Biology subjects

Gupta, H.

Publications and source records attributed to Gupta, H..

16 recordsLinked to original sources

bioRxiv2026

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses

SummaryElectronic health record (EHR)-linked biobanks generate unprecedented genomic and phenotypic datasets, but their scientific utility is constrained by data fragmentation across institutional silos and incompatible computing infrastructures, forcing researchers to rewrite ad-hoc scripts for each new environment. We present the PMBB Geno-Pheno Toolkit, a suite of modular Nextflow pipelines for biobank-scale association analyses. This note focuses on the toolkits SAIGE family of pipelines -- supporting genome-wide (GWAS), exome-wide (ExWAS), and phenome-wide (PheWAS) association testing -- together with the companion GWAMA and ExWAS meta-analysis pipelines that enable cross-biobank replication. All components are containerized (Docker/Apptainer) and orchestrated with Nextflow, allowing the same workflows to run unmodified on local HPC clusters, cloud platforms, and the All of Us Research Workbench. Complementary toolkit pipelines for PLINK-based GWAS, polygenic scoring, LD-based clumping, and phenotype harmonization are also available and briefly noted. AvailabilityThe PMBB Geno-Pheno Toolkit is freely available at https://github.com/PMBB-Informatics-and-Genomics/pmbb-geno-pheno-toolkit under MIT open-source license.

bioinformatics↗

bioRxiv2026

Collapsing retroviruses for efficient delivery of viro-toxic cargoes

Retroviruses are excellent tools for delivering and expressing transgenic cargoes with broad utility in research and therapy. However, many cargoes including virus restriction factors can dramatically limit virus production and/or infectivity. An extreme viro-toxic cargo is the DNA cytosine deaminase APOBEC3B, which potently restricts retrovirus infectivity by a direct cDNA deamination-dependent mechanism. To overcome viro-toxicity, an APOBEC3B minigene cargo is disrupted by a translation stop cassette flanked by a direct repeat of its own sequence. The integrity of the minigene is reconstituted naturally by retroviral recombination during transduction. Efficiency can be improved from 90% to nearly 100% by coupling the minigene to the translation of a downstream selectable marker. Collapsing retrovirus (CRV) technology enables the functional delivery of APOBEC3B to a target cell population and may have broad utility for delivering viro-toxic cargoes. MotivationMany different proteins are detrimental to retrovirus production and/or to virus-producing cells. This problem can be circumvented by interrupting the genetic cargo with a direct repeat-flanked translation stop cassette and allowing transgene integrity to be restored naturally by recombination during reverse transcription. As exemplified by the retrovirus restriction factor APOBEC3B, this process is very efficient. HighlightsO_LICollapsing retroviruses (CRVs) prevent retrovirus restriction by viro-toxic proteins C_LIO_LITruncated tandem repeats recombine during transduction and restore virus integrity C_LIO_LITranslation-coupled selection enables near 100% transduction efficiency C_LIO_LICRVs have broad utility for delivering viro-toxic cargoes such as APOBEC3B C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/735095v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@e96092org.highwire.dtl.DTLVardef@1c343f9org.highwire.dtl.DTLVardef@a3b53dorg.highwire.dtl.DTLVardef@1cfeb69_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Comparative profiling of carnitine palmitoyltransferase 1 isoforms reveals vincamine as a selective carnitine palmitoyltransferase 1b inhibitor

