Biology subjects

Kumar-Singh, S.

Publications and source records attributed to Kumar-Singh, S..

4 recordsLinked to original sources

bioRxiv2025

Comparative characterization of OncoPro and Wnt-Based media reveals distinct phenotypic and pharmacologic states in patient-derived tumor organoids

BackgroundPatient-derived tumor organoids (PDTOs) are strongly influenced by culture medium. We compared OncoPro (OP) Tumoroid Culture medium with conventional Wnt/R-spondin/noggin (Wnt) medium. This recently developed OP medium offers a standardized, serum-free alternative to Wnt-based formulations. MethodsWe compared OP and Wnt media across 36 PDTO lines from various malignancies (colorectal, pancreatic, breast, lung, gastric, gastroesophageal junction, biliary head- and neck and uknown primary), assessing establishment success. Selected PDTO models were subjected to downstream characterization, including morphological assessment and bulk transcriptomic profiling with comparison to public single-cell RNA sequencing reference datasets (n=11), whole-exome sequencing (WES) (n=9), and pharmacological response profiling to a 33-drug panel (n=3). ResultsAdaptation from Wnt medium to OP succeeded in 83.3% (15/18), whereas de novo establishment favored Wnt (33.3% vs 11.1%). Key oncogenic driver alterations were retained across matched organoid cultures, supporting preservation of tumor-relevant genomic features. Transcriptomic profiling confirmed preserved tumor-identity across media, while revealing different epithelial state programs: Wnt upregulated proliferation/stemness-associated genes (e.g. LGR5) and OP enriched adhesion-associated genes and inflammatory/TGF-{beta} programs. In scRNA databases OP signatures preferentially mapped to malignant epithelial compartments in pancreatic cancer, whereas Wnt signatures were linked to non-malignant epithelium. Similarly, in colon cancer OP signature mapped predominantly to the malignant epithelial compartments. Drug (n=33) screening in pancreatic- and colorectal cancer PDTOs (n=3) demonstrated consistent medium-dependent shifts: Wnt-grown PDTOs were globally more sensitive in the screened subset, particularly to MAPK-axis inhibitors and apoptosis-sensitizers, while OP-grown PDTOs exhibited relative resistance. ConclusionsCulture medium composition is a key determinant of PDTO phenotype, transcriptome and drug sensitivity. Wnt medium was associated with drug-sensitive states, whereas OP medium was associated with adhesion- and inflammatory-related programs, relative resistance in the screened subset of 33 drugs and closer alignment with malignant epithelial programs in the analyzed pancreatic / colorectal cancer single-cell atlases.

cancer biology↗

bioRxiv2025

Generation of a T cell receptor, cytokine and cell repertoire synovial fluid atlas to define commonalities and dissimilarities between arthritic diseases through systems immunology approaches

Although different chronic arthritic diseases are defined by clinical factors like gender, psoriasis and auto-antibodies, the biology of inflamed joints while comparing the different diseases remains neglected. Here, after curating an inflamed joint derived T-cell receptor (TCR) database, our new TRIASSIC tool identified 66303 significantly convergent TCR clonotypes. Clustering TCR clonotypes showed that synovial fluid convergence clusters (SFCCs) characterized HLA-B27+ mediated diseases (spondyloarthritis, SpA, and enthesitis-related juvenile idiopathic arthritis, JIA-ERA), Lyme arthritis and oligoarticular JIA. Single-cell transcriptomics and bulk proteomics showed upregulated interferon type I and II and TNF- pathways in oJIA. Adult and juvenile psoriatic arthritis, (JIA-)PsA, was characterized by upregulated HSP expression in monocytes and TXNIP in T-cells. We discovered an abundance of CCL5 expressing CD8+ T-cells in SF from HLA-B27+ JIA-ERA and SpA patients. JIA-ERA patients showed upregulation of CD74 and LGALS1 in Th1 and Th17 cells and IGHV7-4.1 in B-cells. oJIA patients shared a TRBV28 RG-motif on CXCL13 producing helper T-cells. Rheumatoid arthritis and (JIA-)PsA patients carried EBV-reactive cytotoxic CD8+ T-cells. Annexin signalling was shown to be important in the intercellular communication for all arthritis groups. Collectively, our work showed that chronic arthritis is characterized by both disease-specific and broadly shared mechanisms.

immunology↗

bioRxiv2024

Lacticaseibacillus rhamnosus GG in a chewable colonizes the nose and facilitates local immune benefits in allergic rhinoconjunctivitis patients

Current treatments fall short in managing allergic rhinitis (AR), emphasizing the need for additional strategies. Beneficial bacteria application shows promise in AR, however most studies focus on oral probiotic administration without monitoring the applied strains in the upper respiratory tract (URT) and their local effects. In this randomized, double-blind, placebo-controlled trial, the probiotic Lacticaseibacillus rhamnosus GG was administered via chewable tablets in seasonal AR patients, randomized to probiotic (n=33) or placebo (n=31) groups. Per-protocol analysis of the URT microbiome, immune markers and AR symptoms was performed. L. rhamnosus GG trafficked from chewables to the oropharynx (77%, p=0.02) and nasopharynx (41%, p<0.0001). Control of self-reported AR symptoms via validated questionnaires under grass pollen exposure was observed after two weeks of probiotic administration and not upon placebo. A local decrease in salivary interleukin-4 (p < 0.05) and nasal IL-13 (p < 0.0001) was observed in the probiotic group. These data indicate that L. rhamnosus GG chewables can target the URT and exert local effects on key allergy cytokines after temporal probiotic engraftment. ImportanceAllergic rhinitis (AR) or hay fever is a highly prevalent condition, impacting nearly half the population in some countries. Supplementation of beneficial bacteria or probiotics has gained increasing attention in AR, and a key innovative way to do this is direct administration to the upper airways. Our study shows for the first time that the model probiotic strain Lacticaseibacillus rhamnosus GG can traffic to the nose in AR patients when administered via a slow-releasing chewable tablet. This trafficking is associated with local benefits in the airways, including on grass pollen-induced nasal symptoms and allergy-related cytokines.

microbiology↗

bioRxiv2020

Rapid evolution drives the rise and fall of carbapenem resistance during an acute Pseudomonas aeruginosa infection

It is well established that antibiotic treatment selects for resistance in pathogenic bacteria. However, the evolutionary responses of pathogen populations to antibiotic treatment during infections remain poorly resolved, especially in acute infections. Here we map the evolutionary responses to treatment in high definition through genomic and phenotypic characterization of >100 isolates from a patient with P. aeruginosa pneumonia. Antibiotic therapy (meropenem, colistin) caused a rapid crash of the P. aeruginosa population in the lung, but this decline was followed by the spread of meropenem resistance mutations that restrict antibiotic uptake (oprD) or modify LPS biosynthesis (wbpM). Low fitness strains with high-level meropenem resistance (oprD) were then replaced by high fitness strains with anti-resistance mutations in the MexAB-OprM efflux pump, causing a rapid decline in resistance to both meropenem and a collateral loss of resistance to a broad spectrum of antibiotics. In contrast, we did not observe any evolutionary responses to antibiotic treatment in the intestinal population of P. aeruginosa. Carbapenem antibiotics are key to the treatment of infections caused by Gram negative pathogens, and our work highlights the ability of natural selection to drive both the rapid rise and fall of carbapenem resistance during acute infections.

evolutionary biology↗