Biology subjects

Sethi, M.

Publications and source records attributed to Sethi, M..

7 recordsLinked to original sources

bioRxiv2026

Proteomics of highly post-translationally modified proteins in kidney tubulointerstitium

Kidney disease affects over 850 million people and leads to degradation of the kidney cortical compartments and kidney failure. Interstitial fibrosis and tubular atrophy (IFTA) is a universal feature of chronic kidney disease, yet the sequence of tubulointerstitial matrix protein (matrisome) changes that underlie the development and progression of IFTA are not fully understood. In particular, post-translational modifications which may stabilize key matrisome components and result in irreversible and functionally detrimental interstitial fibrosis or tubular basement membrane thickening, have yet to be characterized. Post-translational modifications (e.g., acetylation) have been shown to contribute to kidney diseases, yet they have not been investigated in chronic kidney disease progression. Herein, we established feasibility of matrisome protein quantification in the tubulointerstitium, with concurrent matrisome protein post-translational modification quantification, in archived diagnostic human kidney biopsies, using laser capture microdissection, liquid chromatography tandem mass spectrometry (LC-MS/MS), and bioinformatics analysis. In this pilot study, we focused on two conditions associated with IFTA progression: diabetic nephropathy and kidney transplantation. We examined both healthy and chronically damaged tubulointerstitium in two human kidney biopsies, one representing each condition. We identified signature protein markers of tubulointerstitium (e.g., UMOD, SLC12A1) in abundance, confirming sample composition, and observed uniformity in protein abundance across replicates from the same biopsies. We found increases in certain collagen isoforms (COL1A1, COL6A3) and other ancillary proteins in areas of IFTA. We also successfully quantified post-translational modifications, confirming that hydroxylproline was the most abundant modification in healthy tubulointerstitium from the kidney transplant biopsy, and that hydroxyllysine was also highly abundant and could be confidently quantitated on two collagen isoforms (COL1A1, COL4A2). Lastly, we performed power analysis to determine the required sample size to achieve significant power and false discovery rate. Several proteins exhibited large Hedge effect sizes in the tubulointerstitium (ANPEP, PRODH2), indicating their potential usefulness as fibrosis signatures. Our study is a first step toward comprehensive characterization of tubulointerstitial matrisome changes, including post-translational modifications seen with IFTA progression. Subsequent studies will potentially reveal new molecular markers of key early events in chronic kidney disease progression, and new therapeutic targets for mitigating this process. Data are available via ProteomeXchange identifier PXD079025.

biochemistry↗

bioRxiv2026

Characterization of expression elements for an AAV delivered antibody in nonhuman primates when co-delivered with PD-L1

Successful AAV-expressed antibody therapy for HIV-1 requires broadly neutralizing antibody (bNAbs) concentrations and reduced immune responses to sustain viral suppression without ART. We have previously demonstrated that co-delivery of AAV-expressed PD-L1 reduces immune responses against HIV-1 bNAbs in rhesus macaques. Here we systematically evaluated six AAV9 transgene cassettes encoding 10-1074 with different promoter/intron combinations (CMV, CMV/R, CBA, CASI, CB7, EF1) across in vitro systems, immune-deficient mice, and in rhesus macaques. We show that both promoter and species selection, leads to differences in 10-1074 concentrations with the CB7 promoter leading to greatest expression in mice and CMV/R promoter in macaques. In addition to differences observed, loss of 10-1074 serum concentrations in macaques resulted in higher anti-drug antibody responses and antigen specific IFN-y T cell responses were focused on the 10-1074 heavy-chain variable region. Furthermore, inclusion of the WPRE greatly impacted 10-1074 expression leading to higher concentrations in both mice and nonhuman primates. Lastly, circulating 10-1074 in macaques retained neutralizing activity against diverse HIV-1 pseudovirus isolates. Together these results demonstrate how expression elements influence AAV-expressed antibodies in the context of co-delivery and highlight the need for further improvements to AAV transgene cassettes when co-delivered with AAV expressed PD-L1.