Carnitine palmitoyltransferase 1 (CPT1) catalyzes the rate-limiting step of fatty acid oxidation and has emerged as a therapeutic target for metabolic diseases and cancer. CPT1 exists in three isoforms, CPT1a, CPT1b, and CPT1c, with distinct tissue distributions and enzymatic properties; however, limitations of previous platforms enabling parallel isoform comparison have undermined efforts to identify selective inhibitors that could minimize off-target effects. Here, we describe a DTNB-based enzyme activity assay adapted for high-throughput screening of CPT1b, the predominant isoform in cardiac and skeletal muscle. Mitochondrial extracts from Expi293F cells transfected with CPT1a or CPT1b expression plasmids served as sources of catalytically active enzymes. The assay was validated using three previously confirmed CPT1b inhibitors: (R)-(+)-etomoxir, perhexiline, and malonyl-CoA. We then generated side-by-side inhibitory profiles for both isoforms, identifying vincamine as a lead selective inhibitor of CPT1b. Furthermore, chlorpromazine, previously characterized only as a broad CPT1 inhibitor and subsequently shown to inhibit CPT1a, is demonstrated here to also inhibit CPT1b, expanding its known isoform profile. Together, these results establish a robust platform for comparative isoform profiling and demonstrate that selective modulation of CPT1b is achievable, with implications for targeted therapeutics in metabolic and oncological disease.

cell biology↗

bioRxiv2026

Severe malarial anaemia is associated with parasite enrichment and host alterations in the bone marrow

BackgroundMalaria poses a significant global health challenge, with over 200 million infections and around 500,000 deaths annually, predominantly affecting children under 5 in sub-Saharan Africa. Severe malarial anaemia (SMA), a major contributor to morbidity and mortality in this demographic, results from various factors including red blood cell destruction and immune-mediated clearance. The role of these mechanisms in SMA differs based on age and infection history. Recent studies indicate increased accumulation of P. falciparum in the bone marrow and spleen, highlighting the need for understanding localized host-parasite interactions. MethodsThis study examines the bone marrow response to malarial infection in young children with SMA or mild malarial malaria in Mozambique, contrasting it with responses observed in peripheral blood in the two cohorts. Results and conclusionsThe study demonstrated that SMA is associated with increased red blood cell production, iron metabolism and tissue injury, as well as higher total parasite biomass including peripheral and bone marrow parasitaemia. We also demonstrate that direct analysis of bone marrow aspirates provides far more resolution in stratifying host signatures and drivers of malarial anaemia across a spectrum of severity than systemic measures from blood samples.

microbiology↗

bioRxiv2026

Oncogenic chromodomain mutations allosterically impair TIP60 acetyltransfearse function preventing activation of DNA repair genes under genotoxic stress

TIP60 is a tumor suppressor with histone acetyltransferase activity that regulates chromatin accessibility in diverse processes including DNA repair, apoptosis, mitosis, transcription, and autophagy. Structurally TIP60 contains a C-terminal MYST domain that mediates its HAT activity, while the N-terminal chromodomain are conserved modules that facilitate its association with chromatin by recognizing histone modifications. Mutations within the chromodomain have been implicated in various cancers, yet their functional consequences remain poorly understood, particularly with respect to TIP60s role in maintaining genomic integrity. Here, we uncover a novel allosteric mechanism whereby cancer-associated chromodomain mutations impair TIP60s catalytic activity without disrupting its chromatin binding, underscoring critical interdomain communication between the chromodomain and the MYST domain. Through structural modelling and molecular dynamics simulations, we identified two missense mutations (R53H and R62W) in TIP60s chromodomain that not only altered TIP60s conformation but also destabilized its trimeric assembly, thereby impairing acetyl-CoA docking. Importantly, we found that TIP60 engages acetyl-CoA exclusively in its trimeric state, and the R62W mutation perturbs the trimeric interface, thereby altering the docking sites for acetyl-CoA. Consistent with these structural changes, biochemical assays revealed that chromodomain mutant TIP60 variants, while retaining chromatin loading, exhibited markedly reduced autoacetylation and histone acetyltransferase activity. Moreover, these mutants failed to activate the p21 gene in response to DNA damage, thereby predisposing the genome to the accumulation of mutations and leaving cells unable to arrest the cell cycle for repair of genomic lesions. Together, our findings establish that distal chromodomain mutations allosterically destabilize TIP60 oligomerization, impair acetyl-CoA utilization, and compromise DNA damage responses. The mechanism establishes a link between chromodomain mutations and genomic instability, shedding light on how reader domain alterations may underlie cancer progression.

