Biology subjects

Parmar, K.

Publications and source records attributed to Parmar, K..

12 recordsLinked to original sources

bioRxiv2026

DNA-PK enforces the S/G2 checkpoint in ATM-deficient cells to limit ATR inhibitor efficacy

ATR inhibition has been proposed as a strategy for tumors under replication stress or those harboring ATM deficiency. However, anti-tumor activity is limited by DNA-PK and ATM compensation. Here, we have delineated distinct roles for DNA-PK and ATM during ATR inhibitor exposure. Both kinases are activated in a cell cycle-dependent manner at the S/G2 boundary following ATR inhibition. DNA-PK imposes the S/G2 checkpoint and promotes completion of DNA replication, whereas ATM detects persistent aberrant DNA replication structures with associated DNA damage in late S and G2/M to establish a G2/M checkpoint promoting DNA repair. In ATM-deficient cells and patient tumors, DNA-PK is activated following ATR inhibition and assumes greater versatility by not only enforcing the S/G2 checkpoint but also by detecting aberrant replication structures in S phase in place of ATM, allowing cells to tolerate ATR inhibition. Consequently, DNA-PK inhibition synergizes with ATR inhibition in ATM-deficient cells and enhances ATR inhibitor efficacy in ATM-deficient PDX models. These data support clinical evaluation of combined ATR and DNA-PK inhibition in ATM-deficient cancers.

cancer biology↗

bioRxiv2026

Spatially Organized Tertiary Lymphoid Structures Emerge in Small Cell Lung Cancer and Associate with Improved Survival

Tertiary lymphoid structures (TLS) are ectopic immune aggregates associated with improved prognosis and response to immunotherapy in multiple solid tumors. However, their presence, spatial organization, and functional relevance in small cell lung cancer (SCLC), a malignancy characterized by profound immune evasion, remain poorly understood. Using imaging mass cytometry (IMC) across 320 regions of interest spanning primary lung tumor, tumor-adjacent lung, liver and lymph node metastasis, complemented by Visium HD spatial transcriptomics, we characterized the cellular architecture and molecular programs of TLS-like niches in SCLC. TLS-like niches were identified in a subset of SCLC samples, predominantly primary lung tumor tissues and adjacent lung, spanning a continuum from loose lymphoid aggregates to compact follicle-like immune structures. Organized TLS-like niches contained CD20+ B-cell cores, closely associated with CD4+ and CD8A+ T cells, proliferating lymphocytes, HLA-DR+ antigen-presenting compartments, and SMA+ stromal scaffolds, and were enriched for canonical TLS organizer signals (CXCL13, LTB, FDCSP). Patients with TLS-positive tumors demonstrated improved overall survival, and core TLS-associated transcriptional programs were associated with favorable survival in an independent bulk RNA-seq cohort. To our knowledge, this represents one of the first spatially resolved analyses of TLS-like immune architecture in SCLC, demonstrating that organized lymphoid immunity can emerge in this classically immune-evasive disease and is associated with improved survival.

cancer biology↗

bioRxiv2026

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

Metastatic progression requires cancer cells to adapt to the unique constraints of distant organ microenvironments, yet the mechanisms that drive organ-specific adaptations remain poorly understood. Here, we show that the liver actively rewrites metastatic cancer cell identity, driving tumor cells toward a hepatobiliary progenitor-like state. Through integrated transcriptomic, proteomic, metabolomic, and epigenomic analyses of patient-derived rapid-autopsy samples and experimental models, we identify this state as selectively enriched in liver metastases. It is characterized by co-activation of hepatic and biliary/progenitor regulators HNF4A and SOX9 and is observed across multiple epithelial cancers, indicating a conserved response to the hepatic niche. Mechanistically, hepatocyte-derived TGF-{beta} and hypoxia converge to activate a HIF-1-ACLY axis, increasing nuclear acetyl-coenzyme A availability and histone acetylation at hepatic lineage regulatory elements to drive hepatobiliary reprogramming. This coordinated niche-response program can be captured transcriptionally and is associated with inferior overall survival. Disruption of this pathway suppresses hepatic reprogramming and impairs liver metastatic fitness. These findings identify the liver as an active determinant of metastatic cell fate, linking microenvironmental signaling to metabolic and chromatin remodeling programs that enable lineage plasticity. More broadly, they reveal organ-specific reprogramming as a fundamental principle of metastasis and a therapeutic vulnerability in liver metastases.

cancer biology↗

bioRxiv2026

Maltose aids in the growth of Salmonella Typhimurium in nitrogen-deficient conditions

