Search bioRxiv⌕ Search

Biology subjects

Shwetar, J.

Publications and source records attributed to Shwetar, J..

2 recordsLinked to original sources

Donor HLA DQ reactive B cells clonally expand under chronic immunosuppression and include atypical CD21lowCD27- B cells with high avidity germline B cell receptors.

Long-term allograft survival is limited by humoral-associated chronic allograft rejection, suggesting inadequate constraint of humoral alloimmunity by contemporary immunosuppression. Heterogeneity in alloreactive B cells and the incomplete definition of which B cells participate in chronic rejection in immunosuppressed transplant recipients limits our ability to develop effective therapies. Using a double-fluorochrome single-HLA tetramer approach combined with single-cell in vitro culture, we investigated the B-cell receptor (BCR) repertoire characteristics, avidity, and phenotype of donor HLA-DQ reactive B cells in a transplant recipient with end-stage donor specific antibody (DSA)-associated cardiac allograft vasculopathy while receiving maintenance immunosuppression (tacrolimus, mycophenolate mofetil, prednisone). Donor DQB1*03:02/DQA1*03:01 (DQ8)-reactive IgG+ B cells were enriched for minimally mutated and germline encoded high avidity BCRs (median KD 4.26x10-09) with an atypical, antigen-experienced and proliferative phenotype (CD27-CD21lowCD71+CD11c+/-). These B cells coexisted with a smaller subset of more highly mutated, affinity matured IgG+CD27+ B cells. Circulating donor-reactive B cells and DSA remained detectable after rituximab, contrasting with the marked reduction in DSA after allograft explant and retransplant. Together, these findings define the persistence of germline high-avidity HLA-DQ alloreactive B cells and their co-existence with affinity matured clones that were both driven by the allograft despite conventional immunosuppression.

immunology↗

Proteogenomic analysis of aneuploidy reveals divergent types of gene expression regulation across cellular pathways

How cells control gene expression is a fundamental question. The relative contribution of protein-level and transcript-level regulation to this process remains unclear. Here we perform a proteogenomic analysis of tumors and untransformed cells containing somatic copy number alterations (SCNAs). By revealing how cells regulate transcript and protein abundances of SCNA-containing genes, we provide insights into the rules of gene regulation. While gene compensation mainly occurs at the protein level across tumor types, genes gained or lost show surprisingly low protein compensation in lung and high RNA compensation in colon cancer. Protein complex genes have a strong protein-level regulation while non-complex genes have a strong transcript-level regulation. Exceptions are plasma membrane protein complexes showing a very low protein-level regulation. Strikingly, we find a strong negative association between the degree of transcript-level and protein-level regulation across genes and pathways. Moreover, genes participating in the same pathway show similar degree of transcript- and protein-level regulation. Pathways including translation, splicing and mitochondrial function show a stronger protein-level regulation while cell adhesion and migration pathways show a stronger transcript-level regulation. These results suggest that the evolution of gene regulation is shaped by functional constraints and that many cellular pathways tend to evolve a predominant mechanism of gene regulation, possibly due to energetic constraints. HighlightsO_LIProteogenomic analyses of cancer SCNAs reveal tissue specificity in gene compensation. C_LIO_LIGenes gained or lost show surprisingly low protein compensation in lung cancer and unexpected RNA compensation in colon cancer. C_LIO_LIWe use DNA-RNA and RNA-protein correlations to infer the degree of RNA-level and protein-level regulation. C_LIO_LIProtein complex genes and non-complex genes show high protein-level and RNA-level regulation, respectively. C_LIO_LIPlasma membrane complexes are an exception showing more RNA-level than protein-level regulation than other complex genes. C_LIO_LIGenes participating in the same pathway show similar degree of RNA-level and protein-level regulation. C_LIO_LIThere is a strong negative relationship between the RNA- and protein-level regulation among pathways, suggesting that they are regulated either at the protein or at the RNA level. C_LIO_LIGenes involved in RNA processing and protein synthesis are upregulated in highly aneuploid tumors, especially at the protein level. C_LI

cell biology↗