Biology subjects

Malumbres, M.

Publications and source records attributed to Malumbres, M..

16 recordsLinked to original sources

bioRxiv2026

Polo-like kinase 1 controls activation of adult neural stem cells and represents a druggable entry-point to boost adult neurogenesis

Neural stem cells (NSCs) persist in the mammalian brain after development, but their potential for replacing neural populations lost in brain damage is dramatically restricted. Quiescence, or the ability to transition in and out of the cell cycle is a hallmark of adult NSCs. It deepens as the organism ages and is regarded as a strategy to protect the reservoirs of NSC for the long term. Deciphering the molecular code of dormancy is a major interest in cellular and molecular biology of ageing and in regenerative medicine since it has important implications for potentially manipulating NSCs to improve tissular homeostasis. In this work we have identified the mitotic kinase Polo like kinase 1 (Plk1) as a novel intrinsic regulator of the dynamic transition between NSC quiescence and activation in adult neurogenic niches. Using quantitative phosphoproteomics to pinpoint mechanistical mediators of the role of Plk1, we have identified the quiescence/activation molecular switch formed by E3 ubiquitin ligase Huwe1 and its target, the transcription factor Ascl1/Mash1, as novel effectors of Plk1 in NSCs. We discover that Plk1 restrains the accumulation of Ascl1/Mash1 by acting upstream of Huwe1, providing a direct molecular connection between completion of the cell cycle and the re-establishment of a low activation state following NSC division, which supports the concept that quiescence is an actively maintained state. Moreover we demonstrate that pharmacological inhibition of Plk1 is sufficient to enhance adult neurogenesis in vivo, identifying Plk1 as a viable target to acutely boost endogenous stem cell activation.

neuroscience↗

bioRxiv2026

BULLKpy: An AnnData-Inspired Unified Framework for Comprehensive Bulk OMICs Analysis

Bulk OMICs data, such as RNA-seq and proteomics, remain foundational in biomedical and cancer research. While single-cell transcriptomics has revolutionized our understanding of cellular heterogeneity, bulk OMICs continue to provide a solid ground for large-scale studies, integrative analyses, and robust biomedical correlations. Yet, analytical workflows for bulk OMICs are frequently fragmented across disparate tools, programming languages, and data formats, in contrast to the single-cell field, which benefits from comprehensive and standardized frameworks like Scanpy and the broader scverse ecosystem. Here, we introduce BULLKpy, a Python-based, scverse-inspired framework designed to deliver similar integration, flexibility, and scalability to bulk RNA-seq analysis, with a particular emphasis on cancer research. Beyond standard preprocessing and visualization utilities, BULLKpy offers systematic evaluation of genemetadata associations, categorical enrichment analyses, clustering stability metrics, and advanced visualization strategies that facilitate intuitive exploration of tumor heterogeneity in expression profiles and metaprograms. Cancer-specific visualizations, such as oncoprints, are natively supported and seamlessly integrated with transcriptomic and clinical features, allowing users to relate somatic alterations to expression-derived phenotypes. By standardizing workflows within the Python ecosystem and aligning with AnnData objects and the scverse, BULLKpy aims to democratize advanced transcriptomic and proteomic analyses, facilitate integrative cancer research, and support future developments at the intersection of computational biology, multi-omics integration, and artificial intelligence.

bioinformatics↗

bioRxiv2025

Cyclin Y Overexpression Drives a Fatal Metabolic Syndrome via Defective Glucose Homeostasis

Cyclin Y (CCNY) is a membrane-associated, non-canonical cyclin best known for regulating WNT/beta-catenin signaling via the recruitment of CDK14/16 protein kinases. Whereas its role in the activation of members of the atypical CDK14-18 subfamily is established, its function in systemic metabolism remains poorly defined. Here, we report that CCNY overexpression drives a fatal metabolic syndrome. Using a novel inducible knock-in mouse model, we demonstrate that CCNY overexpression causes severe cachexia and profound hypoglycemia, resulting in death of adult mice independent of tumor burden. While these mutant mice maintain normal food intake and hepatic synthetic function, they succumb to metabolic starving state. Proteomics reveals that CCNY interacts with and stabilizes Pyruvate Dehydrogenase Kinase 4 (PDK4), in agreement with defective pyruvate use at mitochondria and enforcing a Warburg-like shift to aerobic glycolysis. Phosphoproteomic analysis indicates activation of apoptotic pathways and defective phosphorylation of several enzymes critical for glycolysis and gluconeogenesis as well as amino acid metabolism in addition to other metabolic routes. Altogether, these data suggest that CCNY overexpression uncouples nutrient sensing from utilization, a finding with possible therapeutic implications in CCNY-high cancers with similar changes in metabolic pathways.

