Biology subjects

Lopez, M. A.

Publications and source records attributed to Lopez, M. A..

10 recordsLinked to original sources

bioRxiv2026

Pathway-resolved flux decomposition reveals hidden kinetic hierarchy in protein folding

Proteins fold through ensembles of competing pathways, yet the kinetic contribution of each route remains difficult to quantify. Structure-prediction methods such as AlphaFold identify folded endpoints, but do not resolve folding kinetics, pathway heterogeneity, or how flux partitions among competing mechanisms. Here, we introduce a framework that directly decomposes folding flux into pathway-specific kinetic contributions by combining forward-flux sampling with trajectory-level unsupervised learning, avoiding millisecond-scale trajectories, biasing potentials, and a priori state discretization. Applied to 2,637 statistically representative folding events of the TC5b variant of Trp-cage, the framework recovers a folding time in near-quantitative agreement with experiments and identifies four pathways distinguished by the ordering of helix formation, hydrophobic collapse, and salt-bridge stabilization. The resulting decomposition shows that structural prevalence is a poor proxy for kinetic importance: the most populated pathways are not the fastest, whereas a rare helix- salt-bridge route is disproportionately efficient and a premature salt bridge produces a frustrated slow route. By assigning statistical weights to competing pathways, this framework links structural evolution to kinetic relevance in biomolecular rare events and reveals how folding landscapes select kinetically important routes from many plausible structural sequences.

biophysics↗

bioRxiv2025

DOCK7 regulates WNT signaling and NMJ clustering in normal and DMD muscle

Dedicator of cytokinesis (DOCK) proteins have diverse and critical roles in myoblast fusion, glucose metabolism, skeletal muscle regeneration, and neuronal polarity. DOCK7 is part of this 11-member family of atypical guanine exchange factors. While human DOCK7 pathogenic variants are rare, biallelic variants are known to result in hypotonia and ataxia in children. More recently, DOCK variants have been shown to impact disease pathogenesis as secondary modifiers. We used tissue-specific Dock7 conditional knockout mice to evaluate the roles of DOCK7 in the skeletal muscles and motor neurons. Both Dock7 knockout models developed significant nerve and muscle function deficits; however, the Dock7 motor neuron knockout mice showed more severe locomotor pathologies. RNA sequencing of the Dock7 knockout skeletal muscles revealed dysregulation of WNT signaling factors, and skeletal muscle repair and regeneration pathways. Molecular analysis revealed impaired DOCK7-mediated RAC1 activation that impacted acetylcholine receptor (AChR) clustering in both models. Interestingly, haploinsufficiency of Dock7 in mdx mice improved overall dystrophic muscle pathologies. We propose that DOCK7-RAC1 interactions result in activation of the WNT signaling pathway via the LRP4 receptor in the skeletal muscle and facilitate post-synaptic AChR clustering. Graphical AbstractDOCK7 is a regulator of normal and DMD muscle via the RAC1/WNT pathway. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/696254v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1ce84eaorg.highwire.dtl.DTLVardef@17855f1org.highwire.dtl.DTLVardef@15263d2org.highwire.dtl.DTLVardef@1778e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2025

Conditional Dystrophin ablation causes profound effects on muscle development, neurobehavior, and extracellular matrix pathways

