Biology subjects

Marquez, E.

Publications and source records attributed to Marquez, E..

7 recordsLinked to original sources

bioRxiv2026

Stress Granule Coarsening Is a Pathological Inflection Point for Cardiac Electrophysiological Dysfunction

Arrhythmia risk rises early in many forms of cardiac stress, often before contractile failure is evident. Stressed cardiomyocytes accumulate biomolecular condensates, known as stress granules (SGs), whose contribution to this electrical vulnerability has been unclear. We mapped where SGs reside and followed their life cycle under acute and chronic oxidative stress across complementary model systems and assessed electrophysiological consequences with pharmacological tools targeting granule assembly, microtubule integrity, and calcium channel function. Under both stress regimes, SGs localized preferentially to z-lines and intercalated discs, marking these mechanically critical sites as hubs of condensate assembly. Merging of granules, referred to as coarsening, rather than initial formation, emerged as a pathological connection. Early granules were broadly cytoprotective, whereas progressive coarsening was accompanied by disruption of alpha-actinin and L-type calcium channel (Cav1.2) nanodomains and by shortening of action potential (AP) duration. Coarsened granules disorganized Cav1.2 nanodomains through a microtubule-dependent mechanism, and arresting coarsening with nocodazole preserved nanodomain integrity and restored AP morphology. The transition from nascent to coarsened SGs therefore represents a targetable inflection point, and limiting coarsening may prevent proarrhythmic remodeling during cardiac oxidative stress.

bioengineering↗

bioRxiv2026

Modeling mitochondrial inheritance enables high-precision single-cell lineage tracing in humans

Somatic mutations in mitochondrial DNA (mtDNA) provide natural barcodes that enable engineering-free lineage tracing in human tissues, but the complex dynamics of mtDNA inheritance across cell divisions and incomplete sampling of mtDNA introduce uncertainty in reconstructed lineages. Here, we present MitoDrift, a probabilistic framework that integrates Wright-Fisher drift dynamics with sparse single-cell measurements to produce confidence-refined lineage trees enriched for accurate clonal relationships. Validation with gold-standard lentiviral barcoding and whole-genome sequencing demonstrates that MitoDrift outperforms existing tree reconstruction methods in precision while maintaining high clonal recovery, enabling robust analyses linking lineage to cell state. Applying MitoDrift to human hematopoiesis reveals an age-associated decline in clonal diversity with differential impact across cell types and identifies heritable regulatory programs in hematopoietic stem cells in vivo, linking AP-1/stress-associated programs to clonal expansions. In multiple myeloma, MitoDrift captures therapy-associated clonal remodeling undetectable by copy number analysis, revealing phenotypic transitions and linking gene regulatory programs to differential drug sensitivity. Collectively, MitoDrift enables high-precision lineage tracing at scale and establishes quantitative lineage-state analysis in primary human tissues, linking clonal history to transcriptional and epigenetic programs in tissue homeostasis, aging, and disease.

genomics↗

bioRxiv2026

ADAM17 Deletion Protects Against Type1 Diabetes-Associated Kidney Injury by Modulating Inflammatory and Fibrotic Pathways

0BackgroundA Disintegrin and Metalloprotease 17 (ADAM17) is a key sheddase regulating multiple inflammatory and growth factor-related pathways implicated in diabetic kidney disease (DKD). While cell-specific deletion of ADAM17 has shown renoprotective effects, the impact of global ADAM17 ablation in the context of diabetes remains incompletely understood. MethodsWe investigated the effects of tamoxifen-induced global Adam17 deletion in a murine model of type 1 diabetes induced by streptozotocin. Renal function, structural injury, inflammatory responses, stress-related signalling pathways, and fibrotic remodelling were comprehensively assessed and compared between diabetic Adam17 knockout and control mice. ResultsDespite persistent hyperglycaemia and albuminuria, diabetic Adam17 knockout mice exhibited preservation of glomerular filtration rate and marked attenuation of diabetes-associated renal injury. Global Adam17 deletion reduced mesangial expansion and structural damage, limited macrophage infiltration and chemokine expression, and significantly attenuated fibrotic remodelling. At the molecular level, Adam17 deficiency was associated with selective modulation of stress-related signalling pathways, including reduced activation of the PI3K/Akt axis and partial preservation of mitochondrial stress regulators, without evidence of a generalized suppression of cellular stress responses. ConclusionsOur findings demonstrate that global deletion of ADAM17 confers robust protection against diabetes-induced kidney injury through coordinated attenuation of inflammatory activation, stress-related signalling, and fibrotic progression. These results highlight the context-dependent role of ADAM17 in diabetic kidney disease and support the concept that therapeutic strategies targeting ADAM17-related pathways may require tissue- and disease-specific modulation to achieve renoprotective effects.