molecular biology↗

bioRxiv2025

The CENP-A chaperone complex spatially organizes centromeres

Centromeres, defined by CENP-A-containing nucleosomes, direct the assembly of kinetochores for spindle attachment. In mitosis, CENP-A and the constitutive centromere-associated network (CCAN) of the inner kinetochore are arranged into bipartite subdomains within clearings of chromatin. However, it remains unclear whether any of these features exist before mitosis. We show that in interphase, CENP-A and the CCAN assemble [~]200-300 nm shell-like structures that enclose a chromatin-poor central cavity. Strikingly, this cavity is occupied by the interphase-specific CENP-A chaperone complex, which promotes CENP-A assembly once per cell cycle. However, chaperone presence, but not CENP-A incorporation, is required to generate both the shell architecture and the chromatin clearing. The CCAN scaffold CENP-C, which links CENP-A nucleosomes to the chaperone complex, exhibits radial organization spanning the entire structure and is essential for its formation. These data uncover a previously unrecognized structural role for the CENP-A chaperone machinery in establishing interphase centromere architecture and suggest a mechanism by which this machinery configures centromeres for faithful kinetochore assembly and genome stability.

cell biology↗

bioRxiv2025

Murine models for triple-negative breast cancer with differential responsiveness to immunotherapy

Breast cancer is the most common cancer diagnosis in women. Clinical studies with triple-negative breast cancer (TNBC) are encouraging for immunotherapy combined with chemotherapy (anti-PD-1 with paclitaxel and/or carboplatin). However, additional clinical advances may be pursued more rapidly with assistance from preclinical TNBC models including syngeneic mammary tumor cell lines. Here, we report two mammary tumor cell lines that exhibit differential responsiveness to immunotherapy in vivo. Spontaneous mammary tumors from C57BL/6J MMTV-Cre Trp53fl/+ animals were passaged serially in cell culture and in vivo in the mammary fat pad of fully wildtype animals. The resulting lines, MM001i and MM008i, lost Trp53 and formed 1000 mm3 tumors in the mammary fat pad within 21-28 days. Despite originating from the same genetic background, these lines exhibit differential responses to immunotherapy. For anti-PD-1 therapy, MM001i is poorly responsive and MM008i is strongly responsive with near-complete tumor regression. In comparison, both MM001i and MM008i respond rapidly to anti-CTLA-4 therapy. Both models express unique tumor antigens as evidenced by immunity to subsequent engraftments. Primary MM008i tumors exhibit greater T cell infiltration, and CD8-positive T lymphocytes are required for anti-PD-1 responses. These TNBC models are promising for further mechanistic studies and testing future single and combinatorial therapies.

cancer biology↗

bioRxiv2024

Identification of Ephrin type-B receptor 4 as a critical mediator of tissue fibrosis

Pulmonary fibrosis (PF) is a pathology associated with interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF). Fibrosis promotes continual secretion of extracellular matrix (ECM), producing non-functional scar tissue and causing organ failure. This study investigated the tyrosine kinase receptor Ephrin type-B receptor 4 (EphB4) as a mediator of PF. To this end, we generated mice with conditional Col1a2-driven deletion of Ephb4 and used a preclinical mouse model of PF, total and single nuclei RNA (snRNA) sequencing, NanoString, previously published single cell data, computational analysis, and functional assays of mouse and human healthy control and IPF lung fibroblasts. Col1a2-CreERT-driven Ephb4 deletion, or EphB4 inhibition via NVP-BHG712, markedly protected against bleomycin-induced PF. Total RNA-sequencing of fibroblasts isolated from Ephb4-deficient fibrotic mouse lungs exhibited reduced expression of ECM, ER Cargo, and protein trafficking-related genes. NVP-BHG712 reduced expression of these identified genes in mouse lung fibroblasts under fibrotic conditions in vitro. SnRNA sequencing of mouse lungs treated with NVP-BHG712 identified transcriptomic changes of ECM genes in specific fibroblast subpopulations. RNA sequencing, computational, and functional assays using mouse and human IPF fibroblasts identified elastin as a key mediator involved in EphB4 signaling. Combined, our data show that EphB4 is a crucial mediator of PF.

