

developmental biology↗

bioRxiv2017

Micromanagment of stem cell proliferation by the Drosophila testis stem cell niche

Niches have traditionally been characterized as signalling microenvironments that allow stem cells to maintain their fate. This definition implicitly assumes that the various niche signals are integrated towards a binary fate decision between stemness and differentiation. However, observations in multiple systems have demonstrated that stem cell properties such as proliferation and self renewal can be uncoupled at the level of niche signalling input, which is incompatible with this simplified view. We have studied the role of the transcriptional regulator Zfh1, a shared target of the Hedgehog and Jak/Stat niche signalling pathways, in the somatic stem cells of the Drosophila testis. We found that Zfh1 binds and downregulates salvador and kibra, two tumour suppressor genes of the Hippo/Wts/Yki pathway, thereby restricting Yki activation and proliferation to the Zfh1 positive stem cells. These observations provide an unbroken link from niche signal input to an individual aspect of stem cell behaviour that does not, at any step, involve a fate decision. We discuss the relevance of our observations and other reports in the literature for an overall concept of stemness and niche function.\n\nSummary statementWe demonstrate that the fly testis niche controls stem cell proliferation by repressing Hippo pathway genes independent of a binary cell fate decision between stemness and proliferation.

developmental biology↗

bioRxiv2017

A cell based, high throughput assay for quantitative analysis of Hedgehog pathway activation using a Smoothened phosphorylation sensor

The Hedgehog (Hh) signalling cascade is conserved across evolution and plays an important role in development and disease. In the absence of Hh, activity of the key signal transducer Smoothened (Smo) is downregulated by the Hh receptor Patched (Ptc). However, the mechanisms underlying this inhibition, and especially its release upon ligand stimulation, are still poorly understood, in part because tools for directly following Smo activation at the subcellular level were long lacking. Here we present a high throughput, cell culture assay based on a fluorescent sensor for Drosophila Smo phosphorlyation. Using this approach we could first demonstrate that the graded response to increasing Hh levels observed at the population level can be traced back to threshold responses of individual cells exhibiting differential Hh sensitivity. Second, we screened a small molecule inhibitor library for regulators of Smo phosphorylation. We observed increased Smo sensor fluorescence with compounds aimed at two major target groups, the MAPK signalling cascade and polo and aurora kinases. Biochemical validation confirmed the screen results for selected inhibitors (dobrafenib, tak-733, volasertib) and revealed differences in the mode of Smo activation, demonstrating that the assay is in principle suitable for dissecting the cell biological basis of Hh pathway activation.

cell biology↗