pathology↗

bioRxiv2026

Common Genetic Variants of The Cardiac Sodium Channel Alter Patient Response to Class 1b Antiarrhythmics

Several common variants have been identified in SCN5A, which encodes the cardiac sodium channel -subunit Nav1.5 and is targeted by class I antiarrhythmics. Lidocaine and its analog mexiletine both have a primary amine that blocks Na+ current. While lidocaine is highly effective in terminating ventricular tachycardia after acute myocardial infarction, mexiletine has been shown to prevent arrhythmia induction in only [~]20% of patients. The factors underlying this inconsistent drug response are unclear. Here, we use cardiomyocytes that are derived from induced pluripotent stem cells to observe that a common polymorphism in the SCN5A gene, S1103Y, exhibits an altered pharmacological response to mexiletine, with enhanced use-dependent and tonic block of peak sodium current. In addition, an unexpected increase in late sodium current causes action potential prolongation. This paradoxical proarrhythmic phenotype shifts the paradigm of conventional antiarrhythmic therapy with mexiletine, suggesting that background variants may alter pharmacological responses leading to unanticipated consequences. Our results suggest that the unique genetic background of patients should inform therapeutic approaches to treat and prevent arrhythmias associated with common cardiac pathologies.

physiology↗

bioRxiv2023

Gait speed is a biomarker of cancer-associated cachexia decline and recovery

BackgroundProgressive functional decline is a key element of cancer-associated cachexia. No therapies have successfully translated to the clinic due to an inability to measure and improve physical function in cachectic patients. Major barriers to translating pre-clinical therapies to the clinic include lack of cancer models that accurately mimic functional decline and use of non-specific outcome measures of function, like grip strength. New approaches are needed to investigate cachexia-related function at both the basic and clinical science levels. MethodsSurvival extension studies were performed by testing multiple cell lines, dilutions, and vehicle-types in orthotopic implantation of K-rasLSL.G12D/+; Trp53R172H/+; Pdx-1-Cre (KPC) derived cells. 128 animals in this new model were then assessed for muscle wasting, inflammation, and functional decline using a battery of biochemical, physiologic, and behavioral techniques. In parallel, we analyzed a 156-subject cohort of cancer patients with a range of cachexia severity, and who required rehabilitation, to determine the relationship between gait speed via six-minute walk test (6MWT), grip strength (hGS), and functional independence measures (FIM). Cachectic patients were identified using the Weight Loss Grading Scale (WLGS), Fearon consensus criteria, and the Prognostic Nutritional Index (PNI). ResultsUsing a 100-cell dose of DT10022 KPC cells, we extended the survival of the KPC orthotopic model to 8-9 weeks post-implantation compared to higher doses used (p<0.001). In this Low-dose Orthotopic (LO) model, both progressive skeletal and cardiac muscle wasting were detected in parallel to systemic inflammation; skeletal muscle atrophy at the fiber level was detected as early as 3 weeks post-implantation compared to controls (p<0.001). Gait speed in LO animals declined as early 2 week post-implantation whereas grip strength change was a late event and related to end of life. Principle component analysis (PCA) revealed distinct cachectic and non-cachectic animal populations, which we leveraged to show that gait speed decline was specific to cachexia (p<0.01) while grip strength decline was not (p=0.19). These data paralleled our observations in cancer patients with cachexia who required rehabilitation. In cachectic patients (identified by WLGS, Fearon criteria, or PNI, change in 6MWT correlated with motor FIM score changes while hGS did not (r2=0.18, p<0.001). This relationship between 6MWT and FIM in cachectic patients was further confirmed through multivariate regression (r2=0.30, p<0.001) controlling for age and cancer burden. ConclusionOutcome measures linked to gait are better associated with cachexia related function and preferred for future pre-clinical and clinical cachexia studies.

