Biology subjects

Perez, J. M.

Publications and source records attributed to Perez, J. M..

7 recordsLinked to original sources

bioRxiv2026

Testis-Specific MAGEA3/6 Regulate Glycolysis to Promote Metabolic Flexibility and Reveal Therapeutic Vulnerabilities in Pancreatic Cancer Cells

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor characterized by metabolic plasticity that enables cancer cells to survive nutrient deprivation and therapeutic stress. Melanoma-associated antigens A3 and A6 (MAGEA3/6), members of the cancer-testis antigen family with a previously identified protective role in spermatogenesis during nutritional stress, have been implicated in cancer progression and metabolic regulation. However, their contribution to metabolic adaptation in pancreatic cancer remains poorly understood. Here, we investigated the molecular mechanisms underlying MAGEA3/6-mediated resistance to glycolytic inhibition using complementary gain- and loss-of-function models, pharmacological inhibition of metabolic pathways, cellular metabolic assays, and integrated transcriptomic, proteomic, metabolomic, and lipidomic analyses. MAGEA3/6 expression enhanced resistance to 2-deoxy-D-glucose (2-DG), with MAGEA6-expressing MIA PaCa-2 cells exhibiting a greater than 2.5-fold increase in the half-maximal inhibitory concentration (IC50). Conversely, MAGEA3/6 depletion reduced clonogenic growth and migration and increased sensitivity to 2-DG. Resistance persisted despite pharmacological inhibition of mTORC1, the pentose phosphate pathway, or glutaminase, suggesting metabolic adaptations beyond these pathways. Unexpectedly, MAGEA6 expression was associated with increased rather than decreased AMPK1 protein abundance, contrasting with previously reported MAGEA3/6-mediated AMPK degradation and suggesting context-dependent regulation of this master regulator of cellular metabolism. MAGEA6 also reduced hexokinase HK1 and HK2 abundance while increasing several downstream glycolytic enzymes, revealing discordant regulation of glycolysis. Seahorse analyses and integrated multi-omics profiling identified extensive remodeling of mitochondrial metabolism, glutamine-aspartate metabolism, phospholipid composition, lipid storage, and redox homeostasis. Interestingly, despite enhanced resistance to glycolytic inhibition, MAGEA6-expressing cells exhibited increased sensitivity to hydrogen peroxide-induced oxidative stress, revealing a potential metabolic vulnerability. Given that MAGEA3/6 are physiologically expressed primarily in the male germline during early spermatogenesis, a process highly sensitive to metabolic and oxidative stress, these findings also raise important questions about their physiological roles in protecting developing germ cells and maintaining metabolic and redox homeostasis. Together, our findings recognize MAGEA3/6 as regulators of metabolic plasticity in PDAC and highlight how understanding their molecular functions in both spermatogenesis and cancer may uncover previously unrecognized metabolic vulnerabilities and potential therapeutic opportunities.

cancer biology↗

bioRxiv2025

MTBP allosterically activates Cdk8-CycC kinase activity

How the approximately 300 human protein kinases identify their dedicated substrates despite the significant overlap of their phosphorylation consensus sequences is relevant for nearly all cellular processes. We show here that the Cdk8/19-CycC kinase uses mutually exclusive targeting and activation factors to facilitate distinct cellular roles. The Med12 protein is known to target Cdk8/19-CycC to the mediator of transcription complex to control the transcription of specific gene sets upon respective stimuli. We describe that a second Cdk8/19-CycC targeting factor exists, the replication origin firing regulator MTBP that targets the kinase to Med12-independent cellular roles. Both Med12 and MTBP constitute allosteric activators of the enzymatic Cdk8/19-CycC kinase activity in vitro. We describe the structural basis of this activation that involves distinct mechanisms how Med12 and MTBP reposition the T-loop of the kinase independently of T-loop phosphorylation - the canonical mechanism of CDK kinase activation. Our results support the following model: the Cdk8/19-CycC dimer alone has low enzymatic activity, which may help avoid off-target phosphorylation. Med12, MTBP and potentially other as yet unidentified accessory factors, target the kinase to distinct molecular environments, at the same time activating kinase activity for efficient substrate phosphorylation. Our work establishes an unusual mechanism of CDK kinase control and change the current paradigm how Cdk8/19-CycC selects its substrates. Substrate selection of the kinase may be relevant for cancer biology and therapy because Cdk8 is a well-established colorectal cancer promoting factor.

biochemistry↗

bioRxiv2025

Global proteomic analysis of Cryptococcus neoformans clinical strains reveals significant differences between latent and lethal infection

