Biology subjects

Lund, J.

Publications and source records attributed to Lund, J..

10 recordsLinked to original sources

bioRxiv2026

Label Noise Limits TCR-pMHC Specificity Prediction: Improved Performance Through AlphaFold3-Based Structural Modeling and Data Denoising

T cell receptor (TCR) binding to peptides presented by major histocompatibility complex (MHC) molecules is a key step in T cell activation, and forms the basis of adaptive immunity. Predicting this specificity is therefore essential to developing effective TCR-based immunotherapies and vaccines. Despite its clinical relevance, predicting TCR-pMHC specificity for previously unseen peptides remains an open problem, with structural modeling so far the only strategy showing any predictive power in this setting. In this study, we find that this limited performance is substantially driven by label noise in the data used to train and evaluate these methods, an effect that has so far been largely underexplored. Using an AlphaFold3-based pipeline adapted for TCR-pMHC structural modeling, we achieve state-of-the-art specificity prediction, outperforming AlphaFold2.3-based and sequence based methods, and performing at par with the leading Immrep2025 competition submission. Combining this pipeline with a cluster-based denoising algorithm, we show that removing mislabeled points from a large specificity dataset increased binder ranking accuracy by more than 70% relative to the full dataset. Together, these results highlight label noise as a major factor limiting the performance that any method in this field can achieve, and show that combining structural modeling with label denoising substantially improves TCR-pMHC specificity prediction, making such approaches an attractive complement to current sequence-based approaches for refining TCR target selection.

bioinformatics↗

bioRxiv2026

Direct RNA Sequencing reveals epitranscriptomic regulation of brain cells and Alzheimer's Disease pathology

Alternative mRNA splicing and post-transcriptional RNA modification are key mechanisms that regulate transcript function; however, their role in neuronal activity and neurodegenerative disease remains poorly defined. In this study, we evaluated two nanopore-based long-read sequencing (LR-seq) formats: cDNA-PCR sequencing (CPS) and direct RNA sequencing (DRS). We then applied DRS to profile both full-length isoforms and RNA modifications in major brain cell types derived from induced pluripotent stem cells (iPSCs) and post-mortem Alzheimers disease (AD) brains. Relative to CPS, DRS achieved higher accuracy and sensitivity for transcript quantification, de novo transcript model construction, and open reading frame (ORF) annotation across neuropathological gene sets. Focusing on iPSC-derived neurons, we built a multi-omic atlas to connect transcriptional output with translational engagement and protein abundance, by integrating DRS-based mRNA abundance, N6-methyladenosine (m6A) status and poly(A) tail length with ribosome profiling (Ribo-seq) and mass spectrometry (MS). The combination of DRS and Ribo-seq data demonstrated synergism in predicting protein abundance. This analysis also uncovered a significant inverse relationship between m6A modification and mRNA abundance, which was dependent on the engagement of the ribosomal A-site. Lastly, we applied DRS to the epitranscriptomic analysis of AD brain samples, demonstrating that m6A profiles can be used to distinguish early-versus late-stage disease.

neuroscience↗

bioRxiv2025

Genetic and preclinical evidence implicating chondroitin sulfate as a matritherapeutic target for the treatment of type 2 diabetes

Peptide-based treatments for type 2 diabetes (T2D) are often limited by variable patient responses, frequent discontinuation, and substantial costs. Emerging lines of evidence link the extracellular matrix (ECM) to the pathophysiology of T2D, highlighting a largely unexplored modality for managing this heterogenous disease. Chondroitin sulfate (CS), a major glycosaminoglycan in the ECM, has been suggested to improve cardiometabolic health in preclinical research. However, the human genetic and pharmacological basis for CS as an anti-diabetic target is largely unexplored. Here, we uncover novel and robust links between 12 CS-related genes and both glycemic traits and the risk of T2D in hu-mans. Complementing this, administration of CS leads to a profound lowering of blood glucose levels in severely diabetic mice and improves glucose tolerance and cardiac clearance of circulating glucose in diet-induced obese mice without causing hypoglyce-mia or other adverse effects. The improvement in glycemic control is accompanied by increased glucose-stimulated insulin secretion and enhanced insulin action, effects which seem to occur independent of the incretin system. The combination of human genetic evidence and appealing pharmacodynamic features highlights CS as a promising ECM-target for developing novel pharmacotherapies that complement current treatments for T2D.

physiology↗

bioRxiv2025

Neuromuscular, Cardiovascular, and Cognitive Fatigue in Motor Learning: A Systematic Review

