Biology subjects

Straub, J.

Publications and source records attributed to Straub, J..

7 recordsLinked to original sources

bioRxiv2026

Quantum transduction from electron spin state to a signaling state in a wild-type LOV photoreceptor

1Whether coherent spin dynamics can control biological regulation remains an open question. Here we show that the electron spin state in the wild-type Avena sativa phototropin 1 Light-Oxygen-Voltage domain 2 (AsLOV2) modulates FMN-cysteine photoadduct formation, the covalent bond that defines its signaling state. Although AsLOV2 was thought magnetically inactive, we observe a magnetic field effect (MFE) on its fluorescence, emerging above ~100 mT and strengthening to 1300 mT. The MFE establishes a spin-correlated radical pair on the photoadduct pathway, one rendered inaccessible to direct spectroscopy by the same strong coupling that sets the high-field onset. It arises from g-factor asymmetry within the closely spaced FMN-cysteine radical pair overcoming its dipolar coupling to drive coherent singlet-triplet interconversion. We furthermore observe an MFE in UV-Vis absorption that, unlike fluorescence, shows the field modulates productive bond formation itself. LOV domains are ubiquitous biological regulators, suggesting that quantum transduction relying on radical pairs as molecular qubits may be a general property among natural and engineered photoreceptors.

biophysics↗

bioRxiv2025

Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics

Glioblastoma (GB) is one of the most lethal human cancers, marked by profound intratumoral heterogeneity and near-universal treatment resistance. Cellular plasticity, the capacity of cancer cells to transition between phenotypic states, drives GB progression and resistance. However, the regulatory logic that permits or restricts specific state transitions remains poorly understood. Here, we integrated single-nucleus RNA and chromatin accessibility multi-ome profiles from over one million cells across primary IDH-wildtype GBs and developed scDORI, a scalable deep-learning framework to infer enhancer-driven gene regulatory networks (eGRNs) at single-cell resolution. Our analysis revealed a structured hierarchy of GB cell states governed by distinct regulatory programs, with marked variability in epigenetic plasticity that enables or constrains transitions. Neuronal-like tumor cells emerge as a low plasticity state that deploys active repression, in contrast to more permissive progenitor-like and astrocytic states. We identified the neuronal-like state-specific repressor MYT1L as a key regulator that silences master transcription factors of alternative states. MYT1L gain-of-function in patient-derived GB cells reduced chromatin accessibility, induced neuronal-like identity, and restricted proliferation and invasion in vivo, whereas loss-of-function reactivated plasticity and accelerated malignant features. Our findings delineate the epigenetic architecture and associated transcriptional master regulators that shape GB state trajectories, and establish safeguard repressors such as MYT1L as potential therapeutic targets to constrain malignant plasticity.

cancer biology↗

bioRxiv2025

Dual inhibition of lactate transporters MCT1 and MCT4 in pancreatic neuroendocrine tumors targets metabolic heterogeneity and functional redundancy

Our current understanding of the metabolic landscape of pancreatic neuroendocrine tumors (PanNETs) is very limited. Such knowledge could lead the development of novel therapeutic strategies for subgroups of PanNET patients based on the metabolic profile of their tumor. Here, we investigated the expression of lactate transporters MCT1 and MCT4 in two independent PanNET cohorts (n=93; n=70) and analyzed their association with tumor aggressiveness and therapeutic vulnerability in cell lines, spheroids and patient-derived tumoroids of PanNET. Immunohistochemistry revealed four expressor types: MCT1/4-negative, MCT1-positive, MCT4-positive, and MCT1/4-double positive with frequent regional co-expression. Both homogenous and heterogenous expression patterns were observed, indicating metabolic heterogeneity within the latter subset of PanNETs. MCT4 expression correlated with the hypoxia marker CA9, suggesting a hypoxic and acidic tumor microenvironment. Mechanistic studies revealed that MCT1 and MCT4 operate both as lactate efflux systems in PanNET cell lines, providing functional redundancy to their glycolytic roles. Inhibition of lactate efflux in normoxia and hypoxia using the dual MCT1/4 inhibitor syrosingopine significantly impaired lactate secretion, glycolysis, and proliferation across PanNET cell lines and 3D spheroid and patient-derived tumoroid models. In contrast, selective MCT1 or MCT4 inhibitors showed limited efficacy, underscoring the therapeutic need for co-targeting MCT1 and MCT4 due to functional redundancy and heterogenous expression. This work demonstrates MCT1 and MCT4 as metabolic markers and promising therapeutic targets of a subset of PanNETs with clinical features of aggressiveness.