microbiology↗

bioRxiv2025

Viral lineage and mode of exposure modulate within host spatial dynamics of influenza A viruses

The upper and lower respiratory tracts (URT and LRT) present distinct environments for influenza A virus (IAV) replication. Their differential features have major implications for viral evolutionary dynamics, transmission potential, and pathogenesis. To investigate the implications of differential viral replication in the URT and LRT, we assessed dispersal of IAVs throughout the guinea pig respiratory system. Guinea pigs were inoculated intranasally with a 300 L volume to deliver inoculum to both the URT and LRT. Two strains were used to represent the circulating seasonal IAV lineages: influenza A/TX/50/2012 (H3N2) and influenza A/CA/07/2009 (H1N1) virus. The inclusion of a diverse genetic barcode enabled high-resolution tracing of viral dispersal for the H1N1 virus. While infectious virus was consistently detected in the URT, the H1N1 virus could be detected in LRT while the H3N2 virus could not. To determine whether replication of the H1N1 virus in the LRT extends to other modes of infection, virus distribution was evaluated following infection via aerosol exposure or transmission. Infectious virus in lung homogenates was observed in both cases, confirming the LRT tropism of the H1N1 virus. Sequencing genetic barcodes revealed that diversity was largely maintained in nasal samples and trachea but contracted upon dispersal to the lungs. This loss of diversity was associated with increased distance to and branching from the major airways, implicating long distance dispersal through the airways in imposing within-host population bottlenecks. These data underline the implications for within-host viral dynamics of the distinct environments of the upper and lower respiratory tracts. ImportanceThe upper (URT) and lower (LRT) respiratory tracts create different conditions for influenza A virus (IAV) spread and evolution. We studied how the virus moves through guinea pigs airways after infection with H3N2 or H1N1 strains of IAV. Whether delivered intranasally, by aerosol or by transmission, the H1N1 virus replicated in the nasal cavity, trachea, and lungs. By contrast, the H3N2 virus stayed mostly in the nasal cavity. Genetic barcodes were used to track how the H1N1 virus moved and changed. The populations replicating in the nasal cavity and trachea maintained high diversity but those sampled from the lungs showed low diversity. This bottlenecking effect was stronger for viral populations present deeper in the lungs. These findings show that the different environments of the URT and LRT strongly shape how influenza spreads and evolves inside a host.

microbiology↗

bioRxiv2025

Virion aggregation shapes infection dynamics and evolutionary potential

Viral spread is classically thought to be mediated by single viral particles. However, viruses often disseminate in groups - as aggregates, inside membranous vesicles, or as clusters associated with bacterial components or other complex surfaces. The implications of collective dispersal for viral infectivity and evolution remain incompletely defined. Here, we used mammalian orthoreovirus to evaluate the impact of aggregation on the propagation of infection and the generation of viral diversity through reassortment. Aggregation of free virions was induced by manipulating pH and ionic conditions. This treatment promoted coordinated delivery of viruses to cells, increasing the number of virions per infected cell and number of virions per occupied endosome at early times of infection. Likely due to a consolidation of infectious units, aggregation concomitantly reduced the overall infectivity of the viral population and progeny virus yields. When viral populations comprised two genetically distinct viruses, aggregation increased the frequency of mixed infection and of genetic exchange through reassortment. Thus, the formation of collective infectious units lowers the replicative potential of mammalian orthoreovirus populations but increases viral evolutionary potential by promoting genetic diversification. ImportanceA deeper understanding of processes shaping viral evolution will advance our ability to anticipate viral emergence, escape from immune responses and resistance to therapeutics. Although much is known about how genetic variation fuels viral evolution, how modes of viral spread influence the generation and structure of genetic variation remains poorly characterized. Here we examine how the collective dissemination of viruses modulates early infection dynamics and viral diversity. We find that, although infection in groups reduces the number of independently infected cells, it results in a more genetically diverse progeny population, an outcome that may enhance evolutionary potential.

