bioRxiv : the preprint server for biology最新文献

{"title":"Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant.","authors":"Briana L Sobecks, Jiming Chen, Tanner J Dean, Diwakar Shukla","doi":"10.1101/2023.01.18.524622","DOIUrl":"10.1101/2023.01.18.524622","url":null,"abstract":"<p><p><i>Striga hermonthica</i> is a parasitic weed that destroys billions of dollars' worth of staple crops every year. Its rapid proliferation stems from an enhanced ability to metabolize strigolactones (SLs), plant hormones that direct root branching and shoot growth. <i>Striga's</i> SL receptor, <i>Sh</i>HTL7, bears more similarity to the staple crop karrikin receptor KAI2 than to SL receptor D14, though KAI2 variants in plants like <i>Arabidopsis thaliana</i> show minimal SL sensitivity. Recently, studies have indicated that a small number of point mutations to HTL7 residues can confer SL sensitivity to <i>At</i>KAI2. Here, we analyze both wild-type <i>At</i>KAI2 and SL-sensitive mutant Var64 through all-atom, long-timescale molecular dynamics simulations to determine the effects of these mutations on receptor function at a molecular level. We demonstrate that the mutations stabilize SL binding by about 2 kcal/mol. They also result in a doubling of the average pocket volume, and eliminate the dependence of binding on certain pocket conformational arrangements. While the probability of certain non-binding SL-receptor interactions increases in the mutant compared with the wild-type, the rate of binding also increases by a factor of ten. All these changes account for the increased SL sensitivity in mutant KAI2, and suggest mechanisms for increasing functionality of host crop SL receptors.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9a/6f/nihpp-2023.01.18.524622v1.PMC9882355.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10657155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Image-based identification and isolation of micronucleated cells to dissect cellular consequences.","authors":"Lucian DiPeso, Sriram Pendyala, Heather Z Huang, Douglas M Fowler, Emily M Hatch","doi":"10.1101/2023.05.04.539483","DOIUrl":"10.1101/2023.05.04.539483","url":null,"abstract":"<p><p>Recent advances in isolating cells based on visual phenotypes have transformed our ability to identify the mechanisms and consequences of complex traits. Micronucleus (MN) formation is a frequent outcome of genome instability, triggers extensive changes in genome structure and signaling coincident with MN rupture, and is almost exclusively defined by visual analysis. Automated MN detection in microscopy images has proved challenging, limiting discovery of the mechanisms and consequences of MN. In this study we describe two new MN segmentation modules: a rapid model for classifying micronucleated cells and their rupture status (VCS MN), and a robust model for accurate MN segmentation (MNFinder) from a broad range of cell lines. As proof-of-concept, we define the transcriptome of non-transformed human cells with intact or ruptured MN after chromosome missegregation by combining VCS MN with photoactivation-based cell isolation and RNASeq. Surprisingly, we find that neither MN formation nor rupture triggers a strong unique transcriptional response. Instead, transcriptional changes appear correlated with small increases in aneuploidy in these cell classes. Our MN segmentation modules overcome a significant challenge with reproducible MN quantification, and, joined with visual cell sorting, enable the application of powerful functional genomics assays to a wide-range of questions in MN biology.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10187275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9610318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How Occam's razor guides human decision-making.","authors":"Eugenio Piasini, Shuze Liu, Pratik Chaudhari, Vijay Balasubramanian, Joshua I Gold","doi":"10.1101/2023.01.10.523479","DOIUrl":"10.1101/2023.01.10.523479","url":null,"abstract":"<p><p>Occam's razor is the principle that, all else being equal, simpler explanations should be preferred over more complex ones. This principle is thought to guide human decision-making, but the nature of this guidance is not known. Here we used preregistered behavioral experiments to show that people tend to prefer the simpler of two alternative explanations for uncertain data. These preferences match predictions of formal theories of model selection that penalize excessive flexibility. These penalties emerge when considering not just the best explanation but the integral over all possible, relevant explanations. We further show that these simplicity preferences persist in humans, but not in certain artificial neural networks, even when they are maladaptive. Our results imply that principled notions of statistical model selection, including integrating over possible, latent causes to avoid overfitting to noisy observations, may play a central role in human decision-making.