Biology subjects

Bajaj, S.

Publications and source records attributed to Bajaj, S..

5 recordsLinked to original sources

bioRxiv2026

Glutaminase contributes to MYC-induced cell-autonomous autophagy and to RasV12-dependent non-autonomous autophagy in the Drosophila wing disc epithelium

MYC-driven metabolic reprogramming supports rapid cell growth but also creates metabolic demands that require adaptive mechanisms to maintain cellular homeostasis. Here, combining clonal analysis in Drosophila wing imaginal discs with studies in Schneider S2 cells, we identify glutamine metabolism as a component of Myc-induced autophagy. Myc increased the expression of genes involved in glutamine utilization, including glutaminase (GLS), and enhanced ammonia production, a metabolic by-product of glutaminolysis. Genetic depletion of GLS in clones suppressed the accumulation of Myc-induced Atg8a-positive structures and reduced autophagic flux, demonstrating that glutaminase contributes to the autophagic response elicited by Myc. Exogenous NHCl was sufficient to induce Atg8a-positive structures and partially restored their accumulation following GLS depletion, supporting ammonia as a downstream contributor to this response. Mechanistically, Myc-induced autophagy in clones required the core autophagy factor Atg5 but was not suppressed by depletion of Rheb or Atg1, consistent with an autophagic program that can operate independently of canonical TOR-Atg1 signaling. We further found that Myc activity is required for RasV12-driven epithelial overgrowth and that RasV12 cells induce a pronounced non-cell-autonomous accumulation of Atg8a-positive structures in wild-type cells surrounding RasV12 clones. Depletion of either Myc or GLS in RasV12 cells strongly reduced this neighboring autophagic response, linking Myc-dependent glutamine metabolism in transformed cells to autophagy in the surrounding tissue. Together, our findings identify GLS-dependent glutamine metabolism as a previously unrecognized component of Myc-induced autophagy and extend this relationship to Ras-transformed epithelia, where Myc and Gls contribute to non-cell-autonomous autophagic responses in neighboring cells.

cell biology↗

bioRxiv2026

Hierarchical classification of immune cell transcriptomes at population-scale

Accurate immune cell classification is essential for interpreting single-cell RNA sequencing (scRNA-seq) data. However, progress in automating cell type annotation is constrained by the lack of independent, high-resolution benchmarks, as routine data integration introduces statistical dependencies that inflate model generalizability. Here, we present the single-cell universal classification omnibus (Suco), a resource of independent, uniform expert annotations, and Compocyte, a modular hierarchical classifier. Together, they establish a framework that substantially outperforms existing classifiers while facilitating expert review of ambiguous annotations. Applying Compocyte across 50 studies, including three newly generated datasets, we classified 15.6 million leukocytes from 3,965 patients. Within this cohort, we identified a new tumor-associated resorptive macrophage phenotype, a non-canonical monocyte subtype in subclinical cytokine release syndrome, and the programmatic erosion of T cell memory stemness across metastatic sites. Suco and Compocyte thus provide a generalizable framework to uncover the principles governing human immunity at population scale. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/728980v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@13a6e4borg.highwire.dtl.DTLVardef@11f1626org.highwire.dtl.DTLVardef@1e72bd4org.highwire.dtl.DTLVardef@1ee799b_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefThe single-cell universal classification omnibus and the modular hierarchical classifier Compocyte enable annotating single cell RNA sequencing data from 3,965 patients, revealing novel resorptive macrophage and vaccination-associated monocyte states, alongside the erosion of T cell memory stemness as a hallmark of solid tumor metastases. HighlightsO_LISuco, a benchmark enabling novel single cell artificial intelligence models C_LIO_LICompocyte, a hierarchical cell type classifier outperforming current architectures C_LIO_LIMacrophages adopt osteoclast-like gene expression states across cancer types C_LIO_LIStem-like programs erode in metastasis-infiltrating T memory cells across tumors C_LI

bioinformatics↗

bioRxiv2026

Spatial Neuroimmune Crosstalk Driving Perineural Invasion in Head and Neck Squamous Cell Carcinoma

