Biology subjects

Rajpal, D.

Publications and source records attributed to Rajpal, D..

6 recordsLinked to original sources

bioRxiv2024

Unveiling inverted D genes and D-D fusions in human antibody repertoires unlocks novel antibody diversity

Antibodies, fundamental to immune defense, derive their diversity primarily from the intricate rearrangement of variable (V), diversity (D), and joining (J) gene segments. Traditionally, D genes in the forward (5-3) direction contribute to this diversity by rearranging with V and J segments. However, the existence and significance of inverted D genes (InvDs), which are D genes oriented in the inverted (3-5) direction, were previously obscured by limitations in data and detection methods. Here, we carried out a comprehensive analysis of a large-scale public next-generation sequencing (NGS) dataset encompassing antibody repertoires from 13 healthy donors using a novel immunoinformatics workflow. Our analysis, for the first time, uncovers the existence of all 25 unique InvDs across all three reading frames within human antibody repertoires, including both naive and memory B cells. This finding challenges previous assumptions, revealing the extensive presence of InvDs and identifying a broad spectrum of D-D fusions, especially those involving InvDs. Notably, InvDs enrich for unique amino acids such as histidine, proline, and lysine, not commonly found in forward D genes, and exhibit reduced use of certain negatively charged and bulky amino acids, including aspartate, tryptophan, and methionine. The unique amino acid profile of InvDs discloses new diversity and functionality in the human antibody repertoire, evidenced by over two dozen documented antibodies featuring InvDs, targeting a wide array of antigens. By opening exciting avenues for immunogenetics research, including new chromatin compaction models, innovative antibody libraries, and advancements in antibody engineering, these findings hold promise for the development of novel therapeutics and vaccines.

immunology↗

bioRxiv2021

Microglia ferroptosis is prevalent in neurodegenerative disease and regulated by SEC24B

Iron dysregulation has been implicated in multiple neurodegenerative diseases, including Parkinsons Disease (PD), Amyotrophic Lateral Sclerosis (ALS), and Multiple Sclerosis (MS). One prominent feature of affected brain regions are iron-loaded microglia, but how iron overload influences microglia physiology and disease response is poorly understood. Here we show that microglia are highly susceptible to ferroptosis, an iron-dependent form of cell death. In a tri-culture of human iPSC-derived neurons, astrocytes, and microglia, under ferroptosis-inducing conditions, microglia undergo a drastic shift in cell state, with increased ferritin levels, disrupted glutathione homeostasis, and altered cytokine signaling. Similar ferroptosis-associated signature (FAS) microglia were uncovered in PD, and the signature was also found in a large cohort of PD patient blood samples, raising the possibility that ferroptosis can be identified clinically. We performed a genome-wide CRISPR screen which revealed a novel regulator of ferroptosis, the vesicle trafficking gene SEC24B. A small molecule screen also nominated several candidates which blocked ferroptosis, some of which are already in clinical use. These data suggest that ferroptosis sits at the interface of cell death and inflammation, and inhibition of this process in microglia and other brain cells may provide new ways for treating neurodegenerative disease.

neuroscience↗

bioRxiv2021

Single Cell Atlas of Human Putamen Reveals Disease Specific Changes in Synucleinopathies: Parkinson's Disease and Multiple System Atrophy

Understanding disease biology at a cellular level from disease specific tissues is imperative for effective drug development for complex neurodegenerative diseases. We profiled 87,086 nuclei from putamen tissue of healthy controls, Parkinsons Disease (PD), and Multiple System Atrophy (MSA) subjects to construct a comprehensive single cell atlas. Although both PD and MSA are manifestations of -synuclein protein aggregation, we observed that both the diseases have distinct cell-type specific changes. We see a possible expansion and activation of microglia and astrocytes in PD compared to MSA and controls. Contrary to PD microglia, we found absence of upregulated unfolded protein response in MSA microglia compared to controls. Differentially expressed genes in major cell types are enriched for genes associated with PD-GWAS loci. We found altered expression of major neurodegeneration associated genes -- SNCA, MAPT, LRRK2, and APP -- at cell-type resolution. We also identified disease associated gene modules using a network biology approach. Overall, this study creates an interactive atlas from synucleinopathies and provides major cell-type specific disease insights. Link to interactive atlas will be made available at the time of publication.

genomics↗

bioRxiv2021

Single Nuclei Sequencing of Human Putamen Oligodendrocytes Reveals Altered Heterogeneity and Disease-Associated Changes in Parkinson's Disease and Multiple System Atrophy

The role of oligodendrocytes in neurodegenerative diseases remains incompletely understood and largely unexplored at the single cell level. We profiled 87,086 single nuclei from human brain putamen region for healthy control, Parkinsons Disease (PD), and Multiple System Atrophy (MSA). Oligodendrocyte lineage cells were the dominant cell-type in the putamen with oligodendrocyte subpopulations clustered by transcriptomic variation found to exhibit diverse functional enrichment patterns, and this oligodendrocyte heterogeneity was altered in a disease-specific way. Among profiled oligodendrocyte subpopulations, differences in expression of SNCA, HAPLN2, MAPT, APP, and OPALIN were observed for PD and MSA compared with healthy controls. Intriguingly, greater activation of unfolded protein response pathway gene expression was observed in PD nuclei versus MSA. Using network analysis, we then identified specific PD- and MSA-correlated gene co-expression modules enriched with disease relevant pathways; the PD-correlated module was significantly enriched for Parkinsons Disease GWAS loci (p = 0.01046). Our analysis provides a broader understanding of oligodendrocyte heterogeneity and reveals distinctive oligodendrocyte pathological alterations associated with PD and MSA which may suggest potential novel therapeutic targets and new strategies for disease modification.

genomics↗

bioRxiv2021

Lysosomal-Immune Axis Is Associated with COVID 19 Disease Severity: Insights from Patient Single Cell Data

SARS-COV-2 has become a leading cause of illness, hospitalizations, and deaths worldwide yet heterogeneity in disease morbidity remains a conundrum. In this study, we analyzed publicly available single-cell RNA-seq data from 75076 cells sequenced from clinically staged COVID-19 patients using a network approach and identified lysosomal-immune axis as a factor significantly associated with disease severity. Our results suggest modulation of lysosomal-immune pathways may present a novel drug-targeting strategy to attenuate SARS-Cov-2 infections.

genomics↗

bioRxiv2019

Effect of topical soluble epoxide hydrolase inhibition in a preclinical diabetic wound healing model.

The objective of this study was to test a topical formulation of EPHX2 inhibitor, GSK2256294, in a dermal wound diabetic (db/db) mouse model. Comparisons were made between groups treated with EPHX2 inhibitor, matching vehicle control and a currently approved treatment for diabetic ulcers, becaplermin/Regranex, as a positive control which is highly efficacious in this model. Leptin receptor-deficient (db/db) male mice were sequentially assigned to treatment groups (N=10 per group) based on blood glucose levels and body weight. Mice were given a single 8 mm diameter full thickness wound on the back. Wounds were photographed and traced, and fresh test materials applied periodically with fresh dressing. Of ten mice treated with GSK2256294, three had completely healed wounds at the study conclusion, and 8/10 mice reached at least 50% closure. In the vehicle group, no mice achieved complete closure, and only 6/10 reached at least 50% closure by the study conclusion. Nine of ten wounds achieved complete closure in the positive control group by 21 days. Although the EPHX2 inhibitor results were indicative of efficacy, the single-sided p-value criterion of 0.05 was not met in this study.

physiology↗