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9882019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10790279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The distinct roles of MSH2 and MLH1 in basal-like breast cancer and immune modulation.","authors":"Tanzia Islam Tithi, Jiao Mo, Nicholas Borcherding, Sung Jo, Heather R Kates, Edward Cho, Kailey E Cash, Masayoshi Honda, Lei Wang, Kawther K Ahmed, Kalyanee Shirlekar, Li Chen, Katherine Gibson-Corley, Ronald Weigel, Maria Spies, Ryan Kolb, Weizhou Zhang","doi":"10.1101/2023.07.20.549745","DOIUrl":"10.1101/2023.07.20.549745","url":null,"abstract":"<p><p>The mismatch repair (MMR) pathway is known as a tumor suppressive pathway and genes involved in MMR are commonly mutated in hereditary colorectal or other cancer types. However, the function of MMR genes/proteins in breast cancer progression and metastasis are largely undefined. We found that MSH2, but not MLH1, is highly enriched in basal-like breast cancer (BLBC) and that its protein expression is inversely correlated with overall survival time (OS). <i>MSH2</i> expression is frequently elevated due to genomic amplification or gain-of-expression in BLBC, which results in increased MSH2 protein to pair with MSH6 (collectively referred to as MutSα). Genetic deletion of <i>MSH2</i> or <i>MLH1</i> results in a contrasting phenotype in metastasis, with <i>MSH2</i> -deletion leading to reduced metastasis and <i>MLH1</i> -deletion to enhanced liver or lung metastasis. Mechanistically, MSH2 - but not MLH1 - binds to the promoter region of interferon α receptor 1 ( <i>IFNAR1</i> ) and suppresses its expression in BLBC. Deletion of MSH2 initiates a chain of immune reactions via the upregulation of IFNAR1 expression and the activation of type 1 interferon signaling, which explains a highly immune active tumor microenvironment in tumors with MSH2-deficiency. Our study supports the contrasting functions of MSH2 and MLH1 in BLBC progression and metastasis due to the differential regulation of IFNAR1 expression, which challenges the paradigm of the MMR pathway as a universal tumor suppressive mechanism.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/86/bd/nihpp-2023.07.20.549745v2.PMC10515760.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41142416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Latent Activated Olfactory Stem Cell State Revealed by Single-Cell Transcriptomic and Epigenomic Profiling.","authors":"Koen Van den Berge, Dana Bakalar, Hsin-Jung Chou, Divya Kunda, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit, John Ngai, Whitney Heavner","doi":"10.1101/2023.10.26.564041","DOIUrl":"10.1101/2023.10.26.564041","url":null,"abstract":"<p><p>The olfactory epithelium is one of the few regions of the nervous system that sustains neurogenesis throughout life. Its experimental accessibility makes it especially tractable for studying molecular mechanisms that drive neural regeneration in response to injury. In this study, we used single-cell sequencing to identify the transcriptional cascades and epigenetic processes involved in determining olfactory epithelial stem cell fate during injury-induced regeneration. By combining gene expression and accessible chromatin profiles of individual lineage-traced olfactory stem cells, we identified transcriptional heterogeneity among activated stem cells at a stage when cell fates are being specified. We further identified a subset of resting cells that appears poised for activation, characterized by accessible chromatin around wound response and lineage-specific genes prior to their later expression in response to injury. Together these results provide evidence for a latent activated stem cell state, in which a subset of quiescent olfactory epithelial stem cells are epigenetically primed to support injury-induced regeneration.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92157588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precise Spatial Tuning of Visually Driven Alpha Oscillations in Human Visual Cortex.","authors":"Kenichi Yuasa, Iris I A Groen, Giovanni Piantoni, Stephanie Montenegro, Adeen Flinker, Sasha Devore, Orrin Devinsky, Werner Doyle, Patricia Dugan, Daniel Friedman, Nick Ramsey, Natalia Petridou, Jonathan Winawer","doi":"10.1101/2023.02.11.528137","DOIUrl":"10.1101/2023.02.11.528137","url":null,"abstract":"<p><p>Neuronal oscillations at about 10 Hz, called alpha oscillations, are often thought to arise from synchronous activity across occipital cortex, reflecting general cognitive states such as arousal and alertness. However, there is also evidence that modulation of alpha oscillations in visual cortex can be spatially specific. Here, we used intracranial electrodes in human patients to measure alpha oscillations in response to visual stimuli whose location varied systematically across the visual field. We separated the alpha oscillatory power from broadband power changes. The variation in alpha oscillatory power with stimulus position was then fit by a population receptive field (pRF) model. We find that the alpha pRFs have similar center locations to pRFs estimated from broadband power (70-180 Hz) but are several times larger. The results demonstrate that alpha suppression in human visual cortex can be precisely tuned. Finally, we show how the pattern of alpha responses can explain several features of exogenous visual attention.