microbiology↗

bioRxiv2023

Harnessing genetic variations improving seedling vigor for successful crop establishment in deep sown direct-seeded rice

Improving seedling vigour remains key objective for breeders working with direct-seeded rice (DSR). To understand the genetic control of seedling vigour in deep sown DSR, combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes was performed. Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 3.79 Mb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The potential candidate gene, LOC_Os07g25150 codes for Myb-30-related transcription factor. The LOC_Os07g25150 codes for Myb 30-related transcription factor, LOC_Os07g17689 annotated as protein translation factor, LOC_Os07g17770 as tryptophanyl-tRNA synthetase, LOC_Os07g15440 as alanyl-tRNA synthetase family protein, LOC_Os07g24100 as retrotransposon protein and the remaining others as expressed proteins. The antagonistic relationship between Myb-30 and ethylene-mediated signalling (EIN-3) in regulating mesocotyl elongation have been observed. The functional characterization and knocking of LOC_Os07g25150 codes for Myb 30-related transcription factor may provide better understanding of the mechanism behind mesocotyl elongation. The four promising introgression lines with longer mesocotyl length, longer root length and semi-dwarf plant height have been identified.

genomics↗

bioRxiv2021

A multimodal study of a first episode psychosis cohort: potential markers of antipsychotic treatment resistance

Treatment resistant (TR) psychosis is considered to be a significant cause of disability and functional impairment. Numerous efforts have been made to identify the clinical predictors of TR. However, the exploration of molecular and biological markers is still at an early stage. To understand the TR condition and identify potential molecular and biological markers, we analyzed demographic information, clinical data, structural brain imaging data, and molecular brain imaging data in 7 Tesla magnetic resonance spectroscopy, from a first episode psychosis cohort that includes 138 patients. Age, gender, race, smoking status, duration of illness, and antipsychotic dosages were controlled in the analyses. We found that TR patients had a younger age at onset, more hospitalizations, more severe negative symptoms, a significant reduction in the volumes of the hippocampus (HP) and superior frontal gyrus (SFG), and a significant reduction in glutathione (GSH) levels in the anterior cingulate cortex (ACC), when compared to non-TR patients. The combination of multiple markers provided a better classification between TR and non-TR patients compared to any individual marker. Our study shows that ACC GSH, HP and SFG volumes, and age at onset could potentially be trait biomarkers for TR diagnosis, while hospitalization and negative symptoms could be used to evaluate the progression of the disease. Multimodal cohorts are essential in obtaining a comprehensive understanding of brain disorders.

neuroscience↗

bioRxiv2019

Noninvasive sleep monitoring in large-scale screening of knock-out mice reveals novel sleep-related genes

Sleep is a critical process that is well-conserved across mammalian species, and perhaps most animals, yet its functions and underlying mechanisms remain poorly understood. Identification of genes and pathways that can influence sleep may shed new light on these functions. Genomic screens enable the detection of previously unsuspected molecular processes that influence sleep. In this study, we report results from a large-scale phenotyping study of sleep-wake parameters for a population of single-gene knockout mice. Sleep-wake parameters were measured using a high throughput, non-invasive piezoelectric system called PiezoSleep. Knockout mice generated on a C57BL6/N (B6N) background were monitored for sleep and wake parameters for five days. By analyzing data from over 6000 mice representing 343 single gene knockout lines, we identified 122 genes influencing traits like sleep duration and bout length that have not been previously implicated in sleep, including those that affect sleep only during a specific circadian phase. PiezoSleep also allows assessment of breath rates during sleep and this was integrated as a supplemental tool in identifying aberrant physiology in these knockout lines. Sex differences were evident in both normal and altered sleep behavior. Through a combination of genetic and phenotypic associations, and known QTLs for sleep, we propose a set of candidate genes playing specific roles in sleep. The high \"hit rate\" demonstrates that many genes can alter normal sleep behaviors through a variety of mechanisms. Further investigation of these genes may provide insight into the pathways regulating sleep, functional aspects of sleep, or indirect potentially pathological processes that alter normal sleep.

neuroscience↗