Marco Todesco, Gregory L. Owens, Natalia Bercovich, Jean-Sébastien Légaré, Shaghayegh Soudi, Dylan O. Burge, Kaichi Huang, Katherine L. Ostevik, Emily B. M. Drummond, Ivana Imerovski, Kathryn Lande, Mariana A. Pascual-Robles, Mihir Nanavati, Mojtaba Jahani, Winnie Cheung, S. Evan Staton, Stéphane Muños, Rasmus Nielsen, Lisa A. Donovan, John M. Burke, Sam Yeaman, Loren H. Rieseberg <<<

Petri Pölönen, Danika Di Giacomo, Anna Eames Seffernick, Abdelrahman Elsayed, Shunsuke Kimura, Francesca Benini, Lindsey E. Montefiori, Brent L. Wood, Jason Xu, Changya Chen, Zhongshan Cheng, Haley Newman, Jason Myers, Ilaria Iacobucci, Elizabeth Li, Jonathan Sussman, Dale Hedges, Yawei Hui, Caroline Diorio, Lahari Uppuluri, David Frank, Yiping Fan, Yunchao Chang, Soheil Meshinchi, Rhonda Ries, Rawan Shraim, Alexander Li, Kathrin M. Bernt, Meenakshi Devidas, Stuart S. Winter, Kimberly P. Dunsmore, Hiroto Inaba, William L. Carroll, Nilsa C. Ramirez, Aaron H. Phillips, Richard W. Kriwacki, Jun J. Yang, Tiffaney L. Vincent, Yaqi Zhao, Pankaj S. Ghate, Jian Wang, Colleen Reilly, Xin Zhou, Mathijs A. Sanders, Junko Takita, Motohiro Kato, Nao Takasugi, Bill H. Chang, Richard D. Press, Mignon Loh, Evadnie Rampersaud, Elizabeth Raetz, Stephen P. Hunger, Kai Tan, Ti-Cheng Chang, Gang Wu, Stanley B. Pounds, Charles G. Mullighan, David T. Teachey <<<

Siegfried Schloissnig, Samarendra Pani, Jana Ebler, Carsten Hain, Vasiliki Tsapalou, Arda Söylev, Patrick Hüther, Hufsah Ashraf, Timofey Prodanov, Mila Asparuhova, Hugo Magalhães, Wolfram Höps, Jesus Emiliano Sotelo-Fonseca, Tomas Fitzgerald, Walter Santana-Garcia, Ricardo Moreira-Pinhal, Sarah Hunt, Francy J. Pérez-Llanos, Tassilo Erik Wollenweber, Sugirthan Sivalingam, Dagmar Wieczorek, Mario Cáceres, Christian Gilissen, Ewan Birney, Zhihao Ding, Jan Nygaard Jensen, Nikhil Podduturi, Jan Stutzki, Bernardo Rodriguez-Martin, Tobias Rausch, Tobias Marschall, Jan O. Korbel <<<

Abstract Genomic structural variants (SVs) contribute substantially to genetic diversity and human diseases1–4, yet remain under-characterized in population-scale cohorts5. Here we conducted long-read sequencing6 in 1,019 humans to construct an intermediate-coverage resource covering 26 populations from the 1000 Genomes Project. Integrating linear and graph genome-based analyses, we uncover over 100,000 sequence-resolved biallelic SVs and we genotype 300,000 multiallelic variable number of tandem repeats7, advancing SV characterization over short-read-based population-scale surveys3,4. We characterize deletions, duplications, insertions and inversions in distinct populations. Long interspersed nuclear element-1 (L1) and SINE-VNTR-Alu (SVA) retrotransposition activities mediate the transduction8,9 of unique sequence stretches in 5′ or 3′, depending on source mobile element class and locus. SV breakpoint analyses point to a spectrum of homology-mediated processes contributing to SV formation and recurrent deletion events. Our open-access resource underscores the value of long-read sequencing in advancing SV characterization and enables guiding variant prioritization in patient genomes. <<<

Michael Kosicki, Boyang Zhang, Vivian Hecht, Anusri Pampari, Laura E. Cook, Neil Slaven, Jennifer A. Akiyama, Ingrid Plajzer-Frick, Catherine S. Novak, Momoe Kato, Stella Tran, Riana D. Hunter, Kianna von Maydell, Sarah Barton, Erik Beckman, Yiwen Zhu, Diane E. Dickel, Anshul Kundaje, Axel Visel, Len A. Pennacchio <<<

