Biology subjects

Sharif, M. A.

Publications and source records attributed to Sharif, M. A..

3 recordsLinked to original sources

bioRxiv2026

Redox activation of ATG5 licenses autophagy upon nutrient restriction

Dietary restriction (DR) protects against metabolic disease, extends lifespan, and is associated with remodeling of tissue reactive oxygen species (ROS). ROS control biological adaptation through reversible oxidation of protein cysteines, yet the targets of DR-initiated redox signaling are unknown. Here we generate OxiDR, a tissue-resolved atlas of the cysteine redox proteome that quantifies oxidation state under DR. Rather than oxidizing the proteome broadly, DR selectively targets a high-amplitude set of cysteines in a tissue-specific manner, allowing systematic classification of biological processes subject to DR-mediated redox regulation. Among the cysteines most highly oxidized upon DR is Cys19 of the core autophagy protein ATG5. We show oxidation of Cys19 is required for ATG5-mediated autophagosome formation and for autophagy triggered by nutrient restriction in human cells and mice. Reversible oxidation of this cysteine promotes ATG5 binding to ATG10, thus forming the ATG5-ATG12 conjugate that lipidates LC3B/ATG8 and matures the autophagosome. In mice, loss of this redox switch prevents effective initiation of autophagy upon nutrient restriction, resulting in gross tissue pathology and rapid onset of mortality. The autophagic response to nutrient restriction is thus gated by oxidation of a single cysteine.

cell biology↗

bioRxiv2026

Multidirectional Cellular Plasticity in Ewing Sarcoma Reveals a Tumor-CAF Continuum and Novel Immunotherapeutic Targets

Ewing sarcoma (EwS) is an aggressive pediatric malignancy with poor outcomes for patients with metastatic or relapsed disease. Effective immunotherapeutic approaches, including CAR T-cell therapy, are limited by intratumoral heterogeneity, an incompletely characterized tumor microenvironment (TME), and a lack of well-defined, tumor-restricted target antigens. To address these limitations, we performed an integrated analysis of EwS tumor samples using both single-nucleus and single-cell RNA sequencing datasets derived exclusively from patient samples, including matched primary tumors and orthotopic patient-derived xenograft (PDX) models. Our analyses reveal that primary EwS tumors are largely composed of highly heterogeneous malignant cell populations occupying multiple, multidirectional transcriptional states, including neuronal-like, proliferative, angiogenic, and fibroblast-like. We demonstrate that the EwS TME contains both classical cancer-associated fibroblasts (CAFs) and abundant EwS CAF-like tumor cells that transcriptionally resemble stromal cells while retaining tumor identity. Trajectory analyses define a progressive and coordinated tumor-CAF continuum, marked by gradual loss of neuronal programs and activation of mesenchymal and extracellular matrix remodeling programs, suggesting dynamic tumor cell reprogramming that may promote invasion, immune evasion, and therapeutic resistance. Notably, this structured transcriptional continuum was prominent in primary tumors but largely absent in matched PDX models, underscoring the importance of native tumor context for capturing clinically relevant tumor-TME interactions. We also developed a systematic surface-antigen discovery pipeline and identified ten novel putative tumor-associated surface target antigens (TAs), LRRC15, ATP2B3, CACNA1I, DCHS2, DSEL, LPAR4, PRRT4, TMEM229A, UNC5A, and UNC79, none of which have been previously described in EwS tumor biology. Characterization of these surface TAs revealed distinct expression patterns across EwS tumor cells, EwS CAF-like tumor cells, and classical CAFs. Moreover, some TAs expression differed between primary and metastatic tumors and between primary patient samples and matched PDX models, highlighting the critical importance of first validating therapeutic targets in primary tissues (PT). Together, these findings redefine the cellular architecture of EwS by revealing a dynamic tumor-CAF continuum that is uniquely preserved in primary tumors and establishes a framework for identifying clinically relevant tumor-associated surface TAs. These results provide a foundation for the rational development of next-generation immunotherapies and precision-targeted therapies for patients with EwS.

cancer biology↗

bioRxiv2025

NMDA Receptor Kinetics Drive Distinct Routes to Chaotic Firing in Pyramidal Neurons

Neuronal firing patterns emerge from complex interactions between intrinsic membrane properties and synaptic receptor dynamics. N-methyl-D-aspartate (NMDA) receptors critically shape calcium influx and synaptic plasticity through their voltage-dependent Mg2+ block and prolonged activation kinetics. We developed a Hodgkin-Huxley-type computational model incorporating NMDA, AMPA, and GABA receptor kinetics to investigate how NMDA receptor closing rates ({beta}NMDA) and glutamatergic stimulation frequency control neuronal dynamics. Systematic analysis of 2,942,093 inter-spike intervals across 1,961 parameter combinations revealed two mechanistically distinct pathways to firing irregularity. Pathway 1 involves rapid NMDA deactivation ({beta}NMDA > 0.06 ms-1) at elevated stimulation frequencies, producing deterministic chaos with compromised information encoding (entropy: 1.441 bits, mutual information: 0.185 bits). Pathway 2 results from slow NMDA deactivation ({beta}NMDA < 0.02 ms-1) under weak drive, creating irregularity through prolonged receptor activation and sustained calcium influx (entropy: 1.347 bits). An optimal kinetic window emerged at {beta}NMDA = 0.028 ms-1, maximizing information transfer (0.275 bits) while maintaining stable dynamics. Entropy-Lyapunov correlation analysis confirmed deterministic chaos (r = 0.150, p {inverted exclamation} 0.001). Frequency-dependent chaos onset thresholds demonstrated systematic erosion from 0.000 ms-1 at low frequencies to 0.150 ms-1 at high frequencies. GABAergic inhibition provided frequencyselective stabilization, expanding stable parameter space by 34.2 These findings establish NMDA receptor kinetics as fundamental controllers of cortical excitability and information processing. The dual-pathway framework provides mechanistic insights into addiction-related memory formation, where prolonged NMDA activation enables pathological plasticity, and visual processing disorders, where altered kinetics disrupt retinal function and cortical oscillatory balance. The identification of optimal kinetic windows and frequency-selective GABA modulation suggests therapeutic strategies targeting kinetically-specific interventions for neuropsychiatric disorders involving NMDA dysfunction.

neuroscience↗