pathology↗

bioRxiv2024

Cell-TIMP: Cellular Trajectory Inference based on Morphological Parameter

Cellular morphology, shaped by various genetic and environmental influences, is pivotal to studying experimental cell biology, necessitating precise measurement and analysis techniques. Traditional approaches, which rely on geometric metrics derived from stained images, encounter obstacles stemming from both the imaging and analytical domains. Staining processes can disrupt the cells natural state and diminish accuracy due to photobleaching, while conventional analysis techniques, which categorize cells based on shape to discern pathophysiological conditions, often fail to capture the continuous and asynchronous nature of biological processes such as cell differentiation, immune responses, and cancer progression. In this work, we propose the use of quantitative phase imaging for morphological assessment due to its label-free nature. For analysis, we repurposed the genomic analysis toolbox to perform trajectory inference analysis purely based on morphology information. We applied the developed framework to study the progression of leukemia and breast cancer metastasis. Our approach revealed a clear pattern of morphological evolution tied to the diseases advancement, highlighting the efficacy of our method in identifying functionally significant shape changes where conventional techniques falter. This advancement offers a fresh perspective on analyzing cellular morphology and holds significant potential for the broader research community, enabling a deeper understanding of complex biological dynamics.

bioinformatics↗

bioRxiv2023

An ensemble of Gleditsia sinensis Lam. and gut microbiota against alcoholic liver disease

Gleditsia sinensis Lam. (GSL) is a medicinal herb and a noticeable resource of possessing hepatic protective agents such as alcoholic liver disease (ALD). At present, it has been documented that gut microbiota (GM) is related directly to etiology of ALD. Nevertheless, the bioactive molecules in GSL, favorable GM, targets, and key mechanism(s) against ALD are yet to be revealed. Hence, we integrated the significant four components to clarify the nuanced pathogenesis with help of network pharmacology (NP) concept. We retrieved significant metabolites via gutMGene and constructed GSL or GM-Signaling pathways-Targets-Metabolites (GGSTM) networks. Finally, molecular docking test (MDT) was performed to verify the key findings. The gutMGene suggested that 16 GM and 6 metabolites were related to the two signaling pathways through GGSTM networks. Both MDT and frontier molecular orbitals (FMO) theory revealed the most stable conformers: equol from Lactobacillus paracasei JS1 on IL6, Bauer-7-en-3-one, and Urs-12-en-3-one from GSL on PPARA, PPARD, and PPARG, respectively. In conclusion, this study sheds light on the combinatorial effects of GM, and GSL in treating ALD via systems biology concept.

systems biology↗

bioRxiv2023

Autoacetylation of lysine 187 is critical for TIP60 phase separation and functions

TIP60 is an important lysine acetyl transferase protein that participates in various essential cellular activities by catalyzing the post-translational acetylation of lysine residues on histones and various non-histone protein substrates. TIP60 typically localizes to the nucleus in a punctate foci pattern, although defining factors and mechanisms regulating the assembly of TIP60 foci and their spatial distribution inside the nucleus are not understood. In the present study, we report that TIP60 can undergo phase separation to form liquid like droplets in the nuclear compartment, which is facilitated by the presence of an intrinsically disordered region (IDR) located between its chromodomain and catalytic domain. Importantly, we identified that autoacetylation on lysine 187, located within the IDR region of TIP60, is important for nuclear localization, oligomer formation and phase separation. Finally, we observed that the phase separation of TIP60 promotes its interaction with its partner proteins and actively contribute to its cellular functions.

