Biology subjects

Panigrahi, A.

Publications and source records attributed to Panigrahi, A..

5 recordsLinked to original sources

bioRxiv2026

Early Blood Metabolome Remodeling Reveals Metabolic Signatures of Hypoxic-Ischemic Encephalopathy

Hypoxic-ischemic encephalopathy (HIE) is a neonatal brain injury in which a definitive diagnosis within the first 6 hours of life is essential for initiating therapeutic hypothermia and improving neurological outcomes. However, early clinical evaluation and currently available biomarkers lack quantitative specificity during this narrow therapeutic window. We are providing insights into how rapid disturbances in systemic metabolites that regulate cerebral energy metabolism, neurotransmitter cycling, redox balance, and membrane integrity generate a definitive biochemical signature of HIE immediately after birth. We performed quantitative blood-based 1H NMR metabolomics on collected blood samples within [~]1 hour of birth from 81 neonates (HIE, n = 42; non-HIE, n = 39), under optimized handling conditions to preserve metabolic integrity. Metabolite analysis revealed a distinct HIE-associated profile characterized by elevated lactate, alanine, succinate, glutamate, taurine, glycine, choline, and pyroglutamate, alongside significant depletion of glucose and glutamine compared with non-HIE controls (p < 0.05). These coordinated metabolic shifts reflect impaired mitochondrial respiration, enhanced anaerobic glycolysis, excitotoxic amino acid accumulation, altered membrane phospholipid turnover, and oxidative stress. Multivariate analysis demonstrated clear separation between groups (PLS-DA accuracy = 0.83, R{superscript 2}Y = 0.46, Q{superscript 2} = 0.82), with glutamine, lactate, glutamate, and pyroglutamate as key discriminators. Pathway enrichment highlighted perturbations in glycolysis, the glucose-alanine cycle, glutamate-glutamine metabolism, Warburg effect like metabolic reprogramming, and redox homeostasis. Integration into supervised machine-learning models (Random Forest, XGBoost, SVM, KNN) achieved strong diagnostic performance (AUC = 0.97 {+/-} 0.03; sensitivity {approx} 87%). Collectively, this minimally invasive NMR-to-machine-learning framework enables early, mechanistically grounded risk stratification of neonatal HIE within the therapeutic window.

neuroscience↗

bioRxiv2024

dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples

We employed laser microdissection to selectively harvest tumor cells and stroma from the microenvironment of formalin-fixed, paraffin-embedded head and neck squamous cell carcinoma (HNSCC) tissues. The captured HNSCC tissue fractions were analyzed by quantitative mass spectrometry-based proteomics using a data independent analysis approach. In paired samples, we achieved excellent proteome coverage having quantified 6,668 proteins with a median quantitative coefficient of variation under 10%. We observed significant differences in relevant functional pathways between the spatially resolved tumor and stroma regions. Our results identified extracellular matrix (ECM) as a major component enriched in the stroma, including many cancer associated fibroblast signature proteins in this compartment. We demonstrate the potential for comparative deep proteome analysis from very low starting input in a scalable format that is useful to decipher the alterations in tumor and the stromal microenvironment. Correlating such results with clinical features or disease progression will likely enable identification of novel targets for disease classification and interventions.

cancer biology↗

bioRxiv2023

Galectin-3-binding protein inhibits extracellular heparan 6-O-endosulfatse Sulf-2