cancer biology↗

bioRxiv2022

Multiomic profiling defines cell fate plasticity of in vitro-derived islets

Transplantation of insulin-secreting {beta}-cells differentiated from human pluripotent stem cells holds great potential as a cell therapy for treating insulin-dependent diabetes. While these stem cell-derived islets (SC-islets) are able to reverse diabetes in animal models, they are not fully equivalent to their in vivo counterparts. To better define the state of the cell types generated within these SC-islets and provide a resource for identifying deficiencies in lineage specification, we used single-cell multiomic sequencing to simultaneously measure the chromatin accessibility and transcriptional profiles of SC-islets at multiple time points as well as primary human islets. The integrated analysis of both the transcriptional and chromatin landscape for each cell provided greater resolution for defining cell identity, allowing us to derive novel gene lists for identifying each islet cell type. Furthermore, this multiomic analysis revealed that the difference between SC-{beta} cells and enterochromaffin-like cells, which are a major off-target from in vitro differentiation, is a gradient of progressive cell states rather than a stark difference in identity. The chromatin landscape of primary human islets was much more restricted, suggesting that stem cell-derived cells are not fully locked into their cell fate. While long term culture of SC-islets both in vitro and in vivo does close overall chromatin state, only in vivo transplantation directs cells toward their correct identities. Collectively, our multiomic analysis demonstrates that both the chromatin and transcriptional landscapes play significant roles in islet cell identity, and these data can be used as a resource to identify specific deficiencies in the chromatin and transcriptional state of SC-islet cell types.

cell biology↗

bioRxiv2017

Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis-regulatory element use in human islets

Genetic and environmental factors both contribute to islet dysfunction and failure, resulting in type 2 diabetes (T2D). The islet epigenome integrates these cues and can be remodeled by genetic and environmental variation. However, our knowledge of how genetic variants and T2D disease state alter human islet chromatin landscape and cis-regulatory element (RE) use is lacking. To fill this gap, we profiled and analyzed human islet chromatin accessibility maps from 19 genotyped individuals (5 with T2D) using ATAC-seq technology. Chromatin accessibility quantitative trait locus (caQTL) analyses identified 3001 sequence variants (FDR<10%) altering putative cis-RE use/activity. Islet caQTL were significantly and specifically enriched in islet stretch enhancers and islet-specific transcription factor binding motifs, such as FOXA2, NKX6.1, RFX5/6 and PDX1. Importantly, these analyses identified putative functional single nucleotide variants (SNVs) in 13 T2D-associated GWAS loci, including those previously associated with altered ZMIZ1, MTNR1B, RNF6, and ADCY5 islet expression, and linked the risk alleles to increased (n=8) or decreased (n=5) islet chromatin accessibility. Luciferase reporter assays confirmed allelic differences in cis-RE activity for 5/9 caQTL sequences tested, including a T2D-associated SNV in the IL20RA locus. Comparison of T2D and non-diabetic islets revealed 1882 open chromatin sites exhibiting T2D-associated chromatin accessibility changes (FDR<10%). Together, this study provides new insights into genetic variant and T2D disease state effects on islet cis-RE use and serves as an important resource to identify putative functional variants in T2D-and islet dysfunction-associated GWAS loci and link their risk allele to in vivo loss or gain of chromatin accessibility.

genomics↗