Enteric pathogens, such as Salmonella, encounter uncertain nutrients in both the host and the environment. Nutrients such as carbon and nitrogen are essential for growth, and when these nutrients are limited, bacteria have developed various mechanisms to overcome stress and thrive in nutrient-rich environments. In this study, we investigated the role of the disaccharide sugar maltose in the growth and pathogenicity of Salmonella Typhimurium (STM) under nitrogen-deficient culture conditions. Throughout the study, we used Burks medium to mimic nitrogen-deficient conditions. STM growth in Burks medium was minimal, and maltose supplementation enhanced STM growth in both liquid and solid Burks media. The STM grown in Burks medium had a reduced bacterial cell length, which increased upon the addition of maltose and became comparable to that of LB-grown STM WT. Growth was dependent on the NtrBC two-component system and sigma factor RpoE. Deletion of ntrB and rpoE significantly reduced the growth in Burks medium during the log phase. Salmonella grown in Burks medium with maltose had reduced invasion in Caco-2 cells, phagocytosis in RAW 264.7 macrophages, and organ burden in C57BL/6 mice. Our findings revealed the role of maltose in enhancing the growth and length of Salmonella under nitrogen-deficient conditions. However, Salmonella grown in Burks medium with maltose is defective in pathogenesis.

microbiology↗

bioRxiv2025

Disruption of Microhomology-mediated End-joining in Ewing Sarcoma

Ewing sarcoma (EwS) is a group of bone and soft tissue cancers in children and young adults. Since EwS cells have pronounced sensitivity to radiation and chemotherapy-induced DNA damage, the role of the oncoprotein, EWS-FLI1, in DNA repair is likely. Here, we demonstrate that EWS-FLI1 causes a defect in microhomology-mediated end-joining (MMEJ) repair. EWSR1 is a splicing factor that promotes the faithful splicing of the POLQ pre-mRNA, required for the expression of POL{Theta}, a critical protein in the MMEJ pathway. Expression of EWS-FLI1, or loss of EWSR1, causes exon 25 skipping of the POLQ transcript, decreased POL{Theta} expression, impaired MMEJ, and cellular sensitivity to inhibitors of the Fanconi Anemia (FA), NHEJ, or HR pathways, through the mechanism of synthetic lethality. Knockdown of EWS-FLI1 expression restores POL0 mitotic foci and increases MMEJ activity. Inhibitors of the FA, NHEJ, or HR therefore may provide a targeted therapy for patients with EwS. Highlights- Ewing sarcoma tumors have a deficiency in POL{theta} expression and a corresponding loss of MMEJ activity - EWSR1 is a splicing factor that interacts with other splicing factors such as FUBP1 and KHSRP/FUBP2 to accurately splice the POLQ mRNA. - The EWS-FLI1 fusion oncoprotein, or loss of EWSR1, causes a splicing defect, leading to exon25 skipping of the POLQ pre-mRNA and loss of POL{theta} expression - The MMEJ deficiency of EwS cells results in cellular sensitivity to inhibitors of Fanconi Anemia, Homologous Recombination or Non-Homologous End-Joining - Exon 25 skipping of POLQ mRNA is a predictive biomarker for HR inhibitors in human cancers

cancer biology↗

bioRxiv2025

Maltose facilitates Salmonella growth under nitrogen stress while impairing adhesion to epithelial cells

The composition of nutrients in the intestine defines a niche for colonising gut pathogens. The lack of nutrients suitable for pathogens due to competition from resident intestinal microbiota or dietary preferences leads to colonisation failure by pathogens. In this study, we investigated the impact of the disaccharide sugar maltose on Salmonella Typhimurium (STM) pathogenicity during the early phases of infection in C57BL/6 mice and human colon carcinoma cells (Caco-2). We found that supplementation of maltose at lower concentrations inhibited STM colonisation in the ileum of mice. To understand this, we investigated the role of maltose metabolism in human colon epithelial (Caco-2) cells. Deleting the maltose metabolism gene (malQ) increased adhesion to Caco-2 cells. The increased adhesion was due to increased expression of type 1 fimbriae. Inhibiting the type 1 fimbriae-mediated binding to host epithelial cells by incubating with mannose resulted in similar adhesion of STM WT and STM {Delta}malQ. We further identified that malQ regulates the adhesion of Salmonella through the sigma factor RpoE. Overall, malQ in Salmonella inhibits infection in epithelial cells by reducing its adhesion to host epithelial cells.

microbiology↗

bioRxiv2025

Undecaprenyl Pyrophosphate Phosphatase (UppP) is a pivotal element in Salmonella Intramacrophage Survival

