Biology subjects

Kalinina, A.

Publications and source records attributed to Kalinina, A..

5 recordsLinked to original sources

bioRxiv2026

Molecular dissection of the ChAHP complex subunits Adnp and Chd4 reveals common and divergent functions in retinal development

Epigenetic remodelling is thought to regulate the progression of competence states in neural progenitor cells. Here, we examined the functions of the ChAHP chromatin remodelling complex during retinal development. ChAHP consists of the ATP-dependent nucleosome remodeller CHD4, the zinc finger and homeodomain transcription factor ADNP, and the HP1 heterochromatin proteins (Cbx1/3/5). Notably, both CHD4 and ADNP are genetically associated with neurodevelopmental disorders (NDDs), but ChAHP functions in neural development are not fully understood. In the retina, we found that both ADNP and CHD4 proteins were co-expressed ubiquitously in each cell type throughout development, and the two proteins formed a complex in vivo. Next, we generated retina-specific conditional knockouts (cKOs) to both Adnp and Chd4 using the Chx10-Cre driver. We observed phenotypic correspondence and divergence. Developmentally, we observed elevated cell death in both Adnp and Chd4 cKOs, but Adnp cKOs also exhibited deficits in progenitor numbers and proliferation. As a result, mature Adnp cKOs were hypoplastic with reductions in each cell type. We previously described a more complex phenotype in Chd4 cKOs, where cell fates were imbalanced and progenitor proliferation was prolonged, but these features were absent from the Adnp cKO. To understand how ChAHP regulates gene expression, we compared Adnp and Chd4 cKOs via scRNA-seq, which revealed common transcriptional signatures. However, Chd4 cKOs exhibited more severe effects on gene expression in line with its stronger effects on cell fate. We then performed cut&run-seq, which suggested that Adnp and Chd4 are recruited to the same genomic loci - many of which are also occupied by the Ctcf transcription factor. Taken together, our data suggest that ChAHP regulates retinal growth, but that CHD4 has additional ChAHP-independent functions in regulating progenitor fate decisions. These findings point to the idea that during neurogenesis, some brain regions may have greater dependence on ChAHP, and therefore greater vulnerability to genetic mutation.

developmental biology↗

bioRxiv2024

Mitotic Activity and DNA Maintenance of Adult Neural Stem Cells is Regulated by Beclin1

Beclin1 is a tumor suppressor gene that can regulate proliferation under pathological conditions. Whether Beclin1 has a role in regulating proliferation in physiological conditions remains unknown. Here, through the creation of an inducible transgenic mouse that removes Beclin1 from adult neural stem and progenitor cells (NSPCs) and their progeny we uncovered that Beclin1 is required cell-autonomously to sustain proliferating NSCPs in vivo and ex vivo. Flow cytometry analysis and single-cell RNA-sequencing show that Beclin1 is required for mitosis. Additional analysis of the proliferating NSPCs resolved by stage of cell cycle uncovered that Beclin1-null cells have a distinct differential developmental trajectory accompanied by downregulation of genes involved in chromosomal maintenance and upregulation of cell stress genes upon cell cycle exit. These effects align with DNA damage in Beclin1-null cells and ultimately result in less adult-born granular neurons. Together these data identify Beclin1 as a novel regulator of mitosis in adult NSPCs.

neuroscience↗

bioRxiv2021

Isolation of the side population from adult neurogenic niches enriches for endothelial cells

In stem cell research, DNA-binding dyes offer the ability to purify live stem cells using flow cytometry as they form a low-fluorescence side population due to the activity of ABC transporters. Adult neural stem cells exist within the lateral ventricle and dentate gyrus of the adult brain yet the ability of DNA-binding dyes to identify these adult stem cells as side populations remain untested. The following experiments utilize the efflux of a DNA-binding dye, Vyrbant DyeCycle Violet (DCV), to isolate bona fide side populations in the adult mouse dentate gyrus and SVZ and test their sensitivity to ABC transporter inhibitors. A distinct side population was found in both the adult lateral ventricle and dentate gyrus using DCV fluorescence and forward scatter instead of the conventional dual fluorescence approach. These side populations responded strongly to inhibition with the ABC transporter antagonists, verapamil and fumitremorgin C. The cells in the side population were identified as cerebrovascular endothelial cells characterized by their expression of CD31. These findings, therefore, suggest that the side population analysis provides an efficient method to purify endothelial cells, but not adult neural stem cells.

neuroscience↗

bioRxiv2020

Construction of mutant heparinase I with significantly increased specific activity.

The cleavage of heparin by heparin lyases showed great potential as a cost-effective and innoxious method for producing heparin with low molecular weight (LMWH). One of the most studied and sought heparin lyase is heparinase I (HepI). However, the industrial use of HepI was largely hampered by its low specific activity and thermal stability. In this article we describe increasing in specific heparinase I activity by stepwise site-directed mutagenesis. Thus after two cycles of mutagenesis, we obtained mutant heparinase I Flavobacterium heparinum with significantly increased specific activity (25%).

bioengineering↗

bioRxiv2018

Functional properties of CD8+ T cells under lymphopenic conditions

A peripheral pool of T lymphocytes consists of several functionally distinct populations of CD8+ T cells. One of the major surface markers that allow to define different populations of T cells are CD44 and CD62L. Expression profile of these markers depends on the functional status of T lymphocyte. Naive CD8+ T cells express CD62L and do not express CD44 (CD62LhiCD44lo), clones of T cells activated during the primary immune response lose CD62L and express CD44 (CD62LloCD44hi). Central memory CD8+ T cells express both CD44 and CD62L (CD44hiCD62Lhi). However expression of activation markers not always correlate with an antigen experience of T cell. It is known, that in lymphopenic conditions peripheral T cells undergo homeostatic proliferation and acquire the memory like surface phenotype CD44hiCD62Lhi, but data about functional activity of these cells remain controversial. We studied relationship between surface expression of the markers CD44 and CD62L and functional properties of CD8+ T cells under lymphopenic conditions. We proved that surface expression of CD44 in not the only condition for T lymphocyte to acquire the functional properties of memory T-cells. It means that identification of CD8 + T-memory cells based solely on an expression profile of surface markers is not completely correct and requires confirmation by functional tests. Moreover, results of our research may become of practical importance for blood transfusion and bone marrow transplantation.

immunology↗