Biology subjects

Montes, M.

Publications and source records attributed to Montes, M..

9 recordsLinked to original sources

bioRxiv2026

Reduced LANCL1-AS1 in old human skeletal muscle diminishes mitochondrial activity, shortens mt-mRNA poly(A) tails, and suppresses myogenesis

Regeneration of skeletal muscle preserves muscle mass and function, which decline with age. Here, we sought to identify long noncoding (lnc)RNAs involved in skeletal muscle myogenesis and potentially relevant to muscle aging. Cross-sectional analysis of skeletal muscle transcriptomes from healthy 22-through 89-year-old individuals revealed lncRNA LANCL1-AS1 among the top declining transcripts. Conversely, LANCL1-AS1 increased robustly during skeletal myogenesis and promoted myogenic differentiation in culture. Affinity pulldown by ChIRP followed by mass spectrometry revealed that LANCL1-AS1 associated with the mitochondrial protein LRPPRC, enhancing the formation of the chaperone complex LRPPRC-SLIRP, which maintains longer poly(A) tails of mitochondrial (mt-)mRNAs and stabilizes mt-mRNAs. Importantly, while myoblasts from old rhesus monkey muscle expressed lower levels of LANCL1-AS1 and mt-mRNAs, and displayed lower mitochondrial activity than young monkey myoblasts, overexpressing LANCL1-AS1 in old myoblasts restored mitochondrial activity and myogenesis. We propose that the age-associated reduction in LANCL1-AS1 contributes to impaired mitochondrial function and reduced myogenic capacity in aging skeletal muscle.

molecular biology↗

bioRxiv2026

PP-MAPS: dynamic pharmacophore signatures of protein-peptide interfaces from molecular dynamics trajectories

Protein-peptide interactions underlie many cellular signaling and regulatory processes and are increasingly exploited in drug discovery. Characterizing such interfaces often requires the analysis of ensembles of conformations obtained by molecular modeling or molecular dynamics (MD) simulations, where transient contacts and alternative binding modes can be critical. Pharmacophore models provide an intuitive, transferable representation of molecular interactions. Dynophore i.e. "dynamic pharmacophore" approaches have been developed for small-molecule ligands with MD information. We present PP-MAPS (Protein-Peptide Molecular dynamics Assisted Pharmacophore Signatures), an open-source workflow that extracts and aggregates pharmacophore interactions along MD trajectories of protein-peptide complexes. PP-MAPS produces per-residue interaction frequencies and pharmacophore heatmaps that facilitate comparison of peptides, binding sites and receptor variants. PP-MAPS is implemented in Python and is available under an open-source license at https://github.com/camilledepenveiller/PP-MAPS. The workflow relies on GROMACS for trajectory processing and can use either LigandScout or the Chemical Data Processing Toolkit (CDPKit) for pharmacophore feature detection.

bioinformatics↗

bioRxiv2026

Conserved sequence elements in the final exon of MDM2-eight-exon skipping event reveal a cassette regulon model of alternative splicing controlled by a distal regulatory element.

Modern sequencing technologies have revealed that cancers exhibit widespread dysregulation of alternative splicing, which plays a significant role in driving tumor hallmarks. Alternative splicing enables a single gene to generate multiple mRNA variants, a fundamental mechanism that shapes the distinctive characteristics of normal cells as well as cancer cells. These splicing events are governed by complex interactions between cis- and trans-acting factors and understanding these mechanisms is crucial for effectively targeting cancer cells. This study highlights a unique splicing event in which genotoxic stress induces the skipping of eight-exons in the proto-oncogene MDM2, resulting in the formation of MDM2-ALT1, an isoform that is overexpressed in various cancers. To effectively target this splicing event, it is important to unfold the regulatory mechanism behind it. We hypothesize that the event occurs either by the autonomous regulation of individual exons (Exon autonomous model), where each exon is regulated independently or by the coordinated exclusion of an eight-exon-regulon unit (Exon Regulon model). Utilizing in-silico tools, a comprehensive modular minigene system, CRISPR-mutated cell line, and murine models, we demonstrate that this complex MDM2 splicing event is regulated by sequences within a distal terminal exon, which emerge as critical regulators, orchestrating the alternative splicing of MDM2. Constitutive expression of the Mdm2-MS2 isoform (the mouse ortholog of the human MDM2-ALT1 splice variant), achieved by mutating the Srsf2 binding-site on exon 11, modulates proliferation and apoptosis dynamics in NIH3T3 cells. Moreover, in a p53-wildtype in-vivo setting, this isoform confers a protective effect against age-induced neoplasia. Our findings support the Exon Regulon model of MDM2 splicing, regulated by distal elements analogous to distal enhancer elements that control transcription. These finding sheds light on intricacies in the splicing code that could have significant implications for developing splice variant targeting cancer therapies.