Abstract All contemporary Eurasians trace most of their ancestry to a small population that dispersed out of Africa about 50,000 years ago (ka)1–9. By contrast, fossil evidence attests to earlier migrations out of Africa10–15. These lines of evidence can only be reconciled if early dispersals made little to no genetic contribution to the later, major wave. A key question therefore concerns what factors facilitated the successful later dispersal that led to long-term settlement beyond Africa. Here we show that a notable expansion in human niche breadth within Africa precedes this later dispersal. We assembled a pan-African database of chronometrically dated archaeological sites and used species distribution models (SDMs) to quantify changes in the bioclimatic niche over the past 120,000 years. We found that the human niche began to expand substantially from 70 ka and that this expansion was driven by humans increasing their use of diverse habitat types, from forests to arid deserts. Thus, humans dispersing out of Africa after 50 ka were equipped with a distinctive ecological flexibility among hominins as they encountered climatically challenging habitats, providing a key mechanism for their adaptive success. <<<

Akanksha Jain, Gilles Gut, Fátima Sanchis-Calleja, Reto Tschannen, Zhisong He, Nicolas Luginbühl, Fides Zenk, Antonius Chrisnandy, Simon Streib, Christoph Harmel, Ryoko Okamoto, Malgorzata Santel, Makiko Seimiya, René Holtackers, Juliane K. Rohland, Sophie Martina Johanna Jansen, Matthias P. Lutolf, J. Gray Camp, Barbara Treutlein <<<

Abstract Brain organoids enable the mechanistic study of human brain development and provide opportunities to explore self-organization in unconstrained developmental systems1–3. Here we establish long-term, live light-sheet microscopy on unguided brain organoids generated from fluorescently labelled human induced pluripotent stem cells, which enables tracking of tissue morphology, cell behaviours and subcellular features over weeks of organoid development4. We provide a novel dual-channel, multi-mosaic and multi-protein labelling strategy combined with a computational demultiplexing approach to enable simultaneous quantification of distinct subcellular features during organoid development. We track actin, tubulin, plasma membrane, nucleus and nuclear envelope dynamics, and quantify cell morphometric and alignment changes during tissue-state transitions including neuroepithelial induction, maturation, lumenization and brain regionalization. On the basis of imaging and single-cell transcriptome modalities, we find that lumenal expansion and cell morphotype composition within the developing neuroepithelium are associated with modulation of gene expression programs involving extracellular matrix pathway regulators and mechanosensing. We show that an extrinsically provided matrix enhances lumen expansion as well as telencephalon formation, and unguided organoids grown in the absence of an extrinsic matrix have altered morphologies with increased neural crest and caudalized tissue identity. Matrix-induced regional guidance and lumen morphogenesis are linked to the WNT and Hippo (YAP1) signalling pathways, including spatially restricted induction of the WNT ligand secretion mediator (WLS) that marks the earliest emergence of non-telencephalic brain regions. Together, our work provides an inroad into studying human brain morphodynamics and supports a view that matrix-linked mechanosensing dynamics have a central role during brain regionalization. <<<

Dirk A. Lamprecht, Richard J. Wall, Annelies Leemans, Barry Truebody, Joke Sprangers, Patricia Fiogbe, Cadi Davies, Jennefer Wetzel, Stijn Daems, William Pearson, Vanessa Pillay, Samantha Saylock, M. Daniel Ricketts, Ellie Davis, Adam Huff, Tsehai Grell, Shiming Lin, Michelle Gerber, Ann Vos, John Dallow, Sam J. Willcocks, Christine Roubert, Stéphanie Sans, Amandine Desorme, Nicolas Chappat, Aurélie Ray, Mariana Pereira Moraes, Tracy Washington, Hope D’Erasmo, Pavankumar Sancheti, Melissa Everaerts, Mario Monshouwer, Jorge Esquivias, Gerald Larrouy-Maumus, Ruxandra Draghia Akli, Helen Fletcher, Alexander S. Pym, Bree B. Aldridge, Jansy P. Sarathy, Kathleen W. Clancy, Bart Stoops, Neeraj Dhar, Adrie J. C. Steyn, Paul Jackson, Clara Aguilar-Pérez, Anil Koul <<<