cell biology↗

bioRxiv2023

Upregulation of steroidogenesis is associated with coma in human cerebral malaria

P. falciparum parasites manipulate host metabolic processes during malaria to ensure their survival and progression, causing the host and parasite metabolic pathways to become intertwined. We analyzed metabolites to evaluate their potential as biomarkers for cerebral malaria (CM). Our analysis of CM (with coma) and CM-like (without coma) patients identified 835 metabolites, including lipids, amino acids, xenobiotics, peptides, nucleotides, carbohydrates, cofactors, and vitamins. Principal component analysis revealed clear segregation between CM-like and CM patients. Metabolite-by-metabolite analysis identified 103 differentially abundant metabolites, 26 of which were significantly lower in CM-like patients (primarily lipids), while 71% of those higher in CM patients were amino acids and xenobiotics. The results revealed significant differences in circulating levels of long chain free fatty acids and catecholamine metabolism and identified steroid biosynthesis as the most enriched lipid metabolism pathway, with eight endogenous steroids showing significantly higher levels in CM patients compared to CM-like patients (FC > 2, B-H FDR-adjusted P < 0.05). These steroids include pregnenolone sulfate, pregnenediol sulfate, pregnenetriol sulfate, androsterone monosulfate, 16-OH-DHEA-S, DHEA-S, cortisol, and cortisone. High levels of pregnenolone and its downstream metabolic derivatives were significantly associated with coma in CM patients. Our findings suggest that monitoring circulating neurosteroid levels in patients could aid in the early identification of those at risk of coma, and may important implications for the clinical management of CM patients.

systems biology↗

bioRxiv2022

Progressive spreading of DNA methylation in the GSTP1 promoter CpG island across transitions from precursors to invasive prostate cancer

Glutathione S-transferase pi 1 (GSTP1) is lowly expressed in normal prostate luminal cells and becomes induced in most proliferative inflammatory atrophy lesions (PIA). GSTP1 becomes silenced in prostatic intraepithelial neoplasia (PIN) and prostate adenocarcinoma (CaP) via cytosine-phospho-guanine (CpG) island promoter hypermethylation. However, GSTP1 methylation patterns in PIA and PIN, and their relationship to patterns in CaP are poorly understood. We used bisulfite genomic sequencing to examine patterns of GSTP1 promoter CpG island methylation in laser capture microdissected benign, PIA, PIN, and CaP regions from 32 subjects that underwent radical prostatectomy. We analyzed 908 sequence clones across 24 normal epithelium, 37 PIA, 18 PIN, and 23 CaP regions, allowing assessment of 34,863 CpG sites with allelic phasing. Normal and PIA lesions were mostly unmethylated with 0.52 and 1.3% of total CpG sites methylated, respectively. PIN and CaP lesions had greater methylation with 24% and 51% of total CpG sites methylated, respectively. The degree of GSTP1 methylation showed progression from PIA << PIN < CaP. PIN lesions showed more partial methylation compared to CaP lesions. Partially methylated lesions were enriched for methylation changes at AP1 and SP1 transcription factor binding sites. These results demonstrate that methylation density in the GSTP1 CpG island in PIN was intermediate relative to that in normal prostate epithelium/PIA and CaP lesions. These results are consistent with gradual spreading of DNA methylation centered at the SP1/AP1 transcription factor binding sites in precursor lesions, with subsequent spreading of methylation across the entire CpG island in transition to CaP.

cancer biology↗

bioRxiv2021

Phased Mutations and Complex Rearrangements in Human Prostate Cancer Cell Lines through Linked-Read Whole Genome Sequencing