BackgroundPerineural invasion (PNI) is a clinically important feature of aggressive head and neck squamous cell carcinoma (HNSCC) and is associated with recurrence and poor survival. However, the spatial organization and molecular programs that characterize tumor-nerve interactions in HNSCC remain incompletely understood. MethodsSingle-cell-resolution Xenium spatial transcriptomic data from 10 HNSCC patients were analyzed to define nerve-associated regions, cell-type composition, tumor-nerve proximity, and perineural transcriptional programs. Complementary Visium spatial transcriptomic datasets were used to assess broader transcriptomic features of nerve-associated regions, including epithelial-mesenchymal transition and inferred ligand-receptor signaling. Clinical relevance was evaluated using bulk transcriptomic validation cohorts from TCGA-HNSC and GSE65858. ResultsSpatial mapping identified a distinct nerve-proximal microenvironment characterized by depletion of mature dendritic cells and altered immune and stromal composition, consistent with localized disruption of antigen-presenting support at the tumor-nerve interface. HPV- tumors exhibited closer tumor-nerve proximity and a higher exploratory PNI index compared with HPV+ tumors, suggesting subtype-specific differences in nerve-associated tumor behavior. Differential expression analysis of perineural versus distal tumor cells identified a spatially enriched gene program, including NFE2L2, MDM2, and PPARG, that demonstrated a nerve-proximal gradient most evident in HPV- disease. A composite three-gene score was associated with worse overall survival in HPV- patients in TCGA-HNSC and validated in GSE65858, while showing limited prognostic value in HPV+ disease. Visium analyses provided complementary evidence of EMT enrichment and inferred tumor-nerve signaling involving neural guidance and adhesion-associated pathways. ConclusionsThese findings support a model in which PNI in HNSCC reflects a spatially organized, transcriptionally distinct tumor-nerve microenvironment, particularly in HPV- disease. The NFE2L2/MDM2/PPARG signature may provide a candidate biomarker for risk stratification and nominates pathways for future mechanistic and therapeutic investigation.

cancer biology↗

bioRxiv2025

Isoform-Specific Activation of p53B and p53C in Response to Nucleolar Stress in Drosophila wing imaginal discs

Disruption of ribosome biogenesis triggers nucleolar stress, a conserved cellular response that activates p53. We previously demonstrated that depletion of Nucleolar Complex Protein 1 (Noc1) in Drosophila wing imaginal discs impairs rRNA maturation and ribosome assembly, resulting in elevated p53 levels and apoptosis, hallmarks of nucleolar stress. The Drosophila p53 gene produces four mRNA isoforms, yet their individual contributions to nucleolar stress responses remain poorly understood. Using newly designed isoform-specific qPCR primers, we found that although all p53 isoforms exhibit moderate transcriptional changes following Noc1 reduction, the truncated isoform p53E is robustly and preferentially upregulated. Notably, p53E lacks the N-terminal transactivation domain and has been reported to negatively regulate p53-induced apoptosis in specific tissues. Furthermore, our analyses indicate that {gamma}-H2AV accumulation arises from caspase-dependent apoptosis rather than primary genomic lesions, suggesting the activation of a p53-dependent stress pathway distinct from canonical genotoxic pathways. Together, these findings suggest that p53E may be part of a novel mechanism activated during nucleolar stress, providing insight into how cells adapt to defects in ribosome biogenesis.

genetics↗

bioRxiv2023

Synchrony of Bird Migration with Avian Influenza Global Spread; Implications for Vulnerable Bird Orders

Highly pathogenic avian influenza virus (HPAIV) A H5 clade 2.3.4.4 has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, it is unclear how seasonal bird migration facilitates global virus dispersal, and which avian species are exposed to HPAI H5 clade 2.3.4.4 viruses and where. To shed light on ongoing global outbreaks, we sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences. First, based on viral phylogeography and bird migration networks, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing vulnerable bird orders at geographical origins and destinations of HPAIV H5 lineage movements. Notably, we highlight the potential importance of relatively under-discussed Suliformes and Ciconiiformes, in addition to Anseriformes and Charadriiformes, in virus lineage movements. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behaviour and life history in avian influenza studies.

ecology↗