Biology subjects

Kiełbasa, S. M.

Publications and source records attributed to Kiełbasa, S. M..

3 recordsLinked to original sources

bioRxiv2026

Multi-omic profiling of human thymic B cells reveals intrathymic Ig-class switching and differentiation into multiple memory B cell subsets

Primarily recognized as the site for T cell development, the thymus supports a complex interplay between thymic stromal cells and developing thymocytes, which is essential for T cell maturation and the establishment of central tolerance. Emerging evidence indicates that thymic B cells contribute to tolerance induction by functioning as antigen-presenting cells. However, their developmental pathways and functional roles remain poorly understood. Using tissue mass cytometry, we localized B cells in the thymus and their orientation towards other cells in the medulla. We characterized the heterogeneity of thymic B cells using single-cell RNA sequencing of cells isolated from human thymi, identifying naive, germinal center-like, plasma cell, and multiple memory B cell populations. We identified a distinct pre-B cell subset with local thymic B cell development potential, that can develop due to the inhibition of Notch signaling by Deltex1, a Notch antagonist. Using BCR repertoire analysis, we explored clonal diversity, somatic hypermutation patterns and class switch recombination of thymic B cells. Spectral flow cytometry further validated the surface phenotype of thymic B cell populations and confirmed the presence of distinct CD21-CD27- memory compartments with heterogeneous surface immunoglobulin isotype usage. In doing so we provide novel insights into the unique biology of human thymic B cells, their development, and their differentiation in the human thymus. We conclude that the human thymus supports local B cell development and differentiation into medullary memory-like populations that undergo class switching with limited somatic hypermutation, suggesting secondary lymphoid-like B cell programs adapted to central tolerance induction. One Sentence SummaryThe human thymus is not only a primary lymphoid organ for T cell development, but also a secondary site for the development and maturation of unique populations of B cells.

immunology↗

bioRxiv2024

CaClust: linking genotype to transcriptional heterogeneity of follicular lymphoma using BCR and exomic variants

Tumor tissues exhibit high genotypic and transcriptional heterogeneity, resulting from tumor evolution and affecting cancer progression and treatment. These two types of heterogeneity in follicular lymphoma were so far predominantly studied in separation. To comprehensively investigate the evolution and genotype to phenotype maps in follicular lymphoma, we introduce CaClust, a probabilistic graphical model that integrates deep whole exome, single-cell RNA and B-cell receptor sequencing data to infer clone genotypes, cell-to-clone mapping, and single-cell genotyping. CaClust outperforms a state-of-the-art model on simulated and patient data. In-depth analysis of 22492 single cells and whole exomes from four follicular lymphoma samples using CaClust gives insights into effects of driver mutations, follicular lymphoma evolution, and possible therapeutic targets. CaClust single-cell genotyping agrees with genotypes observed in an independent targeted resequencing experiment. Our approach is the first to evaluate the strength of genotype to phenotype links in follicular lymphoma in the evolutionary context of the disease.

bioinformatics↗

bioRxiv2020

CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells

BackgroundDrawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements. Follicular lymphoma, a malignancy of mature B cells that continuously acquire mutations in parallel in the exome and in B-cell receptor loci, presents a unique opportunity to align exome-derived mutations with B-cell receptor clonotypes as an independent measure for clonal evolution. ResultsHere, we propose CACTUS, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. We apply CACTUS to two follicular lymphoma patient samples, integrating three measurements: whole exome sequencing, single cell RNA sequencing, and B-cell receptor sequencing. CACTUS outperforms a predecessor model by confidently assigning cells and B-cell receptor clonotypes to the tumor clones. ConclusionsThe integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors. CACTUS opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies.

cancer biology↗