Yasir Sohail, Chongle Zhang, Dezhen Xue, Jinyu Zhang, Dongdong Zhang, Shaohua Gao, Yang Yang, Xiaoxuan Fan, Hang Zhang, Gang Liu, Jun Sun, En Ma <<<

Hao Huang, Nora R. Balzer, Lea Seep, Iva Splichalova, Nelli Blank-Stein, Maria Francesca Viola, Eliana Franco Taveras, Kerim Acil, Diana Fink, Franzisca Petrovic, Nikola Makdissi, Seyhmus Bayar, Katharina Mauel, Carolin Radwaniak, Jelena Zurkovic, Amir H. Kayvanjoo, Klaus Wunderling, Malin Jessen, Mohamed H. Yaghmour, Lukas Kenner, Thomas Ulas, Stephan Grein, Joachim L. Schultze, Charlotte L. Scott, Martin Guilliams, Zhaoyuan Liu, Florent Ginhoux, Marc D. Beyer, Christoph Thiele, Felix Meissner, Jan Hasenauer, Dagmar Wachten, Elvira Mass <<<

Ahyeon Hwang, Mario Skarica, Siwei Xu, Jensine Coudriet, Che Yu Lee, Lin Lin, Rosemarie Terwilliger, Alexa-Nicole Sliby, Jiawei Wang, Tuan Nguyen, Hongyu Li, Min Wu, Yi Dai, Ziheng Duan, Shushrruth Sai Srinivasan, Xiangyu Zhang, Yingxin Lin, Dianne Cruz, P J Michael Deans, Traumatic Stress Brain Research Group, Bertrand R Huber, Daniel Levey, Jill R Glausier, David A Lewis, Joel Gelernter, Paul E Holtzheimer, Matthew J Friedman, Mark Gerstein, Nenad Sestan, Kristen J Brennand, Ke Xu, Hongyu Zhao, John H Krystal, Keith A Young, Douglas E Williamson, Alicia Che, Jing Zhang, Matthew J Girgenti <<<

Post-traumatic stress disorder (PTSD) is a polygenic disorder occurring after extreme trauma exposure. Recent studies have begun to detail the molecular biology of PTSD. However, given the array of PTSD-perturbed molecular pathways identified so far, it is implausible that a single cell type is responsible. Here we profile the molecular responses in over two million nuclei from the dorsolateral prefrontal cortex of 111 human brains, collected post-mortem from individuals with and without PTSD and major depressive disorder. We identify neuronal and non-neuronal cell-type clusters, gene expression changes and transcriptional regulators, and map the epigenomic regulome of PTSD in a cell-type-specific manner. Our analysis revealed PTSD-associated gene alterations in inhibitory neurons, endothelial cells and microglia and uncovered genes and pathways associated with glucocorticoid signalling, GABAergic transmission and neuroinflammation. We further validated these findings using cell-type-specific spatial transcriptomics, confirming disruption of key genes such as SST and FKBP5. By integrating genetic, transcriptomic and epigenetic data, we uncovered the regulatory mechanisms of credible variants that disrupt PTSD genes, including ELFN1, MAD1L1 and KCNIP4, in a cell-type-specific context. Together, these findings provide a comprehensive characterization of the cell-specific molecular regulatory mechanisms that underlie the persisting effects of traumatic stress response on the human prefrontal cortex. <<<

The multicellular coordination that underlies tissue homeostasis and disease progression is of fundamental interest. However, how diverse cell types are organized within tissue niches for cohesive functioning remains largely unknown. Here we systematically characterized cross-tissue coordinated cellular modules in healthy tissues, uncovering their spatiotemporal dynamics and phenotypic associations, and examined their rewiring in cancer. We first compiled a comprehensive single-cell transcriptomic atlas from 35 human tissues, revealing substantial inter-tissue variability in cellular composition. By leveraging covariance in cellular abundance, we identified 12 cellular modules with distinct cellular compositions, tissue prevalences and spatial organizations, and demonstrated coordinated intercellular communication within cellular modules using in situ spatial and in vivo perturbation data. Among them, two immune cellular modules in the spleen showed contrasting chronological dynamics with ageing. Analysis of multicellular changes in the breast revealed a menopausal trajectory associated with fibroblast dynamics. Furthermore, interrogation across cancer types uncovered simultaneous rewiring of two types of multicellular ecosystem during tumour progression, including the loss of tissue-specific healthy organization and the emergence of a convergent cancerous ecosystem. These findings reveal fundamental organizing principles of multicellular ecosystems in health and cancer, laying a foundation for further investigations into tissue-level functional coordination across diverse contexts. <<<