Duchenne muscular dystrophy (DMD) patients suffer from skeletal and cardiopulmonary weakness, and interestingly up to one third are diagnosed on the autism spectrum. Dystrophin is an essential protein for regulating the transmission of intracellular force to the extracellular matrix within the skeletal muscle, but also plays key roles in neurobehavior and cognitive function. The mouse dystrophin gene (also abbreviated Dmd) is X-linked and has several isoforms with tissue-specific expression, including the large Dp427m muscle transcript found in heart and skeletal muscle, and the Dp427c transcript that encodes the brain-specific dystrophin cerebellar protein. Understanding the functional requirements and pathways that are affected by dystrophin loss will impact dystrophin replacement gene therapy and exon-skipping correction strategies. We generated conditional Dystrophin knockout mice by targeting exon 52 of the mouse Dystrophin (Dmdflox52) locus. We generated dystrophin constitutive and inducible myofiber knockout (Dmd mKO) mice to evaluate the tissue-specific function of the large skeletal muscle dystrophin isoform. Constitutive embryonic deletion of the Dystrophin gene exclusively in skeletal myofibers resulted in a severe skeletal muscle myopathy, dystrophic histopathology, and functional deficits compared to the mdx mouse. Transcriptomic analysis of skeletal myofibers of the Dmd mKO mice revealed the dysregulation of key extracellular matrix and cytokine signaling pathways. Separately, we generated Purkinje neuron cerebellar dystrophin knockout (Dmd:Pcp2 KO) mice that displayed neurobehavioral deficits in social approach, social memory, and spatial navigation and working memory. These studies reveal the essential requirement for dystrophin expression in both the skeletal muscle and brain for normal physiological and neurobehavioral function. Significance StatementDuchenne muscular dystrophy is caused by the lack of a functional dystrophin protein in muscle. The large dystrophin (Dp427m) isoform is expressed in skeletal, cardiac, and smooth muscle, but its tissue-specific requirements remain unknown. We generated and characterized a conditional skeletal muscle knockout mouse (Dmd mKO). Constitutive embryonic genetic ablation of skeletal muscle Dystrophin resulted in muscle histopathologies similar to the mdx mouse, while postnatal muscle Dystrophin ablation resulted in milder pathologies. Ablating cerebellar Dystrophin Dp427c using a Pcp2/L7-Cre driver resulted in sociobehavioral defects. Transcriptomic analysis of the Dmd mKO mice showed a severe reduction of extracellular matrix and cytokine signaling pathways. Our study reveals an essential role for skeletal muscle dystrophin and identifies essential pathways for modulation using dystrophin-replacement therapies.

genetics↗

bioRxiv2024

Late-Stage Skeletal Muscle Transcriptome in Duchenne muscular dystrophy shows a BMP4-Induced Molecular Signature

Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disease due to loss-of-function mutations in the DYSTROPHIN gene. DMD-related skeletal muscle wasting is typified by an aberrant immune response involving upregulation of TGF{beta} family of cytokines. We previously demonstrated that bone morphogenetic protein 4 (BMP4) is increased in DMD and BMP4 stimulation induces a 20-fold upregulation of Smad8 transcription. However, the role of BMP4 in severely affected DMD skeletal muscle is unknown. We hypothesized that transcriptomic signatures in severely affected human DMD skeletal muscle are driven by BMP4 signaling. Transcriptomes from skeletal muscle biopsies of late-stage DMD vs. non-DMD controls and C2C12 muscle cells with or without BMP4 stimulation were generated by RNA-Seq and analyzed for single transcript differential expression as well as by Ingenuity Pathway Analysis and weighted gene co-expression network analyses. A total of 2,328 and 5,291 transcripts in the human muscle and C2C12 muscle cells, respectively, were differentially expressed. We identified an overlapping molecular signature of 1,027 genes dysregulated in DMD muscle that were induced in BMP4-stimulated C2C12 muscle cells. Highly upregulated DMD transcripts that overlapped with BMP4-stimulated C2C12 muscle cells included ADAMTS3, HCAR2, SERPING1, SMAD8, and UNC13C. The DMD transcriptome was characterized by dysregulation of pathways involving immune function, extracellular matrix remodeling, and metabolic/mitochondrial function. In summary, we define a late-stage DMD skeletal muscle transcriptome that substantially overlaps with the BMP4-induced molecular signature in C2C12 muscle cells. This supports BMP4 as a disease-driving regulator of transcriptomic changes in late-stage DMD skeletal muscle and expands our understanding of the evolution of dystrophic signaling pathways and their associated gene networks that could be explored for therapeutic development.

bioinformatics↗

bioRxiv2023

High-Accuracy Machine Learning Techniques for Functional Connectome Fingerprinting and Cognitive State Decoding

