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Biology subjects

Perin, L.

Publications and source records attributed to Perin, L..

2 recordsLinked to original sources

Vincristine treatment reverses podocyte damage in focal segmental glomerulosclerosis

IntroductionFocal segmental glomerulosclerosis (FSGS) is a significant cause of chronic kidney disease and triggered by podocyte damage which can result in cytoskeletal alterations leading to foot process effacement. Vincristine is a chemoprotective drug which alters cytoskeletal microtubules and has been used clinically to reverse FSGS. However, the mechanisms underlying the beneficial effect of vincristine are not understood. MethodsWe exposed immortalised human podocytes to serum obtained from an FSGS patient before, during, and after vincristine treatment. Using RNA-sequencing we determined the effect on the podocyte transcriptome alongside impacts on cytoskeletal structure and filtration barrier integrity using a glomerulus-on-a-chip model. ResultsWe describe an adult index FSGS patient successfully treated on multiple occasions by vincristine. Podocytes exposed to serum obtained during or after vincristine treatment contained lower levels of genes associated with microtubule function compared with cells stimulated with serum collected before treatment during disease presentation. Presentation serum altered the patterning of two key podocyte cytoskeletal components, tubulin and F-actin and increased albumin permeability, changes prevented by vincristine treatment. Immunoglobulin depletion experiments revealed that the podocyte damage initiated by the presentation serum was not due to circulating autoantibodies. Defects in tubulin patterning were observed when podocytes were exposed to serum from other FSGS patients, suggestive of a common disease mechanism. ConclusionVincristine therapy produces a milieu that protects against pathological changes induced by FSGS serum, associated with preservation of tubulin and F-actin organisation. The functional role of vincristine warrants further investigation, to advance our understanding of this alternative FSGS therapeutic.

cell biology↗

Differential detection workflows for multi-sample single-cell RNA-seq data

In single-cell transcriptomics, differential gene expression (DE) analyses typically focus on testing differences in the average expression of genes between cell types or conditions of interest. Single-cell transcriptomics, however, also has the promise to prioritise genes for which the expression differ in other aspects of the distribution. Here we develop a workflow for assessing differential detection (DD), which tests for differences in the average fraction of samples or cells in which a gene is detected. After benchmarking eight different DD data analysis strategies, we provide a unified workflow for jointly assessing DE and DD. Using simulations and two case studies, we show that DE and DD analysis provide complementary information, both in terms of the individual genes they report and in the functional interpretation of those genes.

bioinformatics↗