To establish infection, Salmonella confronts a dynamic barrage of host-induced stresses. The peptidoglycan layer, essential for maintaining cell integrity and counteracting environmental stress, relies on the lipid carrier undecaprenyl phosphate, generated by Undecaprenyl pyrophosphate phosphatase (UppP). While UppP is linked to virulence in other pathogens, its role in Salmonella remains unclear. We show that an uppP mutant in S. Typhimurium exhibits altered cell morphology, reduced stiffness, and impaired survival in RAW 264.7 macrophages. The mutant is also attenuated in systemic infection in C57BL/6 mice. These defects are associated with increased sensitivity to nitrosative stress. Notably, iNOS inhibition or deficiency restores intracellular survival of the uppP mutant in both RAW 264.7 macrophages and the mouse model, implicating UppP in resistance to nitrosative stress. Our findings reveal a critical role for UppP in promoting Salmonella survival within macrophages and contributing to systemic pathogenesis.

microbiology↗

bioRxiv2024

The resilience of Salmonella to bile stress is impaired due to the reduced efflux pump activity mediated by the antioxidant enzyme YqhD

Bile salts play a critical role in modulating the host gut. They have antimicrobial properties wherein they disrupt the bacterial membrane and produce reactive oxygen species, causing DNA damage. Bile-resistant pathogen like Salmonella regulates their metabolic activity to counteract the effects of bile. This study explores the role of YqhD, a putative alcohol dehydrogenase, in Salmonellas bile salt susceptibility. We observed increased survival of yqhD mutant in the in vitro studies in LB media with bile, liver cell line HepG2 and C57BL/6 mice on treatment with 8% sodium cholate in the intestine. Bile salts are produced for the digestion of fat. Replacing the chow diet with a high-fat diet (HFD) in mice increased organ burden in C57BL/6 mice of the yqhD mutant. Mutation of yqhD on bile salt exposure leads to increased reactive oxygen species and modulation of antioxidant genes in the bacteria. The oxidative stress of the yqhD mutant is indispensable for improved survival when exposed to bile salt. The addition of antioxidant glutathione in vitro reduced the enhanced growth of the yqhD mutant. Similarly, in the gp91-/- phox mice, there was a reduced organ burden of yqhD mutant on exposure to HFD compared to chow-fed mice. Furthermore, the yqhD mutant increases AcrAB efflux pump activity regulated by RamA/R regulon. TeaserRedox gene yqhD regulates bile salt susceptibility by modulating Salmonellas ROS and efflux pump activity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/625033v1_figa1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@14e30f0org.highwire.dtl.DTLVardef@6f14a0org.highwire.dtl.DTLVardef@b3291dorg.highwire.dtl.DTLVardef@503988_HPS_FORMAT_FIGEXP M_FIG A. STM {Delta}yqhD has less organ burden in the C57BL/6 mice than STM WT, and there was a similar organ burden in gp91phox-/-. On HFD exposure, the organ burden of STM {Delta}yqhD became similar to STM WT in C57BL/6 mice, and there was reduced organ of STM {Delta}yqhD burden when gp91phox-/- were exposed to HFD. B. On bile salt exposure, YqhD in Salmonella reduces ROS in bacteria and expression of RamA, decreasing the AcrAB efflux pump activity and reducing survival. C_FIG

microbiology↗

bioRxiv2024

Unravelling the Dynamics of Bacterial-Laden Respiratory Droplets: Epidemiological Transfer from Fomites to Susceptible Host

This study provides the first comprehensive investigation into how pathogen-laden respiratory droplets transfer diseases via inanimate surfaces. Respiratory fluid ejections containing pathogens pose a significant health threat, especially in high-traffic areas like hospitals, public transport, restaurants, and schools. When these droplets dry on surfaces, they form deposits that can transfer pathogens to healthy individuals through contact and can be ingested via the oral or nasal route. The study examined the effects of varying salt and mucin concentrations in respiratory fluid droplets containing Pseudomonas aeruginosa (PA). Results showed that PA viability increased tenfold at elevated mucin concentrations, while changes in salt concentration had minimal impact. Adhesive properties of the deposits were analysed using atomic force spectroscopy and scotch tape test. Pathogen transfer from the deposit to a fingerprint patterned model thumb at different relative humidity (RH) levels was assessed using confocal microscopy, showing significant pathogen transfer at elevated RH. Out of 106 CFU/ml pathogens in deposits, 17% to 38% are potentially transferable, with most of the transfer occurring from the droplets edge deposits. The study also explored evaporation, internal flow, and precipitation dynamics, with deposit and pathogen distribution characterized by optical profilometry, scanning electron microscopy, and confocal microscopy.