A limited number of cell lines have fueled the majority of preclinical Prostate cancer (PCa) research. Despite tremendous effort in characterizing their molecular profiles, comprehensive whole genome sequencing with allelic phasing of somatic genome alterations has not been undertaken to date. Here, we utilized whole genome Linked-read sequencing to obtain haplotype information from the seven most commonly used PCa cell lines (PC3, LNCaP, DU145, CWR22Rv1, VCaP, LAPC4, MDA-PCa-2b), four castrate resistant (CR) subclones (LNCaP_Abl, LNCaP_C42b, VCaP-CR, LAPC4-CR), and an immortalized prostate epithelial line RWPE-1. Phasing of mutations allowed derivation of "Gene-level Haplotype" to assess whether a gene harbored heterozygous mutations in one or both alleles, providing a comprehensive catalogue of mono or bi-allelically inactivated genes. Phased structural variant analysis allowed identification of complex rearrangement chains consistent with chromothripsis and chromoplexy, with breakpoints occurred across a single allele, providing further evidence that complex SVs occurred in a concerted event, rather than through accumulation of multiple independent rearrangements. Additionally, comparison of parental and CR subclones revealed previously known and novel genomic alterations associated with the CR clones. This study therefore comprehensively characterized phased genomic alterations in the commonly used PCa cell lines and provided a useful resource for future cancer research.

cancer biology↗

bioRxiv2020

CryoGAN: A New Reconstruction Paradigm for Single-particle Cryo-EM Via Deep Adversarial Learning

We present CryoGAN, a new paradigm for single-particle cryo-EM reconstruction based on unsupervised deep adversarial learning. The major challenge in single-particle cryo-EM is that the imaged particles have unknown poses. Current reconstruction techniques are based on a marginalized maximum-likelihood formulation that requires calculations over the set of all possible poses for each projection image, a computationally demanding procedure. CryoGAN sidesteps this problem by using a generative adversarial network (GAN) to learn the 3D structure that has simulated projections that most closely match the real data in a distributional sense. The architecture of CryoGAN resembles that of standard GAN, with the twist that the generator network is replaced by a model of the cryo-EM image acquisition process. CryoGAN is an unsupervised algorithm that only demands projection images and an estimate of the contrast transfer function parameters. No initial volume estimate or prior training is needed. Moreover, CryoGAN requires minimal user interaction and can provide reconstructions in a matter of hours on a high-end GPU. In addition, we provide sound mathematical guarantees on the recovery of the correct structure. CryoGAN currently achieves a 8.6 [A] resolution on a realistic synthetic dataset. Preliminary results on real {beta}-galactosidase data demonstrate CryoGANs ability to exploit data statistics under standard experimental imaging conditions. We believe that this paradigm opens the door to a family of novel likelihood-free algorithms for cryo-EM reconstruction.

biochemistry↗

bioRxiv2018

Predicting Aquatic Development and Mortality Rates of Aedes Aegypti

Mosquito-borne pathogens continue to be a significant burden within human populations, with Aedes aegypti continuing to spread dengue, chikungunya, and Zika virus throughout the world. Using data from a previously conducted study, a linear regression model was constructed to predict the aquatic development rates based on the average temperature, temperature fluctuation range, and larval density. Additional experiments were conducted with different parameters of average temperature and larval density to validate the model. Using a paired t-test, the model predictions were compared to experimental data and showed that the prediction models were not significantly different for average pupation rate, adult emergence rate, and juvenile mortality rate. The models developed will be useful for modeling and estimating the number of Aedes aegypti in the environment under different temperature, diurnal temperature variations, and larval densities.\n\nAuthor SummaryUsing experimental data from experiments conducted on Aedes aegypti, we formulated regression models to predict pupation, adult emergence, and juvenile mortality rates based on average temperature, temperature fluctuation range, and larval density. The prediction models produced were shown to account for high levels of variation within the data. Validation was performed by comparing omitted data sets to the predictions generated by our models. Our results show that the models produce results that are not significantly different from the experimental results and are capable of predicting aquatic development rates of Ae. aegypti.

ecology↗