molecular biology↗

bioRxiv2025

Nano-Mod-Amp reveals RNA sequence, structural and cell type specific features of pseudouridylation by PUS7

Pseudouridines are abundant mRNA modifications that can impact splicing, translation, and stability to tune gene expression. PUS7 is one of the major mRNA pseudouridine synthase whose dysregulation leads to neurodevelopmental disorders and cancer, underscoring the critical function of PUS7-dependent pseudouridines. Beyond a short and degenerate consensus sequence, the molecular mechanisms underlying PUS7-mediated pseudouridylation remain unknown. A lack of targeted, high-throughput pseudouridine detection methods limits simultaneous interrogation of PUS7 regulatory features across many experimental conditions. We developed novel Nanopore sequencing tools, including Nano-Mod-Amp, to reveal pseudouridine stoichiometry, its RNA structural context, and dependence on PUS7 levels at specific sites across biological conditions. We identified a novel RNA structural signature that is associated with more efficient mRNA modification by PUS7. Pseudouridines are largely responsive to modulations in PUS7 protein levels, demonstrating the regulatory potential of varying PUS7 levels across cellular conditions. Conversely, PUS7 activity is also regulated in a cell-type specific manner, independent of PUS7 expression levels in a manner consistent with regulation by RNA structure and RNA binding proteins. Together, we developed Nanopore sequencing tools and uncovered new mechanisms of PUS7 regulation with a framework that can be applied to other RNA-modifying enzymes to query the regulation of the epitranscriptome. HighlightsO_LINanopore direct RNA sequencing identifies PUS7-dependent pseudouridines with stoichiometry. C_LIO_LINano-Mod-Amp quantifies PUS7-dependent pseudouridines at hundreds of sites in high-throughput. C_LIO_LIMPRAs define RNA sequence and structural features associated with modification by PUS7. C_LIO_LIIndividual PUS7 target pseudouridines are substoichiometric and poised for regulation. C_LIO_LIPUS7 activity is regulated by cell type in the absence of differences in PUS7 protein levels. C_LI

molecular biology↗

bioRxiv2024

A senescence-specific lncRNA controls metabolic rewiring of senescent cells

Despite the classical view of senescence as passive growth arrest, senescent cells remain metabolically active to be able to cope with the energetic demand of the senescence program. However, the mechanisms underlying this metabolic reprogramming remain poorly understood. We have identified sin-lncRNA, a previously uncharacterized lncRNA, that plays a pivotal role in this response. Sin-lncRNA is only expressed by senescent cells, induced by the senescence master regulator C/EBP{beta}. While strongly activated in senescence, sin-lncRNA loss reinforces the senescence program by altering oxidative phosphorylation and rewiring mitochondrial metabolism. By interacting with the TCA enzyme dihydrolipoamide S-succinyltransferase (DLST) it facilitates its localization to the mitochondria. On the other hand, sin-lncRNA depletion results in DLST nuclear translocation linked to DLST-dependent transcriptional alteration of OXPHOS genes. While in highly proliferative cancer cells, sin-lncRNA expression remains undetected, it is strongly induced upon cisplatin-induced senescence. Depletion of sin-lncRNA in ovarian cancer cells results in deficient oxygen consumption and increased extracellular acidification, sensitizing the cells to cisplatin treatment. Altogether, these results indicate that sin-lncRNA is specifically induced in cellular senescence to maintain metabolic homeostasis. Our findings reveal a new regulatory mechanism in which a lncRNA contributes to the adaptive metabolic changes in senescent cells, unveiling the existence of an RNA-dependent metabolic rewiring specific to senescent cells.

cell biology↗

bioRxiv2022

PLO3S : Protein LOcal Surficial Similarity Screening

The study of protein molecular surfaces enable to better understand and predict protein interactions. Different methods have been developed in computer vision to compare surfaces that can be applied to protein molecular surfaces. The present work proposes a method using the the Wave Kernel Signature : Protein LOcal Surficial Similarity Screening (PLO3S). The descriptor of the PLO3S method is a local surface shape descriptor projected on a unit sphere mapped onto a 2D plane and called Surface Wave Interpolated Maps (SWIM). PLO3S allows to rapidly compare protein surface shapes through local comparisons to filter large protein surfaces datasets in protein structures virtual screening protocols.

bioinformatics↗

bioRxiv2020

Splice-switching of the insulin receptor in rhabdomyosarcoma: Rescuing the IR-B isoform for better treatment options.

