Biology subjects

Rai, A. J.

Publications and source records attributed to Rai, A. J..

3 recordsLinked to original sources

bioRxiv2025

A workflow using diaPASEF global quantitative proteomic analysis reveals extracellular vesicle biomarker candidates for non-invasive diagnostics in non-small cell lung cancer

Lung cancer is the second most diagnosed cancer in the world. Non-small cell lung cancer is the most common type of lung cancer in the United States. Tissue biopsy is the gold standard for detecting lung cancer but is highly invasive as it necessitates the extraction of a sample of tissue for histologic analysis. It also carries risks of bleeding and/or infection and is inconvenient from a patient perspective. The development of a minimally invasive test, such as one utilizing a blood or urine sample, and capable of providing accurate results for lung cancer detection and/or subtyping, would significantly enhance the clinical landscape and streamline patient care. In this study we utilize A549 and H1299 human lung cancer cell lines, differing in cell type, location within the lung, and genetic composition (Kras & p53 status), and employ diaPASEF for global quantitative proteomic analysis. We demonstrate that extracellular vesicle protein content provides enhanced resolution to differentiate between these two cell lines relative to protein lysate content and reveals alterations in signaling. Protein clusters are identified showing enrichment for distinct biological processes representing multiple gene ontology categories unique to each lung cancer subtype-oxidative phosphorylation, apical junction, and epithelial-mesenchymal transition. We subsequently delineate a short list of urine-detectable protein candidates that is prognostic in a second cohort of lung cancer patients. This list of protein candidates may be useful for the development of a non-invasive test to distinguish between these two subtypes of human lung cancer.

pathology↗

bioRxiv2023

MitoQuicLy: a high-throughput method for quantifying cell-free DNA from human plasma, serum, and saliva

Circulating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. To evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. Here, we describe MitoQuicLy: Mitochondrial DNA Quantification in cell-free samples by Lysis. We demonstrate high agreement between MitoQuicLy and the commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. Using 10 {micro}L of input volume with MitoQuicLy, we quantify cf-mtDNA levels from three commonly used plasma tube types, two serum tube types, and saliva. We detect, as expected, significant inter-individual differences in cf-mtDNA across different biofluids. However, cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Moreover, in a small sample of healthy women and men (n=34), we show that blood and saliva cf-mtDNAs correlate with clinical biomarkers differently depending on the sample used. The biological divergences revealed between biofluids, together with the lysis-based, cost-effective, and scalable MitoQuicLy protocol for biofluid cf-mtDNA quantification, provide a foundation to examine the biological origin and significance of cf-mtDNA to human health.

molecular biology↗

bioRxiv2021

Identifying Therapeutic Strategies in IgA Nephropathy through Comprehensive Transcriptomic Characterization

IgA nephropathy (IgAN) is an autoimmune disease and the most common primary glomerulonephritis. The four-hit hypothesis describes mechanism of the disease, from synthesis of galactose deficient IgA (GD-IgA), to recognition of GD-IgA by anti-glycan antibodies and deposition of the formed immune complex in the mesangium. Complement and coagulation cascade activation ensues, resulting in mesangial activation and cytokine release, podocyte injury, mesangial sclerosis and tubulointerstitial damage. Currently, there is no disease cure, and 30-40% of patients progress to end stage renal disease. Using complementary bioinformatic approaches, we demonstrate different levels of deviation of the transcriptome of the glomerulus in IgAN from normal, with the aim of identifying therapeutic targets. Approaches used herein include, deconvolution of the transcriptome to estimate immune constitution, co-regulation-based functional analysis of differentially expressed genes, modular co-expression analysis, network analysis of metabolic pathways and differential gene correlation analysis. We describe the immune composition in IgAN and the relatively low fold changes of the abundance of different immune cells and strength of immune signatures compared with control. Additionally, we identify enrichment of the intestinal network for IgA synthesis, repression of expression and dysregulation of networks of amino acid metabolism and PPAR signaling pathways in IgAN glomeruli. We also find loss of correlation between expression of matrix synthesizing and matrix degrading genes in IgAN. We conclude by discussing how therapies based on some nodes in these altered pathways described have been shown to be efficacious in IgAN and/or other inflammatory diseases and the potential of others in effective treatment.

bioinformatics↗