cell biology↗

bioRxiv2025

CDC14 phosphatases control adipogenesis via PPARγ de-phosphorylation

Adipogenesis is a finely tuned process requiring an appropriate balance between proliferation and differentiation. We demonstrate that CDC14, a CDK-counteracting phosphatase, regulates adipogenesis and glucose metabolism in mammals. Simultaneous depletion of CDC14A and CDC14B protects against high-fat diet-induced obesity, hepatic steatosis and glucose intolerance in vivo. Lack of these phosphatases blocks differentiation of stem cells into adipocytes, a defect rescued by the PPAR{gamma} agonist troglitazone. Mechanistically, we show that CDC14 counteracts ERK2 and CDK5-induced phosphorylation of PPAR{gamma}, a master regulator of adipogenesis, by directly dephosphorylating S112, S273 and T296 residues. This study supports the idea that cell cycle regulators in multicellular organisms evolved to coordinate the balance between proliferation and differentiation in different cell types. Furthermore, since PPAR{gamma} is a key target of anti-diabetic drugs and a central regulator of adipogenesis and metabolism, these findings may have important implications for treatment of metabolic diseases such as type 2 diabetes.

cell biology↗

bioRxiv2024

A common CTRB misfolding variant associated with pancreatic cancer risk causes ER stress and inflammation in mice

ObjectiveGenome wide association studies have identified an exon 6 CTRB2 deletion variant that associates with increased risk of pancreatic cancer. To acquire evidence on its causal role, we developed a new mouse strain carrying an equivalent variant in Ctrb1, the mouse orthologue of CTRB2. DesignWe used CRISPR/Cas9 to introduce a 707bp deletion in Ctrb1 encompassing exon 6 (Ctrb1{Delta}exon6). This mutation closely mimics the human deletion variant. Mice carrying the mutant allele were extensively profiled at 3 months to assess their phenotype. ResultsCtrb1{Delta}exon6 mutant mice express a truncated CTRB1 that accumulates in the ER. The pancreas of homozygous mutant mice displays reduced chymotrypsin activity and total protein synthesis. The histological aspect of the pancreas is inconspicuous but ultrastructural analysis shows evidence of dramatic ER stress and cytoplasmic and nuclear inclusions. Transcriptomic analyses of the pancreas of mutant mice reveals acinar program down-regulation and increased activity of ER stress-related and inflammatory pathways. Heterozygous mice have an intermediate phenotype. Agr2 is one of the most up-regulated genes in mutant pancreata. Ctrb1{Delta}exon6 mice exhibit impaired recovery from acute caerulein-induced pancreatitis. Administration of TUDCA or sulindac partially alleviates the phenotype. A transcriptomic signature derived from the mutant pancreata is significantly enriched in normal human pancreas of CTRB2 exon 6 deletion variant carriers from the GTEx cohort. ConclusionsThis mouse strain provides formal evidence that the Ctrb1{Delta}exon6 variant causes ER stress and inflammation in vivo, providing an excellent model to understand its contribution to pancreatic ductal adenocarcinoma development and to identify preventive strategies. SUMMARY BOX What is already known about this subject?- CTRB2 is one of the most abundant proteins produced by human pancreatic acinar cells. - A common exon 6 deletion variant in CTRB2 has been associated with an increased risk of pancreatic ductal adenocarcinoma. - Misfolding of digestive enzymes is associated with pancreatic pathology. What are the new findings?- We developed a novel genetic model that recapitulates the human CTRB2 deletion variant in the mouse orthologue, Ctrb1. - Truncated CTRB1 misfolds and accumulates in the ER; yet, mutant mice display a histologically normal pancreas at 3 months age. - CTRB1 and associated chaperones colocalize in the ER, the cytoplasm, and the nucleus of acinar cells. - Transcriptomics analysis reveals reduced activity of the acinar program and increased activity of pathways involved in ER stress, unfolded protein response, and inflammation. - Mutant mice are sensitized to pancreatic damage and do not recover properly from a mild caerulein-induced pancreatitis. - TUDCA administration partially relieves the ER stress in mutant mice. How might it impact on clinical practice in the foreseeable future?- The new mouse model provides a tool to identify the mechanisms leading to increased pancreatic cancer risk in CTRB2 exon 6 carriers. - The findings suggest that drugs that cause ER stress relief and/or reduce inflammation might provide preventive opportunities.

cancer biology↗

bioRxiv2024

miR-203 controls timing of developmental transitions during early preimplantation embryogenesis

