Biology subjects

Chaturvedi, A.

Publications and source records attributed to Chaturvedi, A..

11 recordsLinked to original sources

bioRxiv2026

RNA-Encoded PGT121-LS Anti-HIV Antibody: Comprehensive Preclinical Characterization and Translational Pharmacokinetics

Human Immunodeficiency Virus (HIV)-1 broadly neutralizing antibodies (bNAbs) have demonstrated clinical efficacy, but face manufacturing challenges associated with recombinant protein production and purification. Here, we present a ribonucleic acid (RNA)-encoded bNAb (RibobNAb) platform that enables in vivo antibody production of the clinically validated bNAb PGT121 via lipid nanoparticle (LNP) delivery, supporting rapid evaluation of Fc variants (LS, del294, LS-del294) in vitro and in vivo. We confirmed expression, sub-nanomolar HIV-1 Env binding, and potent neutralization across all RibobNAb variants in vitro. In mice, single RNA-LNP administrations yielded in vivo expression of all RibobNAb variants, with PGT121-LS exhibiting a prolonged half-life compared with PGT121. In non-human primates (NHPs), a single intravenous administration of PGT121-LS RNA-LNP was well tolerated without anti-drug antibody (ADA) formation over 180 days and resulted in PGT121-LS half-lives comparable to the reference protein. Single intramuscular administration showed RibobNAb expression but resulted in ADA development from Day 14 onwards and lower bioavailability. In vivo-expressed PGT121-LS RibobNAb retained identical antiviral functionality to PGT121-LS reference protein. An NHP pharmacokinetics model integrating RNA transfection and translation dynamics enabled allometric scaling and first-in-human dose prediction. We highlight RibobNAbs as an alternative to conventional purified protein antibodies for rapid development of bNAb-based therapeutic strategies. O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/734219v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@141319forg.highwire.dtl.DTLVardef@120caadorg.highwire.dtl.DTLVardef@1da2782org.highwire.dtl.DTLVardef@158064d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

immunology↗

bioRxiv2026

piRNAs from Y chromosomal protein coding, noncoding and endogenous retrovirus homologous repeat families regulate autosomal gene expression in mouse testis

BackgroundHeterochromatic long arm of mouse Y chromosome harbors the multicopy species-specific sequences Ssty, Sly, Asty and Orly that are transcribed in testis and have known functions in male fertility. Of these Ssty and Sly encode proteins - yet all the transcripts are not translated. To investigate the roles of these Y-heterochromatic transcripts further, we analyzed them. MethodsMice with 2/3rd deletion of the Y-chromosome (XYRIIIqdel) and its wild type (XYRIII) were used in this study. Bioinformatic approaches, small RNA northern blots, Electrophoretic Mobility Shift Assays, Luciferase reporter assays, dPCR analysis, RT-qPCR assays and western blotting techniques were used to identify piRNAs that regulate autosomal genes. ResultsWe demonstrate that the multicopy gene families from mouse Y-long arm generate piRNAs predominantly in testis. We observed sequences homologous to these piRNAs in the UTRs of a few autosomal genes, which are differentially expressed in the sperms of XYRIIIqdel mice. Furthermore, the Endogenous Retrovirus Element (ERV) LTR, found in the Orly1 transcript identified piRNAs in the database, showed homology to UTRs and associated genomic regions of a few autosomal genes. Orly1 showed a reduction in genomic copy number by digital PCR in XYRIIIqdel mice. One of the four autosomal genes containing the ERV segment in their UTRs, showed a differential testicular protein expression in the mutant mice. ConclusionsThus, we further elucidate that different classes of repeats from Y-chromosome regulate autosomal gene expression via piRNAs. Besides, this study also identified novel roles for a Y-derived ERV in autosomal gene regulation in testis.