BackgroundFatigue is multifactorial and task-dependent, arising from the interplay between performance and perceived fatigability. Fatigue-related changes in sensorimotor control and neural activity may alter skill acquisition and retention. ObjectiveTo synthesize behavioral and neurophysiological evidence on how cognitive, cardiovascular, and neuromuscular fatigue influence motor-skill acquisition, consolidation/retention, and transfer. MethodsA systematic search was conducted within PubMed, Web of Science, and Embase. Thirty-four studies (39 experiments) met inclusion criteria (fatigue effects on motor learning in non-disabled participants). Data were extracted on fatigue protocol, learning taxonomy, learning stage (acquisition vs. retention/transfer), interval, and neurophysiology. Methodological quality was appraised with a tailored Downs & Black checklist. ResultsDuring acquisition, 64% of experiments reported impairments under fatigue, particularly for visuomotor precision and fine force control; 10% found facilitation (often after cardiovascular exertion or high cognitive load); 15% were neutral; 10% inconclusive. Retention was tested in a fresh state and in a fatigue state in 34 experiments and 6 experiments, respectively. Results during retention tests were relatively variable, depending on fatigue protocols. Neurophysiological measures were scarce (EEG/TMS in only four studies), and very few studies considered the effects of personal factors such as age or sex. ConclusionsFatigue does not uniformly impair motor learning. Neuromuscular fatigue typically hampers acquisition and sometimes retention, while cardiovascular exertion can transiently prime plasticity and enhance consolidation. Evidence for cognitive fatigue is limited and inconsistent. Future work should use longer retention windows, state-matched testing, and integrated neurophysiology to clarify mechanisms and guide training under fatigue.

neuroscience↗

bioRxiv2024

Overfeeding does not increase energy expenditure or energy excretion in mice

To curb the obesity epidemic, it is imperative that we improve our understanding of the mechanisms controlling fat mass and body weight regulation. While great progress has been made in mapping the biological feedback forces opposing weight loss, the mechanisms countering weight gain remain less well defined. Here, we integrate a mouse model of intragastric overfeeding with a comprehensive evaluation of the regulatory aspects of energy balance, encompassing food intake, energy expenditure, and fecal energy excretion. To evaluate the role of adipose tissue thermogenesis in the homeostatic protection against overfeeding-induced weight gain, we exposed uncoupling protein 1 (UCP1) knockout (KO) mice to overfeeding. Our results confirm that 7 days of 150% overfeeding induces [~]11% weight gain and triggers a potent and prolonged reduction in voluntary food intake that drives body weight back to baseline following overfeeding. Overfeeding has no effects on energy expenditure, consistent with the observation that mice lacking UCP1 are not compromised in their ability to defend against overfeeding-induced weight gain. These data emphasize that whole-body energy expenditure and adipose thermogenesis are not key contributors to protection against overfeeding in mice. Lastly, we show that fecal energy excretion decreases in response to overfeeding, primarily driven by a reduction in fecal output rather than in fecal caloric content. In conclusion, these results challenge the prevailing notion that adaptive thermogenesis contributes to the defense against weight gain induced by overfeeding. Instead, the protection against enforced weight gain in mice is primarily linked to a profound reduction in food intake.

physiology↗

bioRxiv2023

Transcriptional dysregulation and impaired neuronal activity in FMR1 knock-out and Fragile X patients iPSC-derived models.

The lack of fragile X mental retardation protein (FMRP) protein, due to a repression of the FMR1 gene, causes Fragile X syndrome (FXS), one of the most prevalent forms of syndromic autisms. The FMR1 gene codes for an RNA binding protein involved in the regulation of gene expression through RNA processing, control of local translation, and protein-protein interactions; processes that are crucial for proper brain development. Taking advantage of induced pluripotent stem cells (iPSCs) and CRISPR-Cas9 genome editing technologies, we generated iPSC-derived cortical neural progenitors and cortical neurons from an FMR1 knock-out and patient cell line with the aim of identifying common phenotypes between the two cellular models. Using RNA sequencing, quantitative PCR and multielectrode array approaches, we assessed how the absence of the functional FMR1 gene affects the transcriptional profiles and the activities of iPSC-derived cortical neuronal progenitor cells (NPCs) and neurons with both models. We observed that FMR1 KO and FXS patient cells have a decrease in their mean firing rate; a cellular activity that can also be blocked by tetrodotoxin (TTX) application in wild-type active neurons. Relative to wild-type neurons, in FMR1 KO neurons, increased expression of presynaptic mRNA and transcription factors involved in the forebrain specification and decreased levels of mRNA coding AMPA and NMDA subunits were observed. Intriguingly, 40% of the differentially expressed genes were commonly deregulated between NPCs and differentiating neurons with significant enrichments in FMRP targets and Autism Related Genes found amongst downregulated genes. This implies that an absence of functional FMRP affects transcriptional profiles at the NPC stage, resulting in impaired activity and differentiation of the progenitors into mature neurons over time. These findings from the FMR1 KO lines were also shared with FXS patients iPSC-derived cells that also present with an impairment in activity and neuronal differentiation, illustrating the critical role of FMRP protein in neuronal development.

