Colombo, D. | Search bioRxiv

bioRxiv2026

BenchMHC: a reproducible framework for peptide-MHC presentation prediction

Predicting which peptides an MHC molecule presents is the first step in neoantigen and epitope discovery pipelines. Most published predictors are released for inference only, and each is trained on a different dataset, so the effect of a new method cannot be separated from the effect of its training data. We present BenchMHC, an open framework that reproduces, retrains and evaluates pMHC presentation models on public data only, and that records every implementation decision made in a reproduction. Our NetMHCpan-4.1 reproduction reaches 0.794 per-allele Mean Top-K against 0.790 for the official webserver, and 0.0025 Median FRANK against 0.0022. It scores 280,000 peptide/allele pairs in 27 s, about 350 times faster than the original binary. We then examine the training data. In the public NetMHCpan-4.1 eluted-ligand sets, 86 to 99% of hits are found in the human proteome, against about 12% of their decoys, so a model can separate hits from decoys using this difference rather than features related to MHC binding. Redrawing the decoys within the source protein of each hit and matching their cysteine status, with no other change, raises per-allele Mean Top-K on the regenerated v2.0.0 evaluation set from 0.734 to 0.755, and increases Median FRANK on CD8 epitopes from 0.0025 to 0.0053. The same change improves one evaluation set and degrades the other. Code (Apache-2.0) and model checkpoints (CC BY-NC-4.0): https://github.com/instadeepai/BenchMHC-public.

bioinformatics↗

bioRxiv2026

Impaired astrocyte-to-neuron cholesterol trafficking drives synaptic dysfunction in Rett syndrome

Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder caused by loss-of-function mutations in the MECP2 gene and characterized by profound impairments in neuronal maturation and synaptic connectivity. Increasing evidence indicates that astrocyte dysfunction contributes to RTT pathogenesis through non-cell-autonomous mechanisms, although the molecular pathways underlying defective astrocyte-neuron communication are only partially understood. Astrocytes are the primary source of cholesterol in the brain and support neuronal maturation and synaptic function by supplying cholesterol through ApoE-containing lipoproteins. Although alterations in brain cholesterol metabolism have been reported in RTT, the underlying cellular mechanisms and their functional consequences remain poorly investigated. Here, we studied cholesterol homeostasis in Mecp2 knock-out (KO) astrocytes and its impact on neuron-astrocyte communication. Mecp2 KO astrocytes exhibited reduced nuclear localization of the transcriptional regulator Srebp2, together with the downregulation of genes involved in cholesterol biosynthesis and transport. These molecular alterations were associated with intracellular cholesterol and desmosterol accumulation, reduced Abca1 expression and defective ApoE lipidation, despite preserved ApoE expression and cholesterol secretion. Importantly, similar alterations were detected in acutely isolated astrocytes and in the cerebral cortex of Mecp2 deficient mice, demonstrating that impaired cholesterol homeostasis extends beyond in vitro models. Functionally, cholesterol supplementation of astrocyte-conditioned medium rescued the synaptic defects induced in wild-type neurons by Mecp2 KO astrocytes. Moreover, cholesterol treatment restored pre- and post-synaptic density, as well as axon initial segment length in Mecp2 heterozygous (HET) neurons. Together, these findings identify defective astrocyte-to- neuron cholesterol trafficking as a key mechanism contributing to neuronal dysfunction in RTT and suggest that strategies aimed at restoring cholesterol functional availability might represent a promising therapeutic avenue for RTT.

neuroscience↗