To predict the outcomes of disseminated fungal disease, a deeper understanding of host-pathogen interactions at the site of infection is needed to identify targets for clinical intervention and diagnostic development. Cryptococcus neoformans is the causative agent of cryptococcosis, the largest infectious killer of individuals living with HIV. Cryptococcal infection begins in the lungs, with loss of immunological control leading to disseminated central nervous system disease and death. Using advanced mass spectrometry-based proteomic techniques, in vivo infection models, and patient-derived clinical strains, we explored the proteomic profiles of C. neoformans infections related to differences in strain virulence. Our findings reveal that non-lethal latent infection produces a proteomic response that differs significantly from the response caused by lethal infections, and that the proteomic profiles of typical and hypervirulent infections are markedly similar despite differences in time-to-death. Overall, the mouse pulmonary proteomic response in latent infection is defined by enrichment of proteins and pathways involved in extracellular matrix organization, cell adhesion, and structural changes, while the lethal infection is dominated by host-defense, translation, and metabolic processes. These results provide clinically relevant information on how infections caused by different Cryptococcus strains may produce significantly different outcomes. We also identified abundant fungal proteins that could be future drug targets in latent and lethal cryptococcal infection. IMPORTANCECryptococcus neoformans is a fungal pathogen that causes substantial morbidity and mortality in immunocompromised individuals. The initial infection begins in the lungs after exposure to inhaled spores after which local immune cells respond by either killing or containing the fungal cells. Immunosuppression weakens the immune system and allows fungal cells in the lungs to escape through the circulatory system and invade the central nervous system and cause fatal disease. However, differences between fungal strains influence the severity of disease manifestation. Our group has previously described genetic differences that contribute to strain-specific disease manifestations. In this study, we expanded our analysis to investigate the proteomic differences between strains of C. neoformans to identify candidate proteins and pathways that contribute to disease manifestation. We found that latent infection differs significantly from lethal disease from both the host and pathogen proteomic perspectives and have identified several fungal protein targets for future study.

microbiology↗

bioRxiv2025

MACHINE LEARNING FOR MISSING DATA IMPUTATION IN ALZHEIMER'S RESEARCH: PREDICTING MEDIAL TEMPORAL LOBE FLEXIBILITY

BACKGROUNDAlzheimers disease (AD) begins years before symptoms appear, making early detection essential. The medial temporal lobe (MTL) is one of the earliest regions affected, and its network flexibility, a dynamic measure of brain connectivity, may serve as a sensitive biomarker of early decline. Cognitive (acquisition, generalization), genetic (APOE, ABCA7), and biochemical (P-tau217) markers may predict MTL dynamic flexibility. Given the high rate of missing data in AD research, this study uses machine learning with advanced imputation methods to predict MTL dynamic flexibility from multimodal predictors in an aging cohort. METHODSIn an ongoing study at Rutgerss Aging and Brain Health Alliance, data from 656 participants are utilized, including cognitive assessments, genetic and blood-derived biomarkers, and demographics. Due to MRI-related constraints, only 34.15% of participants had measurable MTL dynamic flexibility from resting-state fMRI. To estimate MTL dynamic flexibility from available data, we evaluated four missing data handling methods (case deletion, MICE, MissForest, and GAIN), and trained five regression models: Ridge, k-NN, SVR, regression trees (bagging, random forest, boosting), and ANN. Hyperparameters were optimized via grid search with 3-fold cross-validation. Model performance was assessed using mean absolute error (MAE), root mean squared error (RMSE), and runtime through 5-fold cross-validation repeated 25 times to ensure robustness in clinical data settings. RESULTSA total of 1,866 missing values (25.86%) were identified in the dataset, with only 42 complete cases (6.40%) remaining after listwise deletion, highlighting the need for effective imputation. In the initial analysis using only complete cases, support vector regression (SVR) achieved the lowest mean absolute error (MAE = 0.184), though overall performance was limited due to small sample size. In the second phase, three imputation techniques were applied, significantly improving model accuracy. MissForest combined with Random Forest produced the best results (MAE = 0.083), representing a 54.7% improvement over case deletion. Statistical analysis confirmed significant differences in performance across imputation methods (p < 0.001), with MissForest outperforming GAIN and MICE. GAIN was the fastest imputation method. DISCUSSIONThe findings underscore the importance of using robust imputation strategies to maximize data utility and model reliability in studies with high missingness. Further research is needed, particularly incorporating additional neuroimaging measures, to localize the brain regions most affected by biomarker-driven changes and to refine predictive models for clinical applications.

neuroscience↗

bioRxiv2024

Cell signaling facilitates apical constriction by basolaterally recruiting Arp2/3 via Rac and WAVE

Apical constriction is a critical cell shape change that bends tissues. How precisely-localized actomyosin regulators drive apical constriction remains poorly understood. C. elegans gastrulation provides a valuable model to address this question. The Arp2/3 complex is essential in C. elegans gastrulation. To understand how Arp2/3 is locally regulated, we imaged embryos with endogenously-tagged Arp2/3 and its nucleation-promoting factors (NPFs). The three NPFs - WAVE, WASP, and WASH - colocalized with Arp2/3 and controlled Arp2/3 localization at distinct subcellular locations. We exploited this finding to study distinct populations of Arp2/3 and found that only WAVE depletion caused penetrant gastrulation defects. WAVE localized basolaterally with Arp2/3 at cell-cell contacts, dependent on CED-10/Rac. Establishing ectopic cell contacts recruited WAVE and Arp2/3, identifying contact as a symmetry-breaking cue for localization of these proteins. These results suggest that cell-cell signaling via Rac activates WAVE and Arp2/3 basolaterally, and that basolateral Arp2/3 is important for apical constriction.