Sujing Yuan, Renqiang Sun, Hao Shi, Nicole M. Chapman, Haoran Hu, Cliff Guy, Sherri Rankin, Anil KC, Gustavo Palacios, Xiaoxi Meng, Xiang Sun, Peipei Zhou, Xiaoyang Yang, Stephen Gottschalk, Hongbo Chi <<<

Mirazul Islam, Yilin Yang, Alan J. Simmons, Vishal M. Shah, Krushna Pavan Musale, Yanwen Xu, Naila Tasneem, Zhengyi Chen, Linh T. Trinh, Paola Molina, Marisol A. Ramirez-Solano, Iannish D. Sadien, Jinzhuang Dou, Andrea Rolong, Ken Chen, Mark A. Magnuson, Jeffrey C. Rathmell, Ian G. Macara, Douglas J. Winton, Qi Liu, Hamim Zafar, Reza Kalhor, George M. Church, Martha J. Shrubsole, Robert J. Coffey, Ken S. Lau <<<

Xiekui Cui, Han Yang, Charles Cai, Cooper Beaman, Xiaoyu Yang, Hongjiang Liu, Xingjie Ren, Zachary Amador, Ian R. Jones, Kathleen C. Keough, Meng Zhang, Tyler Fair, Armen Abnousi, Shreya Mishra, Zhen Ye, Ming Hu, Alex A. Pollen, Katherine S. Pollard, Yin Shen <<<

AbstractTabular data, spreadsheets organized in rows and columns, are ubiquitous across scientific fields, from biomedicine to particle physics to economics and climate science1,2. The fundamental prediction task of filling in missing values of a label column based on the rest of the columns is essential for various applications as diverse as biomedical risk models, drug discovery and materials science. Although deep learning has revolutionized learning from raw data and led to numerous high-profile success stories3–5, gradient-boosted decision trees6–9 have dominated tabular data for the past 20 years. Here we present the Tabular Prior-data Fitted Network (TabPFN), a tabular foundation model that outperforms all previous methods on datasets with up to 10,000 samples by a wide margin, using substantially less training time. In 2.8 s, TabPFN outperforms an ensemble of the strongest baselines tuned for 4 h in a classification setting. As a generative transformer-based foundation model, this model also allows fine-tuning, data generation, density estimation and learning reusable embeddings. TabPFN is a learning algorithm that is itself learned across millions of synthetic datasets, demonstrating the power of this approach for algorithm development. By improving modelling abilities across diverse fields, TabPFN has the potential to accelerate scientific discovery and enhance important decision-making in various domains. <<<

Eslem Ben Arous, James A. Blinkhorn, Sarah Elliott, Christopher A. Kiahtipes, Charles D. N’zi, Mark D. Bateman, Mathieu Duval, Patrick Roberts, Robert Patalano, Alexander F. Blackwood, Khady Niang, Eugénie Affoua Kouamé, Edith Lebato, Emily Hallett, Jacopo N. Cerasoni, Erin Scott, Jana Ilgner, Maria Jesús Alonso Escarza, Francois Yodé Guédé, Eleanor M. L. Scerri <<<

Abstract Humans emerged across Africa shortly before 300 thousand years ago (ka)1–3. Although this pan-African evolutionary process implicates diverse environments in the human story, the role of tropical forests remains poorly understood. Here we report a clear association between late Middle Pleistocene material culture and a wet tropical forest in southern Côte d’Ivoire, a region of present-day rainforest. Twinned optically stimulated luminescence and electron spin resonance dating methods constrain the onset of human occupations at Bété I to around 150 ka, linking them with Homo sapiens. Plant wax biomarker, stable isotope, phytolith and pollen analyses of associated sediments all point to a wet forest environment. The results represent the oldest yet known clear association between humans and this habitat type. The secure attribution of stone tool assemblages with the wet forest environment demonstrates that Africa’s forests were not a major ecological barrier for H. sapiens as early as around 150 ka. <<<