Biology subjects

Mikocziova, I.

Publications and source records attributed to Mikocziova, I..

4 recordsLinked to original sources

bioRxiv2025

Adipose tissue-derived fibroblasts engage in immune-stromal crosstalk during obesity-aggravated atherosclerosis in mice

Atherosclerosis involves changes in the vascular wall and surrounding perivascular adipose tissue, yet the cellular contributors to disease progression remain incompletely understood. Obesity exacerbates atherogenesis, but the cell types driving this aggravation are unclear. We aimed to define the key cell populations across tissues in a highly atherogenic mouse model under obese and normal-weight conditions and to identify obesity-associated cellular changes. We employed 5 single-cell RNA sequencing combined with antibody staining in Ldlr-/-Apob100/100 male mice fed either a high-fat or control diet. Aorta, perivascular and epididymal adipose tissues, and spleen were analyzed, with CD45 enrichment of aortic samples and CITE-seq using a 138-antibody panel. Key findings were validated in mice by immunohistochemistry and multiplexed immunofluorescence and explored in human aorta and carotid arteries using spatial transcriptomics. Analysis of [~]46,000 cells enabled characterization of cell states, gene enrichment, regulon activity, and inferred interactions. Adipose-derived fibroblast subsets displayed immune-associated transcriptional programs in obesity. Pi16 progenitor fibroblasts were reduced alongside marked PVAT remodeling, and the top mouse differentially expressed genes exhibited clear spatial patterning in human arteries.

genomics↗

bioRxiv2021

Individualized VDJ recombination predisposes the available Ig sequence space

The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individuals naive Ig repertoire, and consequently (auto)antigen recognition. VDJ recombination follows probabilistic rules that can be modeled statistically. So far, it remains unknown whether VDJ recombination rules differ between individuals. If these rules differed, identical (auto)antigen-specific Ig sequences would be generated with individual-specific probabilities, signifying that the available Ig sequence space is individual-specific. We devised a sensitivity-tested distance measure that enables inter-individual comparison of VDJ recombination models. We discovered, accounting for several sources of noise as well as allelic variation in Ig sequencing data, that not only unrelated individuals but also human monozygotic twins and even inbred mice possess statistically distinguishable immunoglobulin recombination models. This suggests that, in addition to genetic, there is also non-genetic modulation of VDJ recombination. We demonstrate that population-wide individualized VDJ recombination can result in orders of magnitude of difference in the probability to generate (auto)antigen-specific Ig sequences. Our findings have implications for immune receptor-based individualized medicine approaches relevant to vaccination, infection, and autoimmunity.

immunology↗

bioRxiv2021

Alternative splice variants and germline polymorphisms in human immunoglobulin light chain genes

Immunoglobulin loci are rich in germline polymorphisms and identification of novel polymorphic variants can be facilitated by germline inference of B cell receptor repertoires. Germline gene inference is complicated by somatic hypermutations, errors arising from PCR amplification, and DNA sequencing as well as from the varying length of reference alleles. Inference of light chain genes is even more challenging than inference of heavy chain genes due to large gene duplication events on the kappa locus as well as absence of D genes in the rearranged light chain transcripts. Here, we analyzed the light chain cDNA sequences from naive BCR repertoires of a Norwegian cohort of 100 individuals. We optimized light chain allele inference by tweaking parameters within TIgGER functions, extending the germline reference sequences, and establishing mismatch frequency patterns at polymorphic positions to filter out false positive candidates. As a result, we identified 48 previously unreported variants of light chain variable genes. Altogether, we selected 14 candidates for novel light chain polymorphisms for validation and successfully validated 11 by Sanger sequencing. Additional clustering of light chain 5UTR, L-PART1 and L-PART2 revealed partial intron retention in alternative splice variants in 11 kappa and 9 lambda V alleles. The alternatively spliced transcripts were only observed in genes with low expression levels, suggesting a possible role in expression regulation. Our results provide novel insight into germline variation in human light chain immunoglobulin loci.

genetics↗

bioRxiv2020

Polymorphisms in immunoglobulin heavy chain variable genes and their upstream regions

Germline variations in immunoglobulin genes influence the repertoire of B cell receptors and antibodies, and such polymorphisms may impact disease susceptibility. However, the knowledge of the genomic variation of the immunoglobulin loci is scarce. Here, we report 25 novel germline IGHV alleles as inferred from rearranged naive B cell cDNA repertoires of 98 individuals. Thirteen novel alleles were selected for validation, out of which ten were successfully confirmed by targeted amplification and Sanger sequencing of non-B cell DNA. Moreover, we detected a high degree of variability upstream of the V-region in the 5UTR, leader 1, and leader 2 sequences, and found that identical V-region alleles can differ in upstream sequences. Thus, we have identified a large genetic variation not only in the V-region but also in the upstream sequences of IGHV genes. Our findings challenge current approaches used for annotating immunoglobulin repertoire sequencing data.

immunology↗