</p><p><strong>Significance statement: </strong>The alpha oscillation is the largest electrical signal generated by the human brain. An important question in systems neuroscience is the degree to which this oscillation reflects system-wide states and behaviors such as arousal, alertness, and attention, versus much more specific functions in the routing and processing of information. We examined alpha oscillations at high spatial precision in human patients with intracranial electrodes implanted over visual cortex. We discovered a surprisingly high spatial specificity of visually driven alpha oscillations, which we quantified with receptive field models. We further use our discoveries about properties of the alpha response to show a link between these oscillations and the spread of visual attention.Grant support: NIH R01 MH111417 (Petridou, Winawer, Ramsey, Devinsky); JSPS Overseas Research Fellowship (Yuasa)The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9979988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9788874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome Complexity Disentangled: A Regulatory Molecules Approach.","authors":"Amir Asiaee, Zachary B Abrams, Heather H Pua, Kevin R Coombes","doi":"10.1101/2023.04.17.537241","DOIUrl":"10.1101/2023.04.17.537241","url":null,"abstract":"<p><p>Transcription factors (TFs) and microRNAs (miRNAs) are fundamental regulators of gene expression, cell state, and biological processes. This study investigated whether a small subset of TFs and miRNAs could accurately predict genome-wide gene expression. We analyzed 8895 samples across 31 cancer types from The Cancer Genome Atlas and identified 28 miRNA and 28 TF clusters using unsupervised learning. Medoids of these clusters could differentiate tissues of origin with 92.8% accuracy, demonstrating their biological relevance. We developed Tissue-Agnostic and Tissue-Aware models to predict 20,000 gene expressions using the 56 selected medoid miRNAs and TFs. The Tissue-Aware model attained an <math> <mrow><msup><mi>R</mi> <mn>2</mn></msup> </mrow> </math> of 0.70 by incorporating tissue-specific information. Despite measuring only 1/400th of the transcriptome, the prediction accuracy was comparable to that achieved by the 1000 landmark genes. This suggests the transcriptome has an intrinsically low-dimensional structure that can be captured by a few regulatory molecules. Our approach could enable cheaper transcriptome assays and analysis of low-quality samples. It also provides insights into genes that are heavily regulated by miRNAs/TFs versus alternative mechanisms. However, model transportability was impacted by dataset discrepancies, especially in miRNA distribution. Overall, this study demonstrates the potential of a biology-guided approach for robust transcriptome representation.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/07/ad/nihpp-2023.04.17.537241v2.PMC10153180.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9435398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Time or distance encoding by hippocampal neurons with heterogenous ramping rates.","authors":"Raphael Heldman, Dongyan Pang, Xiaoliang Zhao, Brett Mensh, Yingxue Wang","doi":"10.1101/2023.03.12.532295","DOIUrl":"10.1101/2023.03.12.532295","url":null,"abstract":"<p><p>To navigate their environments effectively, animals frequently integrate distance or time information to seek food and avoid threats. This integration process is thought to engage hippocampal neurons that fire at specific distances or times. Using virtual-reality environments, we uncovered two previously unknown functional subpopulations of CA1 pyramidal neurons that encode distance or time through a novel two-phase coding mechanism. The first subpopulation exhibits a collective increase in activity that peaks at similar times, marking the onset of integration; subsequently, individual neurons gradually diverge in their firing rates due to heterogeneous decay rates, enabling time encoding. In contrast, the second subpopulation initially decreases its activity before gradually ramping up. Closed-loop optogenetic experiments revealed that inactivating somatostatin-positive (SST) interneurons disrupts the first subpopulation, behaviorally impairing integration accuracy, while inactivating parvalbumin-positive (PV) interneurons disrupts the second subpopulation, impairing behavior during integration initiation. These findings support the conclusion that SST interneurons establish an integration window, while PV interneurons generate a reset to reinitiate integration. This study elucidates parallel neural circuits that facilitate distinct aspects of distance or time integration, offering new insights into the computations underlying navigation and memory encoding.