Biology subjects

Rohatgi, N.

Publications and source records attributed to Rohatgi, N..

7 recordsLinked to original sources

bioRxiv2026

Pyroptotic cell-derived factors promote osteoclast differentiation

The NLRP3 D301N substitution, the murine ortholog of the human D303N variant, causes NLRP3 constitutive activation (NLRP3CA) and inflammasome assembly. Here, we show that priming signals induced by lipopolysaccharide (LPS) are sufficient to trigger GSDMD-dependent pyroptosis in NLRP3CA-expressing bone marrow-derived macrophages (BMDMs), but not in wild-type (NLRP3WT) cells. NLRP3CA mice exhibit elevated IL-1{beta} secretion and LDH release in bone marrow supernatants under both basal and LPS-challenged conditions. Other cytokines (e.g., TNF-) increased comparably between genotypes, indicating that NLRP3CA specifically amplifies inflammasome-dependent responses. Conditioned medium (CM) from LPS-treated NLRP3CA BMDMs significantly enhanced osteoclast (OC) differentiation in vivo and in vitro compared to NLRP3WT CM, as did bone marrow supernatants from NLRP3CA mice. This osteoclastogenic activity was largely independent of IL-1{beta}, as demonstrated by experiments using IL-1{beta}-deficient NLRP3CA BMDMs, IL-1{beta}-neutralizing antibodies, and genetic deletion of the IL-1 receptor. The osteoclastogenic factors were primarily soluble proteins, as heat inactivation and proteinase K digestion markedly reduced OC formation. Extracellular vesicles (EVs) from NLRP3CA CM modestly promoted OC differentiation, but EV-depleted supernatants retained full activity, indicating that the primary mediators are soluble proteins not carried within EVs. Together, these findings establish NLRP3CA as a well-controlled model for studying pyroptosis and demonstrate that pyroptotic cells release soluble proteins that drive osteoclastogenesis independently of IL-1{beta}.

cell biology↗

bioRxiv2026

The osteoclast intracellular environment fosters bacterial growth during Staphylococcus aureus infection

Bone infections, which are predominantly caused by Staphylococcus (S.) aureus, can be difficult to treat and have high rates of chronicity and reoccurrence. We previously identified that osteoclasts, the cells that break down bone matrix, may contribute to disease progression by allowing S. aureus to replicate intracellularly. There we identified that this bacteriums ability to grow intracellularly is tied to the maturation of osteoclasts. In this study we addressed whether osteoclast differentiation supports intracellular growth by changing the host cells response to infection or by altering the host cell environment to better support S. aureus. Using dual species RNA-sequencing we analyzed host and bacterial transcripts of infected osteoclast and precursor bone marrow macrophage (BMM) cultures. Host transcript analysis suggests that infected osteoclasts are slow to upregulate bacterial response genes compared to BMMs. We also identify that the S. aureus transcriptional response is primarily determined by the host cell type, and that bacteria in osteoclasts upregulate carbon metabolism genes compared to those inside BMMs. By utilizing intracellular survival assays on S. aureus mutants deficient in carbon metabolism and related pathways we determine that S. aureus require glycolysis, acetyl-CoA synthesis, and aspartate biosynthesis for proliferation inside osteoclasts, although bacteria can survive without them. With differentiation, osteoclasts increase glutamine uptake, and this metabolite is required for S. aureus intracellular growth. Taken together, these findings suggest that osteoclasts support S. aureus intracellular growth by providing nutrients required to replicate in the context of a blunted antimicrobial response. IMPORTANCEInfectious osteomyelitis, bone infection, is frequently caused by the bacterium Staphylococcus aureus. Intracellular infection of cells that build bone, osteoblasts, and cells that resorb bone, osteoclasts, have been implicated in disease progression by providing a niche for immune evasion. While S. aureus in osteoblasts are largely quiescent, bacteria in osteoclasts proliferate and therefore may be a source of reemergent infection. Factors that promote this growth in osteoclasts are poorly characterized. In this study we find that osteoclasts have a diminished transcriptional response to infection and show that S. aureus acquire glucose and glutamine, which have high flux in osteoclasts, to support intracellular growth. We further observe that S. aureus in osteoclasts require aspartate synthesis to grow intracellularly. This work highlights the importance of host cellular metabolism for the intracellular fate of S. aureus as an added factor beyond the direct antimicrobial response.

microbiology↗

bioRxiv2025

Convergent genomic and molecular features predict risk of metachronous metastasis in clear cell renal cell carcinoma

The molecular features determining the risk of metachronous metastases in clear cell renal cell carcinoma (ccRCC) are poorly defined. Using a systematic tumor transcriptome deconvolution approach, we investigated the genomic and transcriptomic profiles of 192 ccRCC primary tumors with extended clinical follow-up to identify cancer and stromal cell molecular features associated with metastatic risk. At the genomic level, we identified a significantly higher frequency of copy number loss at 1p31-36 in primary tumors that later progressed with metastases. Tumor transcriptome deconvolution identified significant down-regulation of epithelial cell polarity, including PATJ (1p31), and fatty acid metabolism, including CYP4A11 (1p33), in cancer cells of tumors that developed metastatic progression. We developed and benchmarked a compact 5-feature predictive model (5G) that demonstrated improved accuracy over existing ccRCC gene signatures in the prediction of metachronous metastasis risk. Overall, our study highlights convergent genomic and transcriptomic alterations in chromosome 1p, driving dysregulation of epithelial cell polarity and fatty acid metabolism, as putative novel risk factors of metachronous metastasis in ccRCC.