neuroscience↗

bioRxiv2023

Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer

Single-cell RNA sequencing predominantly employs short-read sequencing to characterize cell types, states and dynamics; however, it is inadequate for comprehensive characterization of RNA isoforms. Long-read sequencing technologies enable single-cell RNA isoform detection but are hampered by lower throughput and unintended sequencing of artifacts. Here we developed Single-cell Targeted Isoform Long-Read Sequencing (scTaILoR-seq), a hybridization capture method which targets over a thousand genes of interest, improving the median number of unique transcripts per cell by 29-fold. We used scTaILoR-seq to identify and quantify RNA isoforms from ovarian cancer cell lines and primary tumors, yielding 10,796 single-cell transcriptomes. Using long-read variant calling we revealed associations of expressed single nucleotide variants (SNVs) with alternative transcript structures. In addition, phasing of SNVs across transcripts facilitated measurement of allelic imbalance within distinct cell populations. Overall, scTaILoR-seq is a long-read targeted RNA sequencing method and analytical framework for exploring transcriptional variation at single-cell resolution.

genomics↗

bioRxiv2022

The GDF15-GFRAL pathway is dispensable for the effects of metformin on energy balance

Metformin is a blood glucose lowering medication with physiological effects that extend beyond its anti-diabetic indication. Recently, it was reported that metformin lowers body weight via induction of growth differentiation factor 15 (GDF15), which suppresses food intake by binding to the GDNF family receptor -like (GFRAL) in the hindbrain. At the same time, we demonstrated that recombinant GDF15 suppresses voluntary exercise in a GFRAL-dependent fashion. Here, we corroborate that metformin increases circulating GDF15 in mice and humans, but that it does not reduce voluntary running activity in mice. Unexpectedly, we fail to confirm previous reports that the GDF15-GFRAL pathway is necessary for the weight-lowering effects of metformin. Instead, our studies in wild-type, GDF15 knockout and GFRAL knockout mice suggest that the GDF15-GFRAL pathway is dispensable for the effects of metformin on energy balance. The data presented here question whether metformin is a sufficiently strong stimulator of GDF15 to drive anorexia and weight loss and emphasize that additional work is needed to untangle the relationship among metformin, GDF15 and energy balance.

physiology↗

bioRxiv2021

Prolonging coagulant activity of factor Xa under hemophilic conditions by site-specific N-glycosylation of the surface-exposed autolysis loop

The regulation of Factor X (FX) is critical to maintain hemostasis. To gain insights to the regulation of the active and zymogen form of coagulation FX, we probed specific molecular interactions by introducing novel N-linked glycosylations on the surface-exposed loop spanning residues 143-150 (chymotrypsin numbering) of FX. Introduction of N-glycans in the autolysis loop of these FX variants decreased Factor VIIa (FVIIa)-mediated activation ~3-fold and prothrombin activation 2- to 10-fold presumably through steric hinderance. Prothrombin activation was, however, recovered in presence of cofactor Factor Va (FVa) despite a reduced prothrombinase assembly. The introduced N-glycans exhibited position-specific effects on the interaction with two FXa inhibitors: tissue factor pathway inhibitor (TFPI) and antithrombin (ATIII). Ki for the inhibition by full-length TFPI of these FXa variants was increased by 7- to 1150-fold, while ATIII inhibition in the presence of the heparin-analogue Fondaparinux was modestly increased by 2- to 15-fold compared to wild type. To probe the in vitro hemostatic effect of the FX variants, the thrombin generation potential in FX-depleted plasma was evaluated. When supplemented in zymogen form, the FX variants exhibited reduced thrombin generation activity relative to wild-type FX, whereas enhanced procoagulant activity was measured for activated FX variants with N-glycosylation at positions 148-150. These results indicate that residues of the surface-exposed autolysis loop and residues close by participate in FX activation, proteolytic activity and inhibition of FXa by TFPI and ATIII. In plasma-based assays, a modest decrease in FX-activation rate appeared to compensate for the collective reduction in inhibitor interactions.

biochemistry↗

bioRxiv2020

Pharmacological but not physiological GDF15 suppresses feeding and the motivation to exercise

Growing evidence supports that pharmacological application of growth differentiation factor 15 (GDF15) suppresses appetite but also promotes sickness-like behaviors in rodents via GDNF family receptor -like (GFRAL)-dependent mechanisms1,2. Conversely, the endogenous regulation and secretion of GDF15 and its physiological effects on energy homeostasis and behavior remain elusive. Here we show, in four independent studies that prolonged, moderate- to high-intensity endurance exercise substantially increases circulating GDF15, in a time-dependent and reversible fashion, to peak levels otherwise only observed in pathophysiological conditions. This exercise-induced increase can be recapitulated in mice following forced treadmill running and is accompanied by increased Gdf15 expression in the liver, skeletal muscle, and heart muscle. Compared to other metabolic stressors, like fasting, acute high-fat diet feeding, severe caloric excess and temperature changes, exercise has a greater impact on circulating GDF15 levels. However, whereas pharmacological GDF15 inhibits appetite and suppresses wheel running activity via GFRAL, in response to exercise, the physiological induction of GDF15 does not. In summary, exercise-induced circulating GDF15 correlates with the duration of endurance exercise. However, higher GDF15 levels after exercise are not sufficient to evoke canonical pharmacological GDF15 effects on appetite or responsible for exercise aversion/fatigue. Thus, the physiological effects of GDF15 as an exerkine remain elusive.

physiology↗