Commonly expressed at developmental transitions, microRNAs operate as fine tuners of gene expression to facilitate cell fate acquisition and lineage segregation. Nevertheless, how they might regulate the earliest developmental transitions in early mammalian embryogenesis remains obscure. Here, in a strictly in vivo approach based on novel genetically-engineered mouse models and single-cell RNA sequencing, we identify miR-203 as a critical regulator of timing and cell fate restriction within the totipotency to pluripotency transition in mouse embryos. Genetically engineered mouse models show that loss of miR-203 slows down developmental timing during preimplantation leading to the accumulation of embryos with high expression of totipotency-associated markers, including MERVL endogenous retroviral elements. A new embryonic reporter (eE-Reporter) transgenic mouse carrying MERVL-Tomato and Sox2-GFP transgenes showed that lack of miR-203 leads to sustained expression of MERVL and reduced Sox2 expression in preimplantation developmental stages. A combination of single-cell transcriptional studies and epigenetic analyses identified the central coactivator and histone acetyltransferase P300 as a major miR-203 target at the totipotency to pluripotency transition in vivo. By fine tuning P300 levels, miR-203 carves the epigenetic rewiring process needed for this developmental transition, allowing a timely and correctly paced development.

developmental biology↗

bioRxiv2023

PP2A-B55alpha,delta phosphatase counteracts Ki67-dependent chromosome individualization during mitosis

Cell cycle progression is regulated by the orderly balance between kinase and phosphatase activities. PP2A phosphatase holoenzymes containing the B55 family of regulatory B subunits (PP2A-B55) function as major CDK1-counteracting phosphatases during mitotic exit in mammals. However, the identification of the specific mitotic roles of these PP2A-B55 complexes has been hindered by the existence of multiple B55 isoforms. Here, through the generation of loss-of-function genetic mouse models for the two ubiquitous B55 isoforms (B55 and B55{delta}), we report that PP2A-B55 /{delta} complexes display overlapping roles in controlling the dynamics of proper chromosome individualization and clustering during mitosis. In the absence of PP2A-B55/{delta} activity, mitotic cells display increased chromosome individualization in the presence of enhanced phosphorylation and perichromosomal loading of Ki-67. These data provide experimental evidence for a new regulatory mechanism by which the balance between kinase and PP2A-B55 phosphatase activity controls the Ki-67-mediated spatial organization of the mass of chromosomes during mitosis.

cell biology↗

bioRxiv2023

miR-203 drives breast cancer cell differentiation

A hallmark of many malignant tumors is dedifferentiated (immature) cells bearing slight or no resemblance to the normal cells from which the cancer originated. Tumor dedifferentiated cells exhibit a higher capacity to survive to chemo and radiotherapies and have the ability to incite tumor relapse. Inducing cancer cell differentiation would abolish their self-renewal and invasive capacity and could be combined with the current standard of care, especially in poorly differentiated and aggressive tumors (with worst prognosis). However, differentiation therapy is still in its early stages and the intrinsic complexity of solid tumor heterogeneity demands innovative approaches in order to be efficiently translated into the clinic. We demonstrate here that microRNA 203, a potent driver of differentiation in pluripotent stem cells (ESCs and iPSCs), promotes the differentiation of mammary gland tumor cells. Combining mouse in vivo approaches and both mouse and human-derived tridimensional organoid cultures, we report here that miR-203 influences the self-renewal capacity, plasticity and differentiation potential of breast cancer cells, and prevents tumor cell growth in vivo. Our work sheds light on differentiation-based antitumor therapies and offers miR-203 as a promising tool for directly confronting the tumor-maintaining and regeneration capability of cancer cells.

cancer biology↗

bioRxiv2022

Bilallelic germline mutations in MAD1L1 induce a novel syndrome of aneuploidy with high tumor susceptibility

Aneuploidy is a frequent feature of human tumors. Germline mutations leading to aneuploidy are very rare in humans, and their tumor-promoting properties are mostly unknown at the molecular level. We report here novel germline biallelic mutations in MAD1L1, the gene encoding the Spindle Assembly Checkpoint (SAC) protein MAD1, in a 36-year-old female with a dozen of neoplasias, including five malignant tumors. Functional studies in peripheral blood cells demonstrated lack of full-length protein and deficient SAC response, resulting in [~]30-40% of aneuploid cells as detected by cytogenetic and single-cell (sc) DNA analysis. scRNA-seq analysis of patient blood cells identified mitochondrial stress accompanied by systemic inflammation with enhanced interferon and NFkB signaling. The inference of chromosomal aberrations from scRNA-seq analysis detected inflammatory signals both in aneuploid and euploid cells, suggesting a non-cell autonomous response to aneuploidy. In addition to random aneuploidies, MAD1L1 mutations resulted in specific clonal expansions of {gamma}{delta} T-cells with chromosome 18 gains and enhanced cytotoxic profile, as well as intermediate B-cells with chromosome 12 gains and transcriptomic signatures characteristic of chronic lymphocytic leukemia cells. These data point to MAD1L1 mutations as the cause of a new aneuploidy syndrome with systemic inflammation and unprecedented tumor susceptibility.