microbiology↗

bioRxiv2024

Weather-related changes in the dehydration of respiratory droplets on surfaces bolster bacterial endurance

HypothesisThe study shows for the first time a fivefold difference in the survivability of the bacterium Pseudomonas Aeruginosa (PA) in a realistic respiratory fluid droplet on fomites undergoing drying at different environmental conditions. For instance, in 2023, the annual average relative humidity (RH) in London (UK) is 71%, whereas in Delhi (India), it is 45%, showing that disease spread from fomites could have a demographic dependence. Respiratory fluid droplet ejections containing pathogens on inanimate surfaces are crucial in disease spread, especially in nosocomial settings. However, the interplay between evaporation dynamics, internal fluid flow and precipitation and their collective influence on the distribution and survivability of pathogens at different environmental conditions are less known. ExperimentsShadowgraphy imaging is employed to study evaporation, and optical microscopy imaging is used for precipitation dynamics. Micro-particle image velocimetry (MicroPIV) measurements reveal the internal flow dynamics. Confocal imaging of fluorescently labelled PA elucidates the bacterial distribution within the deposits. FindingsThe study finds that the evaporation rate is drastically impeded during drying at elevated solutal concentrations, particularly at high RH conditions. MicroPIV shows reduced internal flow under high RH conditions. Evaporation rate influences crystal growth, with delayed efflorescence and extending crystallisation times. PA forms denser peripheral arrangements under high evaporation rates and shows a fivefold increase in survivability under low evaporation rates. These findings highlight the critical impact of environmental conditions on pathogen persistence and disease spread from inanimate surfaces. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/579296v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@6b9876org.highwire.dtl.DTLVardef@1e6a18forg.highwire.dtl.DTLVardef@78d308org.highwire.dtl.DTLVardef@66ebe8_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2019

Inherited duplications of PPP2R3B promote naevi and melanoma via a novel C21orf91-driven proliferative phenotype

The majority of the heredity of melanoma remains unexplained, however inherited copy number changes have not yet been systematically studied. The genetic environment is highly relevant to treatment stratification, and new gene discovery is therefore desirable. Using an unbiased whole genome screening approach for copy number we identify here a novel melanoma predisposing factor, familial duplications of gene PPP2R3B, encoding a regulatory unit of critical phosphatase PP2A. Significant correlation between expression of PPP2R3B in tumour tissue and survival in a large melanoma cohort was confirmed, and associated with a non-immunological expression profile. Mechanistically, construction and extensive characterization of a stable, inducible cellular model for PPP2R3B overexpression revealed induction of pigment cell switching towards proliferation and away from migration. Importantly, this was independent of the known microphthalmia-associated transcription factor (MITF)-controlled pigment cell phenotype switch, and was instead driven by uncharacterised gene C21orf91. Bioinformatic studies point to C21orf91as a novel target of MITF, and therefore a potential hub in the control of phenotype switching in melanoma. This study identifies novel germline copy number variants in PPP2R3B predisposing to melanocytic neoplasia, and uncovers a new potential therapeutic target C21orf91 in the control of pigment cell proliferation.

genomics↗

bioRxiv2019

Cellular heterogeneity during mouse pancreatic ductal adenocarcinoma progression at single-cell resolution

Background & AimsPancreatic ductal adenocarcinoma (PDA) is a major cause of cancer-related death with limited therapeutic options available. This highlights the need for improved understanding of the biology of PDA progression. The progression of PDA is a highly complex and dynamic process featuring changes in cancer cells and stromal cells; however, a comprehensive characterization of PDA cancer cell and stromal cell heterogeneity during disease progression is lacking. In this study, we aimed to profile cell populations and understand their phenotypic changes during PDA progression. MethodsWe employed single-cell RNA sequencing technology to agnostically profile cell heterogeneity during different stages of PDA progression in genetically engineered mouse models. ResultsOur data indicate that an epithelial-to-mesenchymal transition of cancer cells accompanies tumor progression. We also found distinct populations of macrophages with increasing inflammatory features during PDA progression. In addition, we noted the existence of three distinct molecular subtypes of fibroblasts in the normal mouse pancreas, which ultimately gave rise to two distinct populations of fibroblasts in advanced PDA, supporting recent reports on intratumoral fibroblast heterogeneity. Our data also suggest that cancer cells and fibroblasts are dynamically regulated by epigenetic mechanisms. ConclusionThis study systematically outlines the landscape of cellular heterogeneity during the progression of PDA. It strongly improves our understanding of the PDA biology and has the potential to aid in the development of therapeutic strategies against specific cell populations of the disease.

cancer biology↗