Iain S. Forrest, Ha My T. Vy, Ghislain Rocheleau, Daniel M. Jordan, Ben O. Petrazzini, Girish N. Nadkarni, Judy H. Cho, Mythily Ganapathi, Kuan-Lin Huang, Wendy K. Chung, Ron Do <<<

Accurate variant penetrance estimation is crucial for precision medicine. We constructed machine learning (ML) models for 10 diseases using 1,347,298 participants with electronic health records, then applied them to an independent cohort with linked exome data. Resulting probabilities were used to evaluate ML penetrance of 1648 rare variants in 31 autosomal dominant disease-predisposition genes. ML penetrance was variable across variant classes, but highest for pathogenic and loss-of-function variants, and was associated with clinical outcomes and functional data. Compared with conventional case-versus-control approaches, ML penetrance provided refined quantitative estimates and aided the interpretation of variants of uncertain significance and loss-of-function variants by delineating clinical trajectories over time. By leveraging ML and deep phenotyping, we present a scalable approach to accurately quantify disease risk of variants. <<<

Penadés JR, Gottweis J, He L, Patkowski JB, Daryin A, Weng WH, Tu T, Palepu A, Myaskovsky A, Pawlosky A, Natarajan V, Karthikesalingam A, Costa TRD <<<

Miranda V. Hunter, Eshita Joshi, Sydney Bowker, Emily Montal, Yilun Ma, Young Hun Kim, Zhifan Yang, Laura Tuffery, Zhuoning Li, Eric Rosiek, Alexander Browning, Reuben Moncada, Itai Yanai, Helen Byrne, Mara Monetti, Elisa de Stanchina, Pierre-Jacques Hamard, Richard P. Koche, Richard M. White <<<

Abstract Phenotype switching is a form of cellular plasticity in which cancer cells reversibly move between two opposite extremes: proliferative versus invasive states1,2. Although it has long been hypothesized that such switching is triggered by external cues, the identity of these cues remains unclear. Here we demonstrate that mechanical confinement mediates phenotype switching through chromatin remodelling. Using a zebrafish model of melanoma coupled with human samples, we profiled tumour cells at the interface between the tumour and surrounding microenvironment. Morphological analysis of interface cells showed elliptical nuclei, suggestive of mechanical confinement by the adjacent tissue. Spatial and single-cell transcriptomics demonstrated that interface cells adopted a gene program of neuronal invasion, including the acquisition of an acetylated tubulin cage that protects the nucleus during migration. We identified the DNA-bending protein HMGB2 as a confinement-induced mediator of the neuronal state. HMGB2 is upregulated in confined cells, and quantitative modelling revealed that confinement prolongs the contact time between HMGB2 and chromatin, leading to changes in chromatin configuration that favour the neuronal phenotype. Genetic disruption of HMGB2 showed that it regulates the trade-off between proliferative and invasive states, in which confined HMGB2high tumour cells are less proliferative but more drug-resistant. Our results implicate the mechanical microenvironment as a mechanism that drives phenotype switching in melanoma. <<<

The International Mathematical Olympiad (IMO) poses uniquely challengingproblems requiring deep insight, creativity, and formal reasoning. While LargeLanguage Models (LLMs) perform well on mathematical benchmarks like AIME, theystruggle with Olympiad-level tasks. We use Google's Gemini 2.5 Pro on the newlyreleased IMO 2025 problems, avoiding data contamination. Using aself-verification pipeline with careful prompt design, 5 (out of 6) problemsare solved correctly. This result underscores the importance of developingoptimal strategies to harness the full potential of powerful LLMs for complexreasoning tasks. <<<

Elaine Huang, Ting Fu, Ling Zhang, Guanao Yan, Ryo Yamamoto, Sari Terrazas, Thuy Linh Nguyen, Carlos Gonzalez-Figueroa, Armen Khanbabaei, Jae Hoon Bahn, Rajagopal Varada, Kofi Amoah, Jonatan Hervoso, Michelle T. Paulsen, Brian Magnuson, Mats Ljungman, Jingyi Jessica Li, Xinshu Xiao <<<

Andrew J. Scott, Anjali Mittal, Baharan Meghdadi, Alexandra O’Brien, Justine Bailleul, Palavalasa Sravya, Abhinav Achreja, Weihua Zhou, Jie Xu, Angelica Lin, Kari Wilder-Romans, Ningning Liang, Ayesha U. Kothari, Navyateja Korimerla, Donna M. Edwards, Zhe Wu, Jiane Feng, Sophia Su, Li Zhang, Peter Sajjakulnukit, Anthony C. Andren, Junyoung O. Park, Johanna ten Hoeve, Vijay Tarnal, Kimberly A. Redic, Nathan R. Qi, Joshua L. Fischer, Ethan Yang, Michael S. Regan, Sylwia A. Stopka, Gerard Baquer, Krithika Suresh, Jann N. Sarkaria, Theodore S. Lawrence, Sriram Venneti, Nathalie Y. R. Agar, Erina Vlashi, Costas A. Lyssiotis, Wajd N. Al-Holou, Deepak Nagrath, Daniel R. Wahl <<<