Molecular Biology↗

bioRxiv2025

Targeting Ogt in ADPKD mitigates metabolic reprogramming and renal cystogenesis, extending survival

Aberrant cell metabolism drives autosomal dominant polycystic kidney disease (ADPKD). O-GlcNAcylation, a metabolically regulated post-translational modification, is elevated in ADPKD kidneys. Using rapidly and slowly progressive ADPKD mouse models, we demonstrate that deleting O-GlcNAc transferase (Ogt) reduces renal cystogenesis and extends survival in a rapidly progressive model from postnatal day 21 to over a year. Pharmacological OGT inhibition similarly reduced cyst formation of patient-derived renal epithelial cells in vitro. In Pkd1 conditional knockout kidneys, Ogt deletion maintained phosphorylated AMPK and mitochondrial respiratory chain complex levels, preserving cellular energy sensing and production. Further, metabolomic analysis revealed normalization of glycolysis and of the hexosamine and hyaluronic acid biosynthesis pathways. In contrast, dysregulation of these pathways in Pkd1 conditional knockout kidneys culminated in increased tricarboxylic acid cycle entry, increased O-GlcNAc, and increased hyaluronic acid in the extracellular matrix, respectively. These findings identify Ogt as a central metabolic regulator and therapeutic target, linking metabolism to intracellular and extracellular mechanisms of cyst formation.

cell biology↗

bioRxiv2025

mRNA-based tuberculosis vaccines BNT164a1 and BNT164b1 are immunogenic, well-tolerated and efficacious in rodent models

We designed and preclinically tested two mRNA-LNP-based vaccine candidates to protect against tuberculosis (TB). BNT164a1 and BNT164b1 encode the same eight Mycobacterium tuberculosis (Mtb) antigens expressed across different infection stages: Ag85A, Hrp1, ESAT-6, RpfD, RpfA, HbhA, M72, and VapB47. BNT164a1 utilizes nucleoside-unmodified mRNA, while BNT164b1 utilizes N1-methyl pseudouridine-modified mRNA. Prime-boost immunization with BNT164 candidates elicited antibody and/or T-cell responses against all antigens in three mouse strains (C57BL/6, BALB/c, and HLA-A2.1/DR1 humanized mice). The candidates demonstrated favorable safety profiles in a rat toxicity study and significantly reduced bacterial burdens of two Mtb strains in murine aerosol challenge models. BNT164 protection correlated with granuloma infiltration by CD8+ T cells with memory precursor phenotypes. In conclusion, BNT164a1 and BNT164b1 were immunogenic, well tolerated and efficacious in preclinical models and are the first mRNA-based TB vaccines to enter phase I/II clinical trials (NCT05537038, NCT05547464).

immunology↗

bioRxiv2025

Arsenic Toxicity in the Drosophila Brain at Single Cell Resolution

Arsenic is an ubiquitous environmental toxicant with harmful physiological effects, including neurotoxicity. Modulation of arsenic-induced gene expression in the brain cannot be readily studied in human subjects. However, Drosophila allows quantification of transcriptional responses to neurotoxins at single cell resolution across the entire brain in a single analysis. We exposed Drosophila melanogaster to a chronic dose of NaAsO that does not cause rapid lethality and measured survival and negative geotaxis as a proxy of sensorimotor integration. Females survive longer than males but show earlier physiological impairment in climbing ability. Single-nuclei RNA sequencing showed widespread sex-antagonistic transcriptional responses with modulation of gene expression in females biased toward neuronal cell populations and in males toward glial cells. However, differentially expressed genes implicated similar biological pathways. Evolutionary conservation of fundamental processes of the nervous system enabled us to translate arsenic-induced changes in transcript abundances from the Drosophila model to orthologous human neurogenetic networks.

genetics↗

bioRxiv2023

A novel human model to deconvolve cell-intrinsic phenotypes of genetically dysregulated pathways in lung squamous cell carcinoma

