Biology subjects

Stepanova, E.

Publications and source records attributed to Stepanova, E..

5 recordsLinked to original sources

bioRxiv2025

Dual Ribosome Profiling reveals metabolic limitations of cancer and stromal cells in thetumor microenvironment

Cancer cells, immune cells, and stromal cells within the tumor microenvironment (TME) collaboratively influence disease progression and therapeutic responses. The nutrient-limited conditions of the TME, particularly the scarcity of glucose, amino acids, and lipids, challenge cancer cell survival1-4. However, the metabolic constraints faced by immune and stromal cells in comparison to cancer cells, and how these limitations affect therapeutic outcomes, remain poorly understood. Here, we introduce Dual Ribosome Profiling (DualRP), a method that allows for simultaneous analysis of translation and identification of ribosome stalling, revealing amino acid shortages in different cell types within tumors. Using DualRP, we uncover that interactions between cancer cells and fibroblasts trigger an inflammatory response, mitigating amino acid limitations during glucose starvation. In immunocompetent mouse models, we observe that immune checkpoint blockade therapy induces serine and glycine restrictions specifically in T cells, but not in cancer cells. We further demonstrate that these amino acids are essential for optimal T cell function both in vitro and in vivo, highlighting their critical role in effective immunotherapy. Our findings show that therapeutic interventions create distinct metabolic demands across different tumor cell types, with nutrient availability significantly influencing the success of immunotherapy. DualRPs ability to explore cell type-specific metabolic vulnerabilities offers a promising tool for advancing our understanding of tumor biology and improving therapeutic strategies.

cancer biology↗

bioRxiv2024

Axonal spheroids are regulated by Schwann cells after peripheral nerve injury

Axonal spheroids are hallmark features of neurodegeneration, forming along degenerating axons and contributing to disease progression. Despite their ubiquity across degenerative etiologies, the dynamics of spheroid disappearance, as well as their interactions with glial cells, remain poorly understood. Here, using an in vivo zebrafish model of peripheral nerve injury, we identified several patterns of spheroid disappearance that are regulated by Schwann cells. These results describe spheroid dynamics across their lifetimes, establish a role for the extra-axonal environment in altering spheroid outcomes, and identify a cellular mechanism whereby spheroid fates are altered. SummaryO_LIAxonal spheroids (also called "dystrophic neurites," "axonal swellings," and "axonal beading") undergo three fates: shrinking, breakdown, and uniform disappearance C_LIO_LISchwann cells ensheath most axonal spheroids and internalize a subset of them C_LIO_LISchwann cells regulate axonal spheroid fates, identifying a role for axon-extrinsic processes in spheroid regulation C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/622649v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@16084eeorg.highwire.dtl.DTLVardef@1b72b17org.highwire.dtl.DTLVardef@6e2b47org.highwire.dtl.DTLVardef@db4ccb_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Following injury, spheroids are more likely to undergo shrinking and breakdown when Schwann cells (SCs) are present on degenerating axons. When Schwann cells are absent, spheroids are more likely to undergo uniform disappearance. Spheroids expose phosphatidylserine, which could facilitate interactions between spheroids and SCs. C_FIG

neuroscience↗

bioRxiv2024

Sarm1-Dependent Metabolic Reprogramming of Schwann Cells Following Nerve Injury

Schwann cells (SCs) transition into a Repair state after peripheral nerve injury; however, the early SC injury response preceding this transition remains poorly understood. We demonstrate that Sarm1, a key regulator of axon degeneration, is expressed and upregulated in SCs after nerve injury. Cell-type-specific Sarm1 knockout SCs exhibit enhanced axon protection in vitro, and SC- and glia-specific Sarm1 deletion confers axon protection in mouse sciatic nerve and Drosophila wing injury models. Single-nucleus RNA sequencing revealed that Sarm1-deficient SCs are enriched in a distinct cluster expressing genes with developmental roles in axon and myelin protection, with increased oxidative phosphorylation gene expression across all injured SC states. We propose that Sarm1 gates the transition from a Protection-Associated Schwann Cell (PASC) state to a Repair SC state, establishing Sarm1 as a multi-functional regulator with implications for peripheral neuropathies and neurodegenerative diseases.

neuroscience↗

bioRxiv2023

Oncogenic functions of the m6A demethylase FTO in breast cancer cells involving translational upregulation of C/EBPβ-LIP

N6-methyladenosine (m6A) is a prevalent posttranscriptional mRNA modification involved in the regulation of transcript turnover, translation, and other aspects of RNA fate. The modification is mediated by multicomponent methyltransferase complexes (so-called writers) and is reversed through the action of the m6A-demethylases fat mass and obesity-associated (FTO) and alkB homolog 5 (ALKBH5) (so-called erasers). FTO promotes cell proliferation, colony formation and metastasis in models of triple-negative breast cancer (TNBC). However, little is known about genome-wide or specific downstream regulation by FTO. Here, we examined changes in the genome-wide transcriptome and translatome following FTO-knockdown in TNBC cells. Unexpectedly, FTO knockdown had a limited effect on the translatome, while transcriptome analysis revealed that genes related to extracellular matrix (ECM) and epithelial-mesenchymal transition (EMT) are being regulated through yet unidentified mechanisms. Differential translation of the CEBPB mRNA into the C/EBP{beta} transcription factor isoform C/EBP{beta}-LIP is known to act pro-oncogenic in TNBC cells through regulation of EMT genes. Here we show that FTO is required for efficient C/EBP{beta}-LIP expression, suggesting that FTO has oncogenic functions through regulation of C/EBP{beta}-LIP.

cancer biology↗

bioRxiv2020

Metabolic control of tumour extracellular matrix production in cancer-associated fibroblasts

TElevated production of collagen-rich extracellular matrix (ECM) is a hallmark of cancer associated fibroblasts (CAFs) and a central driver of cancer aggressiveness. How to target ECM production to oppose cancer is yet unclear, since targeting CAFs has been shown to restrain but also promote cancer progression. Metabolic rewiring is a hallmark of CAFs. Here we find that proline, which is a highly abundant amino acid in collagen proteins, is newly synthesised from glutamine to make tumour collagen in breast cancer xenografts, and that its production is elevated in breast cancer CAFs. PYCR1 is the rate-limiting enzyme for proline synthesis and is highly expressed in the tumour stroma of breast cancer patients and in CAFs. Reducing PYCR1 levels in CAFs is sufficient to reduce tumour collagen production, tumour growth and metastatic spread in vivo and cancer cell proliferation in vitro. PYCR1 and COL1A1 are overexpressed in patients with invasive ductal carcinoma with poor prognosis. Both collagen and glutamine-derived proline synthesis in CAFs are enhanced by increased pyruvate dehydrogenase-derived acetyl-CoA levels, via gene expression regulation through the epigenetic regulator histone acetyl transferase EP300. Altogether, our work unveils unprecedented roles of CAF metabolism to support pro-tumorigenic collagen production. PYCR1 is a recognised cancer cell vulnerability and potential target for therapy, hence, our work provides evidence that targeting PYCR1 in tumours may have the additional benefit of halting the production of pro-tumorigenic ECM.

cancer biology↗