cancer biology↗

bioRxiv2024

iSCORE-PD: an isogenic stem cell collection to research Parkinson Disease

Parkinsons disease (PD) is a neurodegenerative disorder caused by complex genetic and environmental factors. Genome-edited human pluripotent stem cells (hPSCs) offer a unique experimental platform to advance our understanding of PD etiology by enabling the generation of disease-relevant cell types carrying patient mutations along with isogenic control cells. To facilitate this approach, we generated a collection of 65 human stem cell lines genetically engineered to harbor high risk or causal variants in genes associated with PD (SNCA A53T, SNCA A30P, PRKN Ex3del, PINK1 Q129X, DJ1/PARK7 Ex1-5del, LRRK2 G2019S, ATP13A2 FS, FBXO7 R498X/FS, DNAJC6 c.801 A>G/FS, SYNJ1 R258Q/FS, VPS13C A444P/FS, VPS13C W395C/FS, GBA1 IVS2+1/FS). All mutations were introduced into a fully characterized and sequenced female human embryonic stem cell (hESC) line (WIBR3; NIH approval number NIHhESC-10-0079) using different genome editing techniques. To ensure the genetic integrity of these cell lines, we implemented rigorous quality controls, including whole-genome sequencing of each line. Our analysis of the genetic variation in this cell line collection revealed that while genome editing, particularly using CRISPR/Cas9, can introduce rare off-target mutations, the predominant source of genetic variants arises from routine cell culture and are fixed in cell lines during clonal isolation. The observed genetic variation was minimal compared to that typically found in patient-derived iPSC experiments and predominantly affected non-coding regions of the genome. Importantly, our analysis outlines strategies for effectively managing genetic variation through stringent quality control measures and careful experimental design. This systematic approach ensures the high quality of our stem cell collection, highlights advantages of prime editing over conventional CRISPR/Cas9 methods and provides a roadmap for the generation of gene-edited hPSC collections at scale in an academic setting. Our iSCORE-PD collection represents an easily accessible and valuable platform to study PD, which can be used by investigators to understand the molecular pathophysiology of PD in a human cellular setting.

neuroscience↗

bioRxiv2023

Microglia play beneficial roles in multiple experimental seizure models.

Seizure disorders are common, affecting both the young and the old. Currently available antiseizure drugs are ineffective in a third of patients and have been developed with a focus on known neurocentric mechanisms, raising the need for investigations into alternative and complementary mechanisms that contribute to seizure generation or its containment. Neuroinflammation, broadly defined as the activation of immune cells and molecules in the central nervous system (CNS), has been proposed to facilitate seizure generation, although the specific cells involved in these processes remain inadequately understood. The role of microglia, the primary inflammation-competent cells of the brain, is debated since previous studies were conducted using approaches that were less specific to microglia or had inherent confounds. Using a selective approach to target microglia without such side effects, we show a broadly beneficial role for microglia in limiting chemoconvulsive, electrical, and hyperthermic seizures and argue for a further understanding of microglial contributions to contain seizures.

neuroscience↗

bioRxiv2022

Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain

Stem cells in the adult brain are specialized astrocytes capable of generating neurons and glial cells. While neural stem cells (NSCs) and common astrocytes have clearly distinct functions, they share highly similar transcriptome profiles. How stemness is molecularly encoded is therefore unclear. Here we use single-cell NMT-seq to simultaneously characterize the transcriptome, DNA methylome and chromatin accessibility of astrocytes and the NSC lineage in the healthy and ischemic brain. Our data reveal distinct methylation profiles associated with either astrocyte or stem cell function. Stemness is conferred by methylation of astrocyte genes and demethylation of neurogenic genes that are expressed only later. Surprisingly, ischemic injury unlocks the stemness-methylome in common astrocytes enabling generation of neuroblasts. Furthermore, we show that oligodendrocytes employ Tet-mediated demethylation to regulate expression of myelin-related genes, many of which are abnormally methylated in multiple sclerosis. Overall, we show that DNA methylation is a promising target for regenerative medicine. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/499860v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@149fe11org.highwire.dtl.DTLVardef@c71902org.highwire.dtl.DTLVardef@13ae945org.highwire.dtl.DTLVardef@a8d37e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2018

Structure of APP-C991-99 and Implications for Role of Extra-Membrane Domains in Function and Oligomerization

The 99 amino acid C-terminal fragment of Amyloid Precursor Protein APP-C99 (C99) is cleaved by {gamma}-secretase to form A{beta} peptide, which plays a critical role in the etiology of Alzheimers Disease (AD). The structure of C99 consists of a single transmembrane domain flanked by intra and intercellular domains. While the structure of the transmembrane domain has been well characterized, little is known about the structure of the flanking domains and their role in C99 processing by {gamma}-secretase. To gain insight into the structure of full-length C99, REMD simulations were performed for monomeric C99 in model membranes of varying thickness. We find equilibrium ensembles of C99 from simulation agree with experimentally-inferred residue insertion depths and protein backbone chemical shifts. In thin membranes, the transmembrane domain structure is correlated with extra-membrane structural states. Mean and variance of the transmembrane and G37G38 hinge angles are found to increase with thinning membrane. The N-terminus of C99 forms {beta}-strands that may seed aggregation of A{beta} on the membrane surface, promoting amyloid formation. The N-terminus, which forms -helices that interact with the nicastrin domain of {gamma}-secretase. The C-terminus of C99 becomes more -helical as the membrane thickens, forming structures that may be suitable for binding by cytoplasmic proteins, while C-terminal residues essential to cytotoxic function become -helical as the membrane thins. The heterogeneous but discrete extra-membrane domain states analyzed here open the path to new investigations of the role of C99 structure and membrane in amyloidogenesis.

biophysics↗