Tractable, patient relevant models are needed to investigate cancer progression and heterogeneity. Here, we report an alternative and unique in vitro model of lung squamous cell carcinoma (LUSC) using primary human bronchial epithelial cells (hBECs) from three healthy donors. The co-operation of ubiquitous alterations (TP53 and CDKN2A loss) and components of commonly deregulated pathways including squamous differentiation (SOX2), PI3K signalling (PTEN) and the oxidative stress response (KEAP1) was investigated by generating hBECs harbouring cumulative alterations. Our analyses confirmed that SOX2-overexpression initiates early preinvasive LUSC stages, and co-operation with the oxidative stress response and PI3K pathways to drive more aggressive phenotypes, with expansion of cells expressing LUSC biomarkers and invasive properties. This cooperation was consistent with the classical LUSC subtype. Importantly, we connected pathway dysregulation with gene expression changes associated with cell-intrinsic processes and immunomodulation. Our approach constitutes a powerful system to model LUSC and unravel genotype-phenotype causations of clinical relevance.

cancer biology↗

bioRxiv2023

Notch3 deletion regulates HIV-1 gene expression and systemic inflammation to ameliorate chronic kidney disease

Antiretroviral therapy (ART) has decreased HIV-1 associated morbidity. However, despite ART, immune cells remain latently infected and slowly release viral proteins, leading to chronic inflammation and HIV-1 associated comorbidities. New strategies are needed to target viral proteins and inflammation. We found activation of Notch3 in several renal cells of the HIV-1 mouse model (HIV-Tg26) and in patients with HIV associated Nephropathy. We hypothesized that targeting Notch3 activation constitutes an effective therapy for HIV-related chronic kidney diseases (HIV-CKD). We generated HIV-Tg26 mice with Notch3 knocked out (Tg-N3KO). Compared to HIV-Tg26 mice at 3 months, HIV-Tg-N3KO mice showed a marked reduction in renal injury, skin lesions and mortality rate. Bulk RNA sequencing revealed that N3KO not only reduced renal infiltrating cells but significantly reduced the expression of HIV genes. Moreover, Notch3 activated the HIV-promoter and induction of HIV-1 resulted in increased Notch3 activation indicating a feedback mechanism. Further, bone marrow derived macrophages (BMDMs) from HIV-Tg26 mice showed activation of Notch3 indicating systemic effects. Consistent with that, systemic levels of TNF-, MCP-1 and other inflammatory chemokines and cytokines were reduced in Tg-N3KO mice. Thus, Notch3 inhibition/deletion has a dual therapeutic effect in HIV-CKD and may extend to other HIV-related pathologies.

molecular biology↗

bioRxiv2022

Automated Workflow for Instant Labeling and Real-Time Monitoring of Monoclonal Antibody N-Glycosylation

With the transition toward continuous bioprocessing, process analytical technology (PAT) is becoming necessary for rapid and reliable in-process monitoring during biotherapeutics manufacturing. Bioprocess 4.0 is looking to build an end-to-end bioprocesses that includes PAT-enabled real-time process control. This is especially important for drug product quality attributes that can change during bioprocessing, such as protein N-glycosylation, a critical quality attribute for most monoclonal antibody (mAb) therapeutics. Glycosylation of mAbs is known to influence their efficacy as therapeutics and is regulated for a majority of mAb products on the market today. Currently, there is no method to truly measure N-glycosylation using on-line PAT, hence making it impractical to design upstream process control strategies. We recently described the N-GLYcanyzer: an integrated PAT unit that measures mAb N-glycosylation within 3 hours of automated sampling from a bioreactor. Here, we integrated Agilents Instant PC (IPC) based chemistry workflow into the N-GLYcanzyer PAT unit to allow for nearly 10x faster mAb glycoforms analysis. Our methodology is explained in detail to allow for replication of the PAT workflow as well as present a case study demonstrating use of this PAT to autonomously monitor a mammalian cell perfusion process at the bench-scale to gain increased knowledge of mAb glycosylation dynamics during continuous biomanufacturing of biologics using Chinese Hamster Ovary (CHO) cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/521623v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@16cf139org.highwire.dtl.DTLVardef@150db0borg.highwire.dtl.DTLVardef@15cbe36org.highwire.dtl.DTLVardef@1cbdf6a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Intraflagellar transport-A deficiency ameliorates ADPKD renal cystogenesis in a renal tubular- and maturation-dependent manner