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10054991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9573191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aging reduces motivation through decreased <i>Bdnf</i> expression in the ventral tegmental area.","authors":"Hanyue Cecilia Lei, Kyle E Parker, Chao-Cheng Kuo, Carla M Yuede, Jordan G McCall, Shin-Ichiro Imai","doi":"10.1101/2023.01.19.524624","DOIUrl":"10.1101/2023.01.19.524624","url":null,"abstract":"<p><p>Age-associated reduced motivation is a hallmark of neuropsychiatric disorders in the elderly. In our rapidly aging societies, it is critical to keep motivation levels high enough to promote healthspan and lifespan. However, how motivation is reduced during aging remains unknown. Here, we used multiple mouse models to evaluate motivation and related affective states in young and old mice. We also compared the effect of social isolation, a common stressor in aged populations, to those of aging. We found that both social isolation and aging decreased motivation in mice, but that <i>Bdnf</i> expression in the ventral tegmental area (VTA) was selectively decreased during aging. Furthermore, VTA-specific <i>Bdnf</i> knockdown in young mice recapitulated reduced motivation observed in old mice. These results demonstrate that maintaining <i>Bdnf</i> expression in the VTA could promote motivation to engage in effortful activities and potentially prevent age-associated neuropsychiatric disorders.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9882313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10640089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SOX7: Autism Associated Gene Identified by Analysis of Multi-Omics Data.","authors":"Samantha Gonzales, Jane Zizhen Zhao, Na Young Choi, Prabha Acharya, Sehoon Jeong, Xuexia Wang, Moo-Yeal Lee","doi":"10.1101/2023.05.26.542456","DOIUrl":"10.1101/2023.05.26.542456","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Genome-wide association studies and next generation sequencing data analyses based on DNA information have identified thousands of mutations associated with autism spectrum disorder (ASD). However, more than 99% of identified mutations are non-coding. Thus, it is unclear which of these mutations might be functional and thus potentially causal variants. Transcriptomic profiling using total RNA-sequencing has been one of the most utilized approaches to link protein levels to genetic information at the molecular level. The transcriptome captures molecular genomic complexity that the DNA sequence solely does not. Some mutations alter a gene's DNA sequence but do not necessarily change expression and/or protein function. To date, few common variants reliably associated with the diagnosis status of ASD despite consistently high estimates of heritability. In addition, reliable biomarkers used to diagnose ASD or molecular mechanisms to define the severity of ASD do not exist. Therefore, it is necessary to integrate DNA and RNA testing together to identify true causal genes and propose useful biomarkers for ASD. We performed gene-based association studies with adaptive test using genome-wide association studies (GWAS) summary statistics with two large GWAS datasets (ASD 2019 data: 18,382 ASD cases and 27,969 controls [discovery data]; ASD 2017 data: 6,197 ASD cases and 7,377 controls [replication data]) which were obtained from the Psychiatric Genomics Consortium (PGC). In addition, we investigated differential expression between ASD cases and controls for genes identified in gene-based GWAS with two RNA-seq datasets (GSE211154: 20 cases and 19 controls; GSE30573: 3 cases and 3 controls). We identified 5 genes significantly associated with ASD in ASD 2019 data (&lt;i&gt;KIZ-AS1&lt;/i&gt;, &lt;i&gt;p&lt;/i&gt;=8.67×10&lt;sup&gt;-10&lt;/sup&gt;; &lt;i&gt;KIZ&lt;/i&gt;, &lt;i&gt;p&lt;/i&gt;=1.16×10&lt;sup&gt;-9&lt;/sup&gt;; &lt;i&gt;XRN2&lt;/i&gt;, &lt;i&gt;p&lt;/i&gt;=7.73×10&lt;sup&gt;-9&lt;/sup&gt;; &lt;i&gt;SOX7&lt;/i&gt;, &lt;i&gt;p&lt;/i&gt;=2.22×10&lt;sup&gt;-7&lt;/sup&gt;; &lt;i&gt;LOC101929229&lt;/i&gt; also known as &lt;i&gt;PINX1-DT&lt;/i&gt;, &lt;i&gt;p&lt;/i&gt;=2.14×10&lt;sup&gt;-6&lt;/sup&gt;). Among these 5 genes, gene &lt;i&gt;SOX7&lt;/i&gt; (&lt;i&gt;p&lt;/i&gt;=0.00087) and &lt;i&gt;LOC101929229&lt;/i&gt; (&lt;i&gt;p&lt;/i&gt;=0.009) were replicated in ASD 2017 data. &lt;i&gt;KIZ-AS1&lt;/i&gt; (&lt;i&gt;p&lt;/i&gt;=0.059) and &lt;i&gt;KIZ&lt;/i&gt; (&lt;i&gt;p&lt;/i&gt;=0.06) were close to the boundary of replication in ASD 2017 data. Genes &lt;i&gt;SOX7&lt;/i&gt; (&lt;i&gt;p&lt;/i&gt;=0.036 in all samples; &lt;i&gt;p&lt;/i&gt;=0.044 in white samples) indicated significant expression differences between cases and controls in the GSE211154 RNA-seq data. Furthermore, gene &lt;i&gt;SOX7&lt;/i&gt; was upregulated in cases than in controls in the GSE30573 RNA-seq data (&lt;i&gt;p&lt;/i&gt;=0.0017; Benjamini-Hochberg adjusted &lt;i&gt;p&lt;/i&gt;=0.0085). &lt;i&gt;SOX7&lt;/i&gt; encodes a member of the SOX (SRY-related HMG-box) family of transcription factors pivotally contributing to determining of the cell fate and identity in many lineages. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins leading to autism. Gene &lt;i&gt;SOX7&lt;/i&gt; in the transcrip","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4a/22/nihpp-2023.05.26.542456v1.PMC10245991.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9707839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}