Human extracellular 6-O-endosulfatases Sulf-1 and Sulf-2 are the only enzymes that post-synthetically alter the 6-O sulfation of heparan sulfate proteoglycans (HSPG), which regulates interactions of HSPG with many proteins. Oncogenicity of Sulf-2 in different cancers has been documented and we have shown that Sulf-2 is associated with poor survival outcomes in head and neck squamous cell carcinoma (HNSCC). In spite of its importance, limited information is available on direct protein-protein interactions of the Sulf-2 protein in the tumor microenvironment. In this study, we used monoclonal antibody (mAb) affinity purification and mass spectrometry to identify galectin-3-binding protein (LG3BP) as a highly specific binding partner of Sulf-2 in the secretome of HNSCC cell lines. We validated their direct interaction in vitro using recombinant proteins and have shown that the chondroitin sulfate (CS) covalently bound to the Sulf-2 influences the binding to LG3BP. We confirmed importance of the CS chain for the interaction by generating a mutant Sulf-2 protein that lacks the CS. Importantly, we have shown that the LG3BP inhibits Sulf-2 activity in vitro in a concentration dependent manner. As a consequence, the addition of LG3BP to a spheroid cell culture inhibited invasion of the HNSCC cells into Matrigel. Thus, Sulf-2 interaction with LG3BP has functional relevance, and may regulate physiological activity of the Sulf-2 enzyme as well as its activity in the tumor microenvironment.

cancer biology↗

bioRxiv2023

Heparan-6-O-endosulfatase 2 promotes invasiveness of head and neck squamous carcinoma cell lines in co-cultures with cancer associated fibroblasts

Local invasiveness of head and neck squamous cell carcinoma (HNSCC) is a complex phenomenon supported by interaction of the cancer cells with the TME. We and others have shown that CAFs are a component of the TME that can promote local invasion in HNSCC and other cancers. Here we report that the secretory enzyme Sulf-2 directly affects the CAF-supported invasion of HNSCC cell lines SCC35 and Cal33 into Matrigel. The Sulf-2 knockout (KO) cells differ from their wild type counterparts in their spheroid growths and formation, and the Sulf-2-KO leads to decreased invasion in a spheroid co-culture model with the CAF. Next, we investigated whether a fucosylated chondroitin sulfate isolated from the sea cucumber Holothuria Floridana (HfFucCS), affects activity of the Sulf-2 enzyme. Our results show that HfFucCS not only inhibits efficiently the Sulf-2 enzymatic activity but, like the Sulf-2 knockout, inhibits Matrigel invasion of the SCC35 and Cal33 cells co-cultured with the primary HNSCC CAF. These findings suggest that the heparan 6-O-endosulfatases regulate local invasion and could be therapeutically targeted with the inhibitory activity of a marine glycosaminoglycan. Simple SummaryLocal invasion of cancer cells is an early step in the cascade of metastasis that requires cooperation of multiple factors and cell types in the tumor microenvironment (TME). One important factor is the crosstalk of cancer cells with cancer associated fibroblasts (CAF). Here we explore the impact of a secretory enzyme heparan-6-O-endosulfatase 2 (Sulf-2) on the CAF-assisted invasion of head and neck squamous carcinoma cells into matrigel. We show that Sulf-2 knock out inhibits cancer cell invasion in a spheroid co-culture model and we identified a novel Sulf-2 inhibitor that, in the same model, limits cancer cell invasion.

cancer biology↗

bioRxiv2021

Proteogenomic Discovery of Neoantigens Facilitates Personalized Multi-antigen Targeted T cell Immunotherapy for Brain Tumors

Neoantigen discovery in pediatric brain tumors is hampered by their low mutational burden and scant tissue availability. We developed a low-input proteogenomic approach combining tumor DNA/RNA sequencing and mass spectrometry proteomics to identify tumor-restricted (neoantigen) peptides arising from multiple genomic aberrations to generate a highly target-specific, autologous, personalized T cell immunotherapy. Our data indicate that novel splice junctions are the primary source of neoantigens in medulloblastoma, a common pediatric brain tumor. Proteogenomically identified tumor-specific peptides are immunogenic and generate MHC II-based T cell responses. Moreover, polyclonal and polyfunctional T cells specific for tumor-specific peptides effectively eliminated tumor cells in vitro. Targeting novel tumor-specific antigens obviates the issue of central immune tolerance while potentially providing a safety margin favoring combination with other immune-activating therapies. These findings demonstrate the proteogenomic discovery of immunogenic tumor-specific peptides and lay the groundwork for personalized targeted T cell therapies for children with brain tumors.

cancer biology↗