Primary cilia are sensory organelles built and maintained by intraflagellar transport (IFT) multi-protein complexes. Deletion of different IFT-B genes attenuates polycystic kidney disease (PKD) severity in juvenile and adult Autosomal Dominant (AD) PKD mouse models, while deletion of an IFT-A adaptor, Tulp3, attenuates PKD severity in adult mice only. These studies indicate that dysfunction of specific cilia components has potential therapeutic value. To broaden our understanding of cilia dysfunction and its therapeutic potential, here we investigate the impact of global deletion of an IFT-A gene, Thm1, in juvenile and adult ADPKD mouse models. Both juvenile and adult models exhibited increased kidney weight:body weight (KW/BW) ratios, renal cysts, inflammation, lengthened renal cilia, and increased levels of the nutrient sensor, O-linked {beta}-N-acetylglucosamine (O-GlcNAc). Thm1 deletion in juvenile ADPKD mice reduced KW/BW ratios and cortical collecting duct cystogenesis, but increased proximal tubular and glomerular dilations and did not reduce inflammation, cilia lengths, and O-GlcNAc signaling. In contrast, Thm1 deletion in adult ADPKD mice markedly attenuated renal cystogenesis, inflammation, cilia lengths, and O-GlcNAc. Thus, unlike IFT-B genes, the role of Thm1 deletion in ADPKD mouse models is development-specific. Unlike an IFT-A adaptor gene, deleting Thm1 in juvenile ADPKD mice is partially ameliorative. Our studies suggest that different microenvironmental factors found in distinct nephron segments and between developing and mature kidneys modify ciliary homeostasis and ADPKD pathobiology. Further, elevated levels of O-GlcNAc, which regulates cellular metabolism and ciliogenesis, may be a novel feature and critical regulator of certain key ADPKD pathological processes.

genetics↗

bioRxiv2018

Transcripts from multicopy gene families localizing to mouse Y long arm encode piRNAs and proteins

Heterochromatic long arm of mouse Y chromosome harbors the multicopy species-specific sequences Ssty, Sly, Asty, and Orly that are transcribed in testis. Of these Ssty and Sly genes encode proteins - yet all the copies of these RNAs are not translated. Using bioinformatic approaches, small RNA northern blots and electrophoretic mobility shift assays, we demonstrate here that these multicopy gene families from mouse Y-long arm generate piRNAs predominantly in testis. Thus, we identified a piRNA cluster on mouse Y chromosome and also unraveled the dual role of Y-chromosome-encoded transcripts to act as primary transcripts of piRNAs in addition to their role as protein-coding RNAs.\n\nHIGHLIGHTSO_LIFirst report of a cluster of piRNAs on a mammalian Y chromosome\nC_LIO_LIReport of primary transcripts of piRNAs\nC_LIO_LIThese piRNAs putatively regulate autosomal genes expressed in mouse testis Ssty and Sly genes code for proteins as well as generate piRNAs\nC_LI

molecular biology↗

bioRxiv2018

Y chromosomal noncoding RNA regulates autosomal gene expression via piRNAs in mouse testis

Majority of the genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility, sterility and sperm abnormalities. The connection between Yq deletion and autosomal gene regulation is not well understood. We describe a novel mouse Yq-derived long noncoding RNA, Pirmy, which shows unprecedented number of splice variants in testis. Further, Pirmy transcript variants act as templates for several piRNAs. We identified ten differentially expressed autosome-encoded sperm proteins in mutant mice. Pirmy transcript variants have homology to 5/3UTRs of these deregulated autosomal genes. Thus, subfertility in Y-deleted mice appears to be a polygenic phenomenon that is partially regulated epistatically by the Y-chromosome. Our study provides novel insights into possible role of MSY-derived ncRNAs in male fertility and reproduction. Finally, sperm phenotypes from the Y-deleted mice seem to be similar to that reported in inter-specific male-sterile hybrids. Taken together, this study provides novel insights into possible role of Y-derived ncRNAs in male sterility and speciation.

genomics↗