Biology subjects

Guadarrama, E.

Publications and source records attributed to Guadarrama, E..

5 recordsLinked to original sources

bioRxiv2026

Heterogeneity of white matter structure in the human brain

White-matter, which contains the long-range axons connecting different brain regions, makes up nearly half the human brain, yet the three-dimensional organization of individual axons has not been characterized. While advances in diffusion MRI have enabled macroscopic mapping of major WM pathways1, these methods are unable to resolve individual axons: their trajectories, density, and relative orientations2. Here, we present a histological and imaging pipeline optimized for post-mortem human white-matter that shows the 3D trajectories of densely stained large (diameter greater than ~1 m) projection axons. Applying our approach to multiple centimeter-scale WM regions in an adult human brain, we observed striking regional diversity in axonal organization. Specifically, we identified distinct architectural motifs ranging from loosely packed, multi-orientation meshworks (in most superficial white matter), to laminar lattice-like structures (near the basal ganglia), to tightly packed bundles of fibers (e.g. in the corpus callosum). We speculate that these patterns reflect local adaptations to spatial constraints, axonal density, and the diversity of axonal sources and targets, offering region-specific solutions to anatomical optimization problems. These findings offer new insights into the principles shaping brain connectivity and underscore the need for regionally detailed atlases of human white matter..

neuroscience↗

bioRxiv2026

An upstream open reading frame represses translation of the neuronal potassium channel KCNQ2

Upstream open reading frames (uORFs) within the 5-untranslated region (5-UTR) of mRNA transcripts can regulate protein translation. Despite widespread prevalence within the human genome, they remain unidentified for many clinically relevant genes. A gene frequently associated with neonatal-onset epilepsy is KCNQ2, which encodes a neuronal voltage-gated potassium channel subunit that functions to dampen neuronal excitability. Heterozygous loss-of-function pathogenic KCNQ2 variants are known to cause a range of neurodevelopmental disorders and epileptic encephalopathies, but there remains an unmet clinical need for patients harboring these variants. We identified a single uORF in KCNQ2 that is highly repressive of protein translation and demonstrated that mutations disabling the uORF start codon enhance translation of encoded potassium channels. Additionally, we show that adenine base editing of the uORF start codon can weaken ribosome engagement at the uORF and enhance translation of the protein in a neuron-like cell line. This study establishes a previously underexplored regulatory feature for KCNQ2 and highlights the importance of understanding uORFs for clinically relevant genes, both for assessing disease risk and therapeutic potential.

molecular biology↗

bioRxiv2025

Classification models distinguish functional and trafficking effects of KCNQ1 variants to enhance variant interpretation

Missense mutations compromise protein fitness by altering stability and function, which can lead to various clinical disease states. The potassium ion channel KCNQ1 underlies the majority of congenital long QT syndrome (LQTS) cases, one of the most common genetic arrhythmia syndromes. During genetic testing for LQTS, variants of uncertain significance (VUS) confound diagnosis and clinical management. KCNQ1 protein fitness metrics enable mechanistic classification of variants, directly informing the molecular basis for dysfunction and providing clinical interpretation of variants linked to LQTS and other channelopathies. We developed structure-aware random forest classifier models to predict seven metrics of KCNQ1 fitness, four functional electrophysiology measurements (peak current density, voltage-dependence, gating kinetics), and three trafficking values measured by flow cytometry. Our trained models outperformed AlphaMissense in predicting protein fitness, enhancing interpretation of ClinVar VUS and variants classified as ambiguous by AlphaMissense. We demonstrate the classifiers distinguish benign and pathogenic variants from ClinVar and gnomAD and identify systematic patterns of dysfunction and mistrafficking along the functionally critical S4 helix. Our method advances variant effect prediction with a mechanistic classifier that reliably links missense mutations in KCNQ1 to their specific disease-causing mechanisms. As a resource for precision medicine approaches for LQTS or other KCNQ1 channelopathies, we provide the predictions and scores for all KCNQ1 missense variants across the structured region of the protein.

biophysics↗

bioRxiv2025

Defining the Polycystin Pharmacophore Through HTS & Computational Biophysics.

Background and PurposePolycystins (PKD2, PKD2L1) are voltage-gated and Ca2+-modulated members of the transient receptor potential (TRP) family of ion channels. Loss of PKD2L1 expression results in seizure-susceptibility and autism-like features in mice, whereas variants in PKD2 cause autosomal dominant polycystic kidney disease. Despite decades of evidence clearly linking their dysfunction to human disease and demonstrating their physiological importance in the brain and kidneys, the polycystin pharmacophore remains undefined. Contributing to this knowledge gap is their resistance to drug screening campaigns, which are hindered by these channels unique subcellular trafficking to organelles such as the primary cilium. PKD2L1 is the only member of the polycystin family to form constitutively active ion channels on the plasma membrane when overexpressed. Experimental ApproachHEK293 cells stably expressing PKD2L1 F514A were pharmacologically screened via high-throughput electrophysiology to identify potent polycystin channel modulators. In-silico docking analysis and mutagenesis were used to define the receptor sites of screen hits. Inhibition by membrane-impermeable QX-314 was used to evaluate PKD2L1s binding site accessibility. Key ResultsScreen results identify potent PKD2L1 antagonists with divergent chemical core structures and highlight striking similarities between the molecular pharmacology of PKD2L1 and voltage-gated sodium channels. Docking analysis, channel mutagenesis, and physiological recordings identify an open-state accessible lateral fenestration receptor within the pore, and a mechanism of inhibition that stabilizes the PKD2L1 inactivated state. Conclusion and ImplicationOutcomes establish the suitability of our approach to expand our chemical knowledge of polycystins and delineates novel receptor moieties for the development of channel-specific antagonists in TRP channel research.

pharmacology and toxicology↗

bioRxiv2018

Regenerative capacity in the lamprey spinal cord is not altered after a repeated transection

The resilience of regeneration in vertebrate tissues is not well understood. Yet understanding how well tissues can regenerate after repeated insults, and identifying any limitations, is an important step towards elucidating the underlying mechanisms of tissue plasticity. This is particularly challenging in tissues such as the nervous system, which contain a large number of terminally differentiated cells (i.e. neurons) and that often exhibits limited regenerative potential in the first place. However, unlike mammals that exhibit very little spinal cord regeneration, many non-mammalian vertebrate species, including lampreys, fishes, amphibians and reptiles, regenerate their spinal cords and functionally recover even after a complete spinal cord transection. It is well established that lampreys undergo full functional recovery of swimming behaviors after a single spinal cord transection, which is accompanied by tissue repair at the lesion as well as axon and synapse regeneration. Here, using the lamprey model, we begin to explore resilience of spinal cord regeneration after a second spinal re-transection. We report that by all functional and anatomical measures tested, the lampreys regenerated after spinal re-transection just as robustly as after single transections. Recovery of swimming behaviors, axon regeneration, synapse and cytoskeletal distributions, and neuronal survival were nearly identical after a single spinal transection or a repeated transection. Thus, regenerative potential in the lamprey spinal cord is largely unaffected by spinal re-transection, indicating a greater persistent regenerative potential than exists in some other highly-regenerative models. These findings establish a new path for uncovering pro-regenerative targets that could be deployed in non-regenerative conditions.

neuroscience↗