Abstract The diversity of T-cell receptors (TCRs) and B-cell receptors (BCRs) underpins the adaptive immune system’s ability to recognize and respond to a wide array of antigens. Recent advancements in RNA sequencing have expanded its application beyond transcriptomics to include the analysis of immune repertoires, enabling the exploration of TCR and BCR sequences across various physiological and pathological contexts. This review highlights key methodologies and considerations for TCR and BCR repertoire analysis, focusing on the technical aspects of receptor sequence extraction, data processing, and clonotype identification. We compare the use of bulk and single-cell sequencing, discuss computational tools and pipelines, and evaluate the implications of examining specific receptor regions such as CDR3. By integrating immunology, bioinformatics, and clinical research, immune repertoire analysis provides valuable insights into immune function, therapeutic responses, and precision medicine approaches, advancing our understanding of health and disease. <<<

Over time, cells in the brain and in the body accumulate damage, which contributes to the ageing process. In the human brain, the prefrontal cortex undergoes age-related changes that can affect cognitive functioning later in life. Here, using single-nucleus RNA sequencing (snRNA-seq), single-cell whole-genome sequencing (scWGS) and spatial transcriptomics, we identify gene-expression and genomic changes in the human prefrontal cortex across lifespan, from infancy to centenarian. snRNA-seq identified infant-specific cell clusters enriched for the expression of neurodevelopmental genes, as well as an age-associated common downregulation of cell-essential homeostatic genes that function in ribosomes, transport and metabolism across cell types. Conversely, the expression of neuron-specific genes generally remains stable throughout life. These findings were validated with spatial transcriptomics. scWGS identified two age-associated mutational signatures that correlate with gene transcription and gene repression, respectively, and revealed gene length- and expression-level-dependent rates of somatic mutation in neurons that correlate with the transcriptomic landscape of the aged human brain. Our results provide insight into crucial aspects of human brain development and ageing, and shed light on transcriptomic and genomic dynamics. <<<

Mingzhi Luo, Xiangrong Zhang, Jia Guo, Rong Gu, Youyuan Qin, Kai Ni, Lei Liu, Yan Pan, Jingjing Li, Honglei Shi, Linhong Deng <<<

Abstract Embryonic development follows a conserved sequence of events across species, yet the pace of development is highly variable and particularly slow in humans. Species-specific developmental timing is largely recapitulated in stem cell models, suggesting a cell-intrinsic clock. Here we use directed differentiation of human embryonic stem cells into neuroectoderm to perform a whole-genome CRISPR-Cas9 knockout screen and show that the epigenetic factors Menin and SUZ12 modulate the speed of PAX6 expression during neural differentiation. Genetic and pharmacological loss-of-function of Menin or SUZ12 accelerate cell fate acquisition by shifting the balance of H3K4me3 and H3K27me3 at bivalent promoters, thereby priming key developmental genes for faster activation upon differentiation. We further reveal a synergistic interaction of Menin and SUZ12 in modulating differentiation speed. The acceleration effects were observed in definitive endoderm, cardiomyocyte and neuronal differentiation paradigms, pointing to chromatin bivalency as a general driver of timing across germ layers and developmental stages. <<<

Nadine Serhan, Nasser S. Abdullah, Nadine Gheziel, Alexia Loste, Rüçhan Ekren, Elodie Labit, Anne-Alicia Gonzalez, Giulia Oliva, Pauline Tarot, Camille Petitfils, Gaëlle Payros, Paolo D’Avino, Allison Voisin, Holly Freya Grace Tinsley, Rebecca Gentek, Carole Brosseau, Marie Bodinier, Laurent Reber, Pierre Val, Cezmi A. Akdis, Yasutaka Mitamura, Anand Kumar Andiappan, Jerry Kok Yen Chan, Florent Ginhoux, Amaury François, Nicolas Cénac, Lilian Basso, Nicolas Gaudenzio <<<

A central component of wayfinding is the ability to maintain a consistent representation of one's facing direction (FD) when moving about the world. In rodents, head direction cells are believed to support this “neural compass,” but identifying a similar mechanism in humans during dynamic naturalistic navigation has been challenging. To address this issue, we acquired fMRI data from male and female human participants while they freely navigated through a virtual reality city. Encoding model analyses revealed voxel clusters in the posterior–medial cortex (the “retrosplenial complex”) and superior parietal lobule that exhibited reliable tuning as a function of FD. Crucially, these directional tunings were consistent across perceptually different versions of the city, spatially separated locations within the city, and motivationally distinct phases of the behavioral task. Analysis of the model weights indicated that these regions represent a broad range of possible FDs and that they do so by representing heading relative to the principal axis of the environment. These findings reveal specific mechanisms in the human brain that allow us to maintain a sense of direction during naturalistic, dynamic navigation. <<<