cancer biology↗

bioRxiv2021

Haspin participates in Aurora phosphorylation at centromeres and contributes to chromosome congression in male mouse meiosis

Chromosome segregation requires that centromeres properly attach to spindle microtubules. This is an essential step towards the accuracy of cell division and therefore must be precisely regulated in both mitosis and meiosis. One of the main centromeric regulatory signaling pathways is the Haspin-H3T3ph-chromosomal passenger complex (CPC) cascade, which is responsible for the recruitment of the CPC to the centromeres. In mitosis, Haspin kinase phosphorylates H3 at threonine 3 (H3T3ph), the essential histone mark that recruits the CPC whose catalytic component is Aurora B kinase. To date, no data has yet been presented about the action of the centromeric Haspin-H3T3ph-CPC pathway in mammalian male meiosis. We have analyzed the consequences of Haspin chemical inhibition in cultured spermatocytes using LDN-192960. Our in vitro studies suggest that Haspin kinase activity is required for proper chromosome congression during both meiotic divisions and for the recruitment of phosphorylated Aurora B at meiotic centromeres. These results have been confirmed by the characterization of the meiotic phenotype of the genetic mouse model Haspin-/-, which displays similar defects. In addition, our work demonstrates that the absence of H3T3ph histone mark does not alter SGO2 localization to meiotic centromeres. These results add new and relevant information regarding the regulation of centromere function during meiosis.

cell biology↗

bioRxiv2020

A cell cycle kinase-phosphatase module restrains PI3K-Akt activity in an mTORC1-dependent manner

The AKT-mTOR pathway is a central regulator of cell growth and metabolism. Upon sustained mTOR activity, AKT activity is attenuated by a feedback loop that restrains upstream signaling. However, how cells control the signals that limit AKT activity is not fully understood. Here we show that MASTL/Greatwall, a cell-cycle kinase that supports mitosis by phosphorylating the PP2A/B55 inhibitors ENSA/ARPP19, inhibits PI3K-AKT activity by sustaining mTORC1- and S6K1-dependent phosphorylation of IRS1 and GRB10. Genetic depletion of MASTL results in an inefficient feedback loop and AKT hyperactivity. These defects are rescued by expression of phospho-mimetic ENSA/ARPP19 or inhibition of PP2A/B55 phosphatases. MASTL is directly phosphorylated by mTORC1, thereby limiting the PP2A/B55-dependent dephosphorylation of IRS1 and GRB10 downstream of mTORC1. Downregulation of MASTL results in increased glucose uptake in vitro and increased glucose tolerance in adult mice, suggesting the relevance of the MASTL-PP2A/B55 kinase-phosphatase module in controlling AKT and maintaining metabolic homeostasis.

cell biology↗

bioRxiv2020

miR-203 imposes an intrinsic barrier during cellular reprogramming by targeting NFATC2

Cellular reprogramming from somatic to pluripotent cells is the basis for multiple applications aimed to replace damaged tissues in regenerative medicine. However, this process is limited by intrinsic barriers that are induced in response to reprogramming factors. In this manuscript we report that miR-203, a microRNA with multiple functions in differentiation and tumor suppression, acts as an endogenous barrier to reprogramming. Genetic ablation of miR-203 results in enhanced reprogramming whereas its expression prevents the formation of pluripotent cells both in vitro and in vivo. Mechanistically, this effect correlates with the direct repression of NFATC2, a transcription factor involved in the early phases of reprogramming. Inhibition of NFATC2 mimics miR-203 effects whereas NFATC2 overexpression rescues inducible cell pluripotency in miR-203-overexpressing cultures. These data suggest that miR-203 repression may favor the efficiency of reprogramming in a variety of cellular models.

cell biology↗

bioRxiv2020

Lack of adaptation to centriolar defects leads to p53-independent microcephaly in the absence of Cep135

