Biology subjects

Sokolov, D.

Publications and source records attributed to Sokolov, D..

5 recordsLinked to original sources

bioRxiv2026

Adaptive plasticity of aspartate metabolism in succinate dehydrogenase-deficient cancer cells

Succinate dehydrogenase (SDH) supports cancer cell proliferation by enabling oxidative biosynthesis of the amino acid aspartate, yet SDH loss can also drive tumorigenesis. To cope with SDH loss, cancer cells can engage alternative aspartate synthesis pathways; however, the variables dictating pathway usage and adaptive mechanisms involved are incompletely understood. Here, we systematically profile the adaptation of SDH-knockout cancer cells and find that cells can adapt to SDH loss via at least two distinct mechanisms: suppression of respiratory complex I or upregulation of pyruvate carboxylase. Each route gives rise to distinct metabolic states with both shared and unique dependencies, but either route allows cells to overcome aspartate limitation, improve proliferative fitness, and mitigate pyrimidine-dependent replication stress. Overall, this work provides a comprehensive view of adaptive aspartate synthesis in SDH-deficient cancer cells, highlights a remarkable redox-constrained metabolic plasticity, and nominates potential metabolic vulnerabilities likely to be shared among SDH-deficient cancer cells.

cancer biology↗

bioRxiv2025

An Evidence-Grounded Research Assistant for Functional Genomics and Drug Target Assessment

The growing availability of biological data resources has transformed research, yet their effective use remains challenging: selecting appropriate sources requires domain knowledge, data are fragmented across databases, and synthesizing results into reliable conclusions is labor-intensive. Although large language models promise to address these barriers, their impact in biomedicine has been limited by unsupported statements, incorrect claims, and lack of provenance. We introduce Alvessa, an evidence-grounded agentic research assistant designed around verifiability. Alvessa integrates entity recognition, orchestration of pre-validated biological tools, and data-constrained answer generation with statement-level verification against retrieved records, explicitly flagging unsupported claims and guiding revision when reliability criteria are not met. We evaluate Alvessa on dbQA from LAB-Bench and GenomeArena, a benchmark of 720 questions spanning gene and variant annotation, pathways, molecular interactions, miRNA targets, drug-target evidence, protein structure, and gene-phenotype associations. Alvessa substantially improves accuracy relative to general-purpose language models and performs comparably to coding-centric agents while producing fully traceable outputs. Using adversarial perturbations, we show that detection of fabricated statements depends critically on access to retrieved evidence. We further demonstrate application to drug discovery, where evidence-grounded synthesis enables identification of candidate targets missed or misattributed by literature-centered reasoning alone. Alvessa and GenomeArena are released to the community to support reproducible, verifiable AI-assisted biological research.

bioinformatics↗

bioRxiv2025

Succinate Dehydrogenase loss causes cascading metabolic effects that impair pyrimidine biosynthesis

Decreased availability of the amino acid aspartate can constrain cell function in diverse biological contexts, but the temporal interplay between aspartate, downstream metabolic changes, and functional effects remains poorly understood. Using an aspartate biosensor and live-cell imaging, we examine the interaction between aspartate abundance and cell proliferation in several models of aspartate limitation. While aspartate deficiencies intuitively interface with proliferation in some contexts, aspartate limitation from succinate dehydrogenase (SDH) inhibition causes strikingly nonintuitive dynamics resulting from an outsized impairment of pyrimidine synthesis. Mechanistically, we find that SDH loss impairs pyrimidine biosynthesis by decreasing aspartate and accumulating succinate, which competitively inhibits mammalian aspartate transcarbamylase (ATCase). This metabolic interaction persists in multiple models of SDH deficiency, causing pyrimidine insufficiency, replication stress, and sensitivity to ATR kinase inhibition. These findings define a novel role for succinate in modulating cellular nucleotide homeostasis, suggest a potential therapeutic vulnerability of SDH-deficient tumors, and demonstrate how cascading metabolic interactions can unfold to impact cell function.

cell biology↗

bioRxiv2023

Light-sensitive phosphorylation regulates enzyme activity and filament assembly of human IMPDH1 retinal splice variants

Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanosine triphosphate (GTP) synthesis and is controlled by feedback inhibition and allosteric regulation. IMPDH assembles into micron-scale filaments in cells, which desensitizes the enzyme to feedback inhibition by GTP and boosts nucleotide production. The vertebrate retina expresses two tissue-specific splice variants IMPDH1(546) and IMPDH1(595). IMPDH1(546) filaments adopt high and low activity conformations, while IMPDH1(595) filaments maintain high activity. In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of phosphorylation in IMPDH1 variants. The S477D mutation re-sensitized both variants to GTP inhibition, but only blocked assembly of IMPDH1(595) filaments and not IMPDH1(546) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of the high activity assembly interface, still allowing assembly of low activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, phosphorylation at S477 acts as a mechanism for downregulating retinal GTP synthesis in the dark, when nucleotide turnover is decreased. Like IMPDH1, many other metabolic enzymes dynamically assemble filamentous polymers that allosterically regulate activity. Our work suggests that posttranslational modifications may be yet another layer of regulatory control to finely tune activity by modulating filament assembly in response to changing metabolic demands. SIGNIFICANCE STATEMENTOver 20 different metabolic enzymes form micron-scale filaments in cells, suggesting that filament assembly is a conserved mechanism for regulating diverse metabolic pathways. Filament assembly regulates catalytic activity of many of these enzymes, including inosine monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme in de novo GTP biosynthesis. The vertebrate retina expresses two IMPDH1 splice variants that are critical for maintaining nucleotide levels required for phototransduction. Here, we show that filament assembly by these variants is itself controlled by phosphorylation at a single residue, adding further complexity to the tight regulation of nucleotide metabolism in the retina. Phosphorylation and other posttranslational modifications are likely to be a general regulatory mechanism controlling filament assembly by enzymes in many different metabolic pathways.

biochemistry↗

bioRxiv2021

NMNAT1 facilitates energy metabolism and gene regulation in developing retinal neurons

Despite mounting evidence that the mammalian retina is exceptionally reliant on proper NAD+ homeostasis for health and function, the specific roles of subcellular NAD+ pools in retinal development, maintenance, and disease remain obscure. Here, we show that deletion of the nuclear-localized NAD+ synthase nicotinamide mononucleotide adenylyltransferase-1 (NMNAT1) in the developing murine retina causes early and severe degeneration of photoreceptors and select inner retinal neurons via multiple distinct cell death pathways. This severe phenotype is associated with disruptions to retinal central carbon metabolism, purine nucleotide synthesis, and amino acid pathways. Furthermore, large-scale transcriptomics reveals dysregulation of a collection of photoreceptor and synapse-specific genes in NMNAT1 knockout retinas prior to detectable morphological or metabolic alterations. Collectively, our study reveals previously unrecognized complexity in NMNAT1-associated retinal degeneration and suggests a yet-undescribed role for NMNAT1 in gene regulation during photoreceptor terminal differentiation.

molecular biology↗