Rhabdomyosarcoma (RMS) is an aggressive pediatric tumor with poor prognosis for metastasis and recurrent disease. Large scale sequencing endeavors demonstrate that RMS tumors have limited mutations and a dearth of driver mutations that are precisely targetable. However, IGF2 signaling is known to be grossly altered in RMS. The IGF2 signalling molecule binds both its innate IGF1 receptor as well as the insulin-receptor-variant-A (IR-A) with high affinity. Mitogenic and proliferative signalling via the canonical IGF2 pathway is therefore augmented by IR-A. The insulin receptor (IR) which is a transmembrane tyrosine-kinase receptor exists in two alternatively spliced isoforms, IR-A and IR-B. In this study, we show that RMS patients express increased IR-A compared to control tissues that express predominantly the IR-B isoform. We also found that Hif1a is significantly increased in RMS tumors, portraying their hypoxic phenotype. Furthermore, the alternative-splicing of IR adapts to produce more IR-A in response to hypoxic stress. Upon examining the pre-mRNA structure of the gene, we identified a hypoxia-responsive-element, which is also the binding site for the RNA-binding protein CUG-BP1. We designed Splice-Switching-Oligonucleotides (SSO) against this binding site to decrease the levels of IR-A in RMS cell-lines and consequently rescue the IR-B expression levels. SSO treatment resulted in significant reductions in proliferation, migration and angiogenesis. Our data show promising insight into how impeding the IGF-2 pathway by reducing IR-A expression mitigates tumor growth. Our data reveal that RMS tumors use IR alternative-splicing as yet another survival strategy which can be exploited as therapeutic intervention in conjunction with already established anti-IGF-1 receptor therapies.

cancer biology↗

bioRxiv2019

Exploring the Conformational Transition Between the Fully Folded and Locally Unfolded Substates of the Escherichia coli Thiol Peroxidase

Thiol peroxidase from Escherichia coli (EcTPx) is a peroxiredoxin that catalyzes the reduction of different hydroperoxides. During the catalytic cycle of EcTPx, the peroxidatic cysteine (CP) is oxidized to a sulfenic acid by peroxide, then the resolving cysteine (CR) condenses with the sulfenic acid of CP to form a disulfide bond, which is finally reduced by thioredoxin. Purified EcTPx as dithiol and disulfide behaves as a monomer in close to physiological conditions. Although secondary structure rearrangements are present when comparing different redox states of the enzyme, no significant differences in unfolding free energies are observed under reducing and oxidizing conditions. A conformational change denominated fully folded (FF) to locally unfolded (LU) transition, involving a partial unfolding of H2 and H3 helices, must occur to enable the formation of the disulfide bond since the catalytic cysteines are 12 [A] apart in the FF conformation of EcTPx. To explore this crucial process, the mechanism of the FF[->]LU and the LU[->]FF transitions were studied using long time scale conventional molecular dynamic simulations and an enhanced conformational sampling technique for different oxidation and protonation states of CP and/or CR. Our results suggest that the FF[->]LU transition has a higher associated energy barrier than the refolding LU[->]FF process in agreement with the relatively slow experimental turnover number of EcTPx. Furthermore, in silico designed single-point mutants of the H3 enhanced locally unfolding events, suggesting that the native FF interactions in the active site are not evolutionary optimized to fully speed-up the conformational transition of wild-type EcTPx.

biophysics↗

bioRxiv2019

SRSF2 regulation of MDM2 reveals splicing as a therapeutic vulnerability of the p53 pathway

MDM2 is an oncogene and critical negative regulator of tumor suppressor p53. Genotoxic stress causes alternative splicing of MDM2 transcripts, which leads to alterations in p53 activity and contributes to tumorigenesis. MDM2-ALT1 is one of transcripts predominantly produced in response to genotoxic stress and is comprised of terminal coding exons 3 and 12. Previously, we found that SRSF1 induces MDM2-ALT1 by promoting MDM2 exon 11 skipping. Here we report that splicing regulator SRSF2 antagonizes the regulation of SRSF1 by facilitating the inclusion of exon 11 through binding at two conserved exonic splicing enhancers. Overexpression of SRSF2 reduced the generation of MDM2-ALT1 in genotoxic stress condition, whereas knockdown induces the expression of MDM2-ALT1 in absence of genotoxic stress. Consistently, blocking the exon 11 SRSF2 binding sites using oligonucleotides promotes MDM2-ALT1. The regulation of MDM2 splicing by SRSF2 is also conserved in mouse as mutation of one SRSF2 binding site in Mdm2 exon 11, using CRISPR-Cas9, increases the expression MDM2-ALT1 homolog Mdm2-MS2 and proliferation of NIH 3T3 cells. Taken together, these findings underscore the relevance of MDM2 alternative splicing in cancer and suggest that p53 levels can be modulated by artificially regulating MDM2 splicing.

cancer biology↗