The human brain is a complex network comprised of functionally and anatomically interconnected brain regions. A growing number of studies have suggested that empirical estimates of brain networks may be useful for discovery of biomarkers of disease and cognitive state. A prerequisite for realizing this aim, however, is that brain networks also serve as reliable markers of an individual. Here, using Human Connectome Project data, we build upon recent studies examining brain-based fingerprints of individual subjects and cognitive states based on cognitively-demanding tasks that assess, for example, working memory, theory of mind, and motor function. Our approach achieves accuracy of up to 99% for both identification of the subject of an fMRI scan, and for classification of the cognitive state of a previously-unseen subject in a scan. More broadly, we explore the accuracy and reliability of five different machine learning techniques on subject fingerprinting and cognitive state decoding objectives, using functional connectivity data from fMRI scans of a high number of subjects (865) across a number of cognitive states (8). These results represent an advance on existing techniques for functional connectivity-based brain fingerprinting and state decoding. Additionally, 16 different pre-processing pipelines are compared in order to characterize the effects of different aspects of the production of functional connectomes (FCs) on the accuracy of subject and task classification, and to identify possible confounds.

neuroscience↗

bioRxiv2022

OsPSTOL1 is prevalent in upland rice and its expression in wheat enhances root growth and hastens low phosphate signaling

PHOSPHORUS-STARVATION TOLERANCE 1 (OsPSTOL1) benefits crown root growth and phosphorus (P) sufficiency in rice (Oryza sativa L.). To better understand the importance of this variably present gene, we carried out a biogeographic survey of landraces and cultivars, confirming that functional OsPSTOL1 alleles prevail in low nutrient and drought-prone rainfed ecosystems, whereas loss-of-function alleles and absence haplotypes predominate in control-irrigated paddy varieties of east Asia. To address the evolutionary history of OsPSTOL1 and related genes in cereal crops, phylogenetic and transcript meta-analyses were performed. Finally, to evaluate its potential value in another Gramineae, wheat (Triticum aestivum L.) lines overexpressing OsPSTOL1 were evaluated under field and controlled low P conditions. OsPSTOL1 enhances growth, crown root number, and overall root plasticity under low P in wheat. Survey of root and shoot crown transcriptomes at two developmental stages identifies transcription factors that are differentially regulated in OsPSTOL1 wheat that are similarly controlled by the gene in rice. In wheat, OsPSTOL1 alters the timing and amplitude of regulators of root development in dry soils and hastens induction of the core P-starvation response. Based on these findings, OsPSTOL1 and related genes may aid more sustainable cultivation of cereal crops. Summary statementMight a rice gene that controls root plasticity confer a similar benefit in another grain crop. Here, we evaluate the genetic variation and evolutionary history of OsPSTOL1 and demonstrate its impact in wheat.

plant biology↗

bioRxiv2021

miR-486 is an epigenetic modulator of Duchenne muscular dystrophy pathologies

Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle disorder resulting in muscle weakness and cardiomyopathy. MicroRNAs have been shown to play essential roles in muscle development, metabolism, and disease pathologies. We demonstrated that miR-486 expression is reduced in DMD muscles and its expression levels correlate with dystrophic disease severity. MicroRNA-486 knockout mice developed disrupted myofiber architecture, decreased myofiber size, decreased locomotor activity, increased cardiac fibrosis, and metabolic defects that were exacerbated on the dystrophic mdx5cv background. We integrated RNA-sequencing and chimeric eCLIP-sequencing data to identify direct in vivo targets of miR-486 and associated dysregulated gene signatures in skeletal muscle. In comparison to our DMD mouse muscle transcriptomes, we identified several of these miR-486 muscle targets including known modulators of dystrophinopathy disease symptoms. Together, our studies identify miR-486 as a driver of muscle remodeling in DMD, a useful biomarker for dystrophic disease progression, and highlight chimeric eCLIP-sequencing as a useful tool to identify direct in vivo microRNA target transcripts. O_FIG O_LINKSMALLFIG WIDTH=122 HEIGHT=200 SRC="FIGDIR/small/448387v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@13eeaf5org.highwire.dtl.DTLVardef@1b3b2dborg.highwire.dtl.DTLVardef@a36782org.highwire.dtl.DTLVardef@1e0b95f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2020

Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer

Fibroblasts are functionally heterogeneous cells, capable of promoting and suppressing tumour progression. Across cancer types, the extent and cause of this phenotypic diversity remains unknown. We used single-cell RNA sequencing and multiplexed immunohistochemistry to examine fibroblast heterogeneity in human lung and non-small cell lung cancer (NSCLC) samples. This identified seven fibroblast subpopulations: including inflammatory fibroblasts and myofibroblasts (representing terminal differentiation states), quiescent fibroblasts, proto-myofibroblasts (x2) and proto-inflammatory fibroblasts (x2). Fibroblast subpopulations were variably distributed throughout tissues but accumulated at discrete niches associated with differentiation status. Bioinformatics analyses suggested TGF-{beta}1 and IL-1 as key regulators of myofibroblastic and inflammatory differentiation respectively. However, in vitro analyses showed that whilst TGF-{beta}1 stimulation in combination with increased tissue tension could induce myofibroblast marker expression, it failed to fully re-capitulate ex-vivo phenotypes. Similarly, IL-1{beta} treatment only induced upregulation of a subset of inflammatory fibroblast marker genes. In silico modelling of ligand-receptor signalling identified additional pathways and cell interactions likely to be involved in fibroblast activation, which can be examined using publicly available R shiny applications (at the following links: myofibroblast activation and inflammatory fibroblast activation). This highlighted a potential role for IL-11 and IL-6 (among other ligands) in myofibroblast and inflammatory fibroblast activation respectively. This analysis provides valuable insight into fibroblast subtypes and differentiation mechanisms in NSCLC.

cancer biology↗

bioRxiv2020

DOCK3 is a dosage-sensitive regulator of skeletal muscle and Duchenne muscular dystrophy-associated pathologies.

DOCK3 is a member of the DOCK family of guanine nucleotide exchange factors that function to regulate cell migration, fusion, and overall viability. Previously, we identified a miR-486/Dock3 signaling cascade that was dysregulated in dystrophin-deficient muscle which resulted in the overexpression of DOCK3, however not much else is known about the role of DOCK3 in muscle. In this work, we characterize the functional role of DOCK3 in normal and dystrophic skeletal muscle. By utilizing Dock3 global knockout (Dock3 KO) mice, we found reducing Dock3 gene via haploinsufficiency in DMD mice improved dystrophic muscle histology, however complete loss of Dock3 worsened overall muscle function on a dystrophin-deficient background. Consistent with this, Dock3 KO mice have impaired muscle architecture and myogenic differentiation defects. Moreover, transcriptomic analyses of Dock3 knockout muscles reveal a decrease in factors known for myogenesis, suggesting a possible mechanism of action. These studies identify DOCK3 as a novel modulator of muscle fusion and muscle health and may yield additional therapeutic targets for treating dystrophic muscle symptoms.

genetics↗

bioRxiv2019

Identification of positive chemotaxis in the protozoan pathogen Trypanosoma brucei

To complete its infectious cycle, the protozoan parasite, Trypanosoma brucei, must navigate through diverse tissue environments in both its tsetse fly and mammalian hosts. This is hypothesized to be driven by yet unidentified chemotactic cues. Prior work has shown that parasites engaging in social motility in vitro alter their trajectory to avoid other groups of parasites, an example of negative chemotaxis. However, movement of T. brucei toward a stimulus, positive chemotaxis, has so far not been reported. Here we show that upon encountering E. coli, socially behaving T. brucei parasites exhibit positive chemotaxis, redirecting group movement toward the neighboring bacterial colony. This response occurs at a distance from the bacteria and involves active changes in parasite motility. By developing a quantitative chemotaxis assay, we show that the attractant is a soluble, diffusible signal dependent on actively growing E. coli. Time-lapse and live video microscopy revealed that T. brucei chemotaxis involves changes in both group and single cell motility. Groups of parasites change direction of group movement and accelerate as they approach the source of attractant, and this correlates with increasingly constrained movement of individual cells within the group. Identification of positive chemotaxis in T. brucei opens new opportunities to study mechanisms of chemotaxis in these medically and economically important pathogens. This will lead to deeper insights into how these parasites interact with and navigate through their host environments.\n\nImportanceAlmost all living things need to be able to move, whether it is toward desirable environments or away from danger. For vector-borne parasites, successful transmission and infection require that these organisms be able to sense where they are and use signals from their environment to direct where they go next, a process known as chemotaxis. Here we show that Trypanosoma brucei, the deadly protozoan parasite that causes African sleeping sickness, can sense and move toward an attractive cue. To our knowledge, this is the first report of positive chemotaxis in these organisms. In addition to describing a new behavior in T. brucei, our findings enable future studies of how chemotaxis works in these pathogens, which will lead to deeper understanding of how they move through their hosts and may lead to new therapeutic or transmission-blocking strategies.

microbiology↗