cancer biology↗

bioRxiv2024

Seed sequences mediate off-target activity in the CRISPR-interference (CRISPRi) system

The CRISPR interference (CRISPRi) system is a powerful tool that is widely used to selectively and efficiently silence genes in functional genomics research applications. However, the extent of off-target activity associated with the CRISPRi system has not been systematically investigated. Here, we utilized a genome-wide CRISPRi Cas9 single guide RNA (sgRNA) library to investigate the presence of off-target activity and its effects on gene expression. Our findings suggest that off-target effects in CRISPRi are quite pervasive and have direct and indirect impact on gene expression. Most of the identified off-target activities can be accounted for by complementarity of the PAM-proximal genomic sequence with the 3 half of the sgRNA spacer sequence, the seed sequence. We also report that not all PAM proximal positions are equally important for binding of sgRNA to the DNA and that mismatches in the PAM-proximal regions can be tolerated depending on the sequence context.

bioinformatics↗

bioRxiv2023

Tmem178 negatively regulates IL-1β production through inhibition of the NLRP3 inflammasome

ObjectiveInflammasomes modulate the release of bioactive IL-1{beta}. Excessive IL-1{beta} levels are detected in patients with systemic juvenile idiopathic arthritis (sJIA) and cytokine storm syndrome (CSS) with mutated and unmutated inflammasome components, raising questions on the mechanisms of IL-1{beta} regulation in these disorders. MethodsTo investigate how the NLRP3 inflammasome is modulated in sJIA, we focused on Tmem178, a negative regulator of calcium levels in macrophages, and measured IL-1{beta} and caspase-1 activation in wild-type (WT) and Tmem178-/- macrophages following calcium chelators, silencing of Stim1, a component of store-operated calcium entry (SOCE), or by expressing a Tmem178 mutant lacking Stim1 binding site. Mitochondrial function in both genotypes was assessed by measuring oxidative respiration, mitochondrial reactive oxygen species (mtROS), and mitochondrial damage. CSS development was analyzed in Perforin-/-/Tmem178-/- mice infected with LCMV in which inflammasome or IL-1 signaling was pharmacologically inhibited. Human TMEM178 and IL-1B transcripts were analyzed in a dataset of peripheral blood monocytes from healthy controls and active sJIA patients. ResultsTMEM178 levels are reduced in monocytes from sJIA patients while IL-1B show increased levels. Accordingly, Tmem178-/- macrophages produce elevated IL-1{beta} compared to WT cells. The elevated intracellular calcium levels following SOCE activation in Tmem178-/- macrophages induce mitochondrial damage, release mtROS, and ultimately, promote NLRP3 inflammasome activation. In vivo, inhibition of inflammasome or IL-1 neutralization prolongs Tmem178-/- mouse survival to LCMV-induced CSS. ConclusionDownregulation of Tmem178 levels may represent a new biomarker to identify sJIA/CSS patients that could benefit from receiving drugs targeting inflammasome signaling.

immunology↗

bioRxiv2020

A pan-cancer metabolic atlas of the tumor microenvironment

Tumors are heterogeneous cellular environments with entwined metabolic dependencies. Here, we used a tumor transcriptome deconvolution approach to profile the metabolic states of cancer and non-cancer (stromal) cells in bulk tumors of 20 solid tumor types. We identified metabolic genes and processes recurrently altered in cancer cells across tumor types, including pan-cancer upregulation of deoxythymidine triphosphate (dTTP) production. In contrast, the tryptophan catabolism rate limiting enzymes, IDO1 and TDO2, were highly overexpressed in stroma, suggesting that kynurenine-mediated suppression of antitumor immunity is predominantly constrained by the stroma. Oxidative phosphorylation was unexpectedly the most upregulated metabolic process in cancer cells compared to both stromal cells and a large atlas of cancer cell lines, suggesting that the Warburg effect may be less pronounced in cancer cells in vivo. Overall, our analysis highlights fundamental differences in metabolic states of cancer and stromal cells inside tumors and establishes a pan-cancer resource to interrogate tumor metabolism.

cancer biology↗

bioRxiv2019

Data-driven inference of crosstalk in the tumor microenvironment

Signaling between cancer and nonmalignant (stromal) cells in the tumor microenvironment (TME) is key to tumorigenesis yet challenging to decipher from tumor transcriptomes. Here, we report an unbiased, data-driven approach to deconvolute bulk tumor transcriptomes and predict crosstalk between ligands and receptors on cancer and stromal cells in the TME of 20 solid tumor types. Our approach recovers known transcriptional hallmarks of cancer and stromal cells and is concordant with single-cell and immunohistochemistry data, underlining its robustness. Pan-cancer analysis reveals previously unrecognized features of cancer-stromal crosstalk. We find that autocrine cancer cell cross-talk varied between tissues but often converged on known cancer signaling pathways. In contrast, many stromal cross-talk interactions were highly conserved across tumor types. Interestingly, the immune checkpoint ligand PD-L1 was overexpressed in stromal rather than cancer cells across all tumor types. Moreover, we predicted and experimentally validated aberrant ligand and receptor expression in cancer cells of basal and luminal breast cancer, respectively. Collectively, our findings validate a data-driven method for tumor transcriptome deconvolution and establishes a new resource for hypothesis generation and downstream functional interrogation of the TME in tumorigenesis and disease progression.

cancer biology↗