Autosomal Recessive Primary Microcephaly (MCPH) is a rare disease associated to proteins involved in centrosomal and spindle dynamics including Cep135 (MCPH8). Although Cep135 has been associated to centriolar assembly, the mechanisms associated to the pathogenesis underlying MCPH8 mutations are unclear. By using a series of CRISPR/Cas9-edited murine Cep135 alleles, we report here that lack of Cep135 results in perinatal lethality accompanied by significant microcephaly in a dosis-dependent manner. Cep135 deficiency, but not that of other centrosomal microcephaly proteins such as Aspm or Cdk5rap2, induces centrosome duplication defects, and perturbed centriole structure and dynamics. Whereas other cell types are able to quickly adapt to these defects, neural progenitors display a prolonged response leading to chromosomal instability and cell death in later developmental stages. Genetic ablation of Trp53 in these mutant embryos prevents apoptotic cell death but does not rescue the microcephaly induced by Cep135 loss. These results suggest that microcephaly can arise from the lack of adaptation to centriole defects in neural progenitors of the developing neocortex in a p53-independent manner.

cell biology↗

bioRxiv2019

A novel microRNA-based strategy to expand the differentiation potency of stem cells

Full differentiation potential along with self-renewal capacity is a major property of pluripotent stem cells (PSCs). However, the differentiation capacity frequently decreases during expansion of PSCs in vitro. We show here that transient exposure to a single microRNA, expressed at early stages during normal development, improves the differentiation capacity of already-established murine and human PSCs. Short exposure to miR-203 in PSCs (miPSCs) results in expanded differentiation potency as well as improved efficiency in stringent assays such as tetraploid complementation and human-mouse interspecies chimerism. Mechanistically, these effects are mediated by direct repression of de novo DNA methyltransferases Dnmt3a and Dnmt3b, leading to transient and reversible erasing of DNA methylation. As a proof of concept, miR-203 improves differentiation and maturation of PSCs into cardiomyocytes in vitro as well as cardiac regeneration in vivo, after cardiac injury. These data support the use of transient exposure to miR-203 as a general and single method to reset the epigenetic memory in PSCs, and improve their use in regenerative medicine.

cell biology↗

bioRxiv2018

Plk1 overexpression suppresses tumor development by inducing chromosomal instability

Polo-like kinase 1 (Plk1) is a protein kinase currently considered as an attractive cancer target due to its critical role in the cell division cycle. Plk1 is overexpressed in a wide spectrum of human tumors, being frequently considered as an oncogene. However, its contribution to tumor development is unclear. Using a new inducible knock-in mouse model we report here that Plk1 overexpression does not favor cell proliferation but rather results in abnormal chromosome segregation and cytokinesis, leading to the formation of polyploid cells with reduced proliferative potential. Mechanistically, these cytokinesis defects correlate with defective loading of Cep55 and ESCRT complexes to the abscission bridge during cytokinesis in a Plk1 kinase-dependent manner. In vivo, elevated levels of Plk1 markedly prevent the development of mammary gland tumors induced either by KrasG12D or Her2, in the presence of increased rates of chromosome instability. In patients, higher Plk1 expression levels are associated with significantly increased overall survival in breast cancer subtypes. These data suggest that, despite the therapeutic benefits of inhibiting Plk1 due to its essential role in tumor cell cycles, Plk1 overexpression has tumor suppressive properties by perturbing mitotic progression and cytokinesis.

cancer biology↗

bioRxiv2018

Biochemical analyses reveal amino acid residues critical for cell cycle-dependent phosphorylation of human Cdc14A phosphatase by cyclin-dependent kinase 1

Cdc14 enzymes compose a family of highly conserved phosphatases that are present in a wide range of organisms, including yeast and humans, and that preferentially reverse the phosphorylation of Cyclin-Dependent Kinase (Cdk) substrates. The budding yeast Cdc14 orthologue has essential functions in the control of late mitosis and cytokinesis. In mammals, however, the two Cdc14 homologues, Cdc14A and Cdc14B, do not play a prominent role in controlling late mitotic events, suggesting that some Cdc14 functions are not conserved across species. Moreover, in yeast, Cdc14 is regulated by changes in its subcellular location and by phosphorylation events. In contrast, little is known about the regulation of human Cdc14 phosphatases. Here, we have studied how the human Cdc14A orthologue is regulated during the cell cycle. We found that Cdc14A is phosphorylated on Ser411, Ser453 and Ser549 by Cdk1 early in mitosis and becomes dephosphorylated during late mitotic stages. Interestingly, in vivo and in vitro experiments revealed that, unlike in yeast, Cdk1-mediated phosphorylation of human Cdc14A did not control its catalytic activity but likely modulated its interaction with other proteins in early mitosis. These findings point to differences in Cdk1-mediated mechanisms of regulation between human and yeast Cdc14 orthologues.

biochemistry↗