cell biology↗

bioRxiv2024

A deep dive into the FALSIFLORA contribution to tomato reproductive development through a comprehensive allelic series analysis

Plants undergo continuous growth and development thanks to meristems, specialized groups of pluripotent stem cells that remain in their undifferentiated state throughout the plants life cycle. Meristem transition from the vegetative to the reproductive phase heavily influences plant reproductive success and agricultural productivity. In tomato (Solanum lycopersicum L.), FALSIFLORA (FA), the orthologue of the Arabidopsis LEAFY gene, promotes floral transition by specifying floral meristem identity and regulating the expression of genes responsible for floral organ identity and development. In this study, the allelic series of FA has been expanded by combining the screening of a tomato EMS mutant collection with overexpression, gene silencing and CRISPR/Cas9 genome editing approaches, aimed to deepen the understanding of the functional role of FA during tomato reproductive development. The phenotypic and molecular characterization of the FA allelic series revealed the multifaceted role of FA acting in both early and late stages of floral ontogeny. Thus, in addition to promoting floral transition and specifying floral meristem identity, FA also plays a role in inflorescence meristem maturation and termination, thereby regulating the inflorescence architecture. Furthermore, FA exerts regulatory control over the expression of the tomato homologs of AGAMOUS (TOMATO AGAMOUS1, TAG1) and WUSCHEL (SlWUS), underscoring its function in promoting carpel development and suppressing floral stem cell activity, thereby establishing floral determinacy. In conclusion, our findings demonstrate the potential of employing mutant allelic series as powerful tools for elucidating gene functions and deciphering the intricate molecular basis underlying biological processes. Plain Language SummaryOur research aims to gain a deeper understanding of the role of FALSIFLORA in tomato reproductive development. The FALSIFLORA allelic spectrum was expanded through mutant screening, along with overexpression, silencing, and CRISPR/Cas9 editing approaches. Our findings reveal that FALSIFLORA has a dual function in early and late floral development stages. In addition to promoting floral transition and specifying floral meristem identity, FA regulates the expression of tomato genes homologous to WUSCHEL and AGAMOUS, which play an essential role in stem cell regulation and carpel development. This study highlights the value of allelic series in elucidating gene functions and intricate biological mechanisms.

plant biology↗

bioRxiv2020

Functional pathway redundancy in the metabolism of plant-derived phenolics by Novosphingobium aromaticivorans

Lignin is a plant heteropolymer composed of phenolic subunits. Because of its heterogeneity and recalcitrance, the development of efficient methods for its valorization still remains an open challenge. One approach to utilize lignin is its chemical deconstruction into mixtures of monomeric phenolic compounds followed by biological funneling into a single product. Novosphingobium aromaticivorans DSM12444 has been previously engineered to produce 2-pyrone-4,6-dicarboxylic acid (PDC) from depolymerized lignin by simultaneously metabolizing multiple aromatics through convergent routes involving the intermediates 3-methoxygallic acid (3-MGA) and protocatechuic acid (PCA). We investigated enzymes predicted to be responsible for O-demethylation and oxidative aromatic ring opening, two critical reactions involved in the metabolism of phenolics compounds by N. aromaticivorans. The results showed the involvement of DesA in O-demethylation of syringic and vanillic acids, LigM in O-demethylation of vanillic acid and 3-MGA, and a new O-demethylase, DmtS, in the conversion of 3-MGA into gallic acid (GA). In addition, we found that LigAB was the main aromatic ring opening dioxygenase involved in 3-MGA, PCA, and GA metabolism, and that a previously uncharacterized dioxygenase, LigAB2, had high activity with GA. Our results indicate a metabolic route not previously identified in N. aromaticivorans that involves O-demethylation of 3-MGA to GA. We predict this pathway channels [~]15% of the carbon flow from syringic acid, with the rest following ring opening of 3-MGA. The new knowledge obtained in this study allowed for the creation of an improved engineered strain for the funneling of aromatic compounds that exhibits stoichiometric conversion of syringic acid into PDC. IMPORTANCEFor lignocellulosic biorefineries to effectively contribute to reduction of fossil fuel use, they need to become efficient at producing chemicals from all major components of plant biomass. Making products from lignin will require engineering microorganisms to funnel multiple phenolic compounds to the chemicals of interest, and N. aromaticivorans is a promising chassis for this technology. The ability of N. aromaticivorans to efficiently and simultaneously degrade many phenolic compounds may be linked to having functionally redundant aromatic degradation pathways and enzymes with broad substrate specificity. A detailed knowledge of aromatic degradation pathways is thus essential to identify genetic engineering targets to maximize product yields. Furthermore, knowledge of enzyme substrate specificity is critical to redirect flow of carbon to desired pathways. This study described an uncharacterized pathway in N. aromaticivorans and the enzymes that participate in this pathway, allowing the engineering of an improved strain for production of PDC from lignin.

microbiology↗