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Gene-environment interactions within a precision environmental health framework. 精准环境健康框架下的基因-环境相互作用。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-25 DOI: 10.1016/j.xgen.2024.100591
Alison A Motsinger-Reif, David M Reif, Farida S Akhtari, John S House, C Ryan Campbell, Kyle P Messier, David C Fargo, Tiffany A Bowen, Srikanth S Nadadur, Charles P Schmitt, Kristianna G Pettibone, David M Balshaw, Cindy P Lawler, Shelia A Newton, Gwen W Collman, Aubrey K Miller, B Alex Merrick, Yuxia Cui, Benedict Anchang, Quaker E Harmon, Kimberly A McAllister, Rick Woychik

Understanding the complex interplay of genetic and environmental factors in disease etiology and the role of gene-environment interactions (GEIs) across human development stages is important. We review the state of GEI research, including challenges in measuring environmental factors and advantages of GEI analysis in understanding disease mechanisms. We discuss the evolution of GEI studies from candidate gene-environment studies to genome-wide interaction studies (GWISs) and the role of multi-omics in mediating GEI effects. We review advancements in GEI analysis methods and the importance of large-scale datasets. We also address the translation of GEI findings into precision environmental health (PEH), showcasing real-world applications in healthcare and disease prevention. Additionally, we highlight societal considerations in GEI research, including environmental justice, the return of results to participants, and data privacy. Overall, we underscore the significance of GEI for disease prediction and prevention and advocate for integrating the exposome into PEH omics studies.

了解遗传和环境因素在疾病病因学中的复杂相互作用以及基因-环境相互作用(GEIs)在人类各发育阶段的作用非常重要。我们回顾了基因-环境互作研究的现状,包括测量环境因素所面临的挑战以及基因-环境互作分析在理解疾病机制方面的优势。我们讨论了基因-环境互作研究从候选基因-环境研究到全基因组互作研究(GWIS)的演变过程,以及多组学在介导基因-环境互作效应中的作用。我们回顾了 GEI 分析方法的进展以及大规模数据集的重要性。我们还探讨了将基因互作研究结果转化为精准环境健康(PEH)的问题,展示了在医疗保健和疾病预防方面的实际应用。此外,我们还强调了环境基因组学研究中的社会考虑因素,包括环境正义、将结果返还给参与者以及数据隐私。总之,我们强调了基因组学信息对疾病预测和预防的重要意义,并倡导将暴露组纳入 PEH 全息研究。
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引用次数: 0
Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms. 合成 DNA 条形码识别 scRNA-seq 数据集中的单体并评估双体算法。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-25 DOI: 10.1016/j.xgen.2024.100592
Ziyang Zhang, Madeline E Melzer, Keerthana M Arun, Hanxiao Sun, Carl-Johan Eriksson, Itai Fabian, Sagi Shaashua, Karun Kiani, Yaara Oren, Yogesh Goyal

Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.

单细胞 RNA 测序(scRNA-seq)数据集除了包含真正的单细胞(或称单细胞)外,还包含在测序过程中聚合的细胞(或称双细胞)。在 scRNA-seq 中高保真地识别单细胞是避免假阴性和假阳性发现的必要条件。虽然已经提出了几种方法,但它们通常都是在高度异构的数据集上进行测试,缺乏对真正单体的先验知识。在这里,我们利用带有合成引入的 DNA 条形码的数据集进行了一项迄今为止尚未探索过的应用:提取地面真实单体。我们展示了我们的框架 "singletCode "的可行性,以评估各种情况下的现有双码检测方法。我们还利用我们的地面实况单点来训练一个概念验证机器学习分类器,该分类器的性能优于其他双重检测算法。我们的综合框架可以识别地面实况单字,并在非条码数据集中实现稳健的双字检测。
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引用次数: 0
Evolutionary and biomedical implications of sex differences in the primate brain transcriptome. 灵长类动物大脑转录组性别差异对进化和生物医学的影响。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-27 DOI: 10.1016/j.xgen.2024.100589
Alex R DeCasien, Kenneth L Chiou, Camille Testard, Arianne Mercer, Josué E Negrón-Del Valle, Samuel E Bauman Surratt, Olga González, Michala K Stock, Angelina V Ruiz-Lambides, Melween I Martínez, Susan C Antón, Christopher S Walker, Jérôme Sallet, Melissa A Wilson, Lauren J N Brent, Michael J Montague, Chet C Sherwood, Michael L Platt, James P Higham, Noah Snyder-Mackler

Humans exhibit sex differences in the prevalence of many neurodevelopmental disorders and neurodegenerative diseases. Here, we generated one of the largest multi-brain-region bulk transcriptional datasets for the rhesus macaque and characterized sex-biased gene expression patterns to investigate the translatability of this species for sex-biased neurological conditions. We identify patterns similar to those in humans, which are associated with overlapping regulatory mechanisms, biological processes, and genes implicated in sex-biased human disorders, including autism. We also show that sex-biased genes exhibit greater genetic variance for expression and more tissue-specific expression patterns, which may facilitate rapid evolution of sex-biased genes. Our findings provide insights into the biological mechanisms underlying sex-biased disease and support the rhesus macaque model for the translational study of these conditions.

人类在许多神经发育障碍和神经退行性疾病的发病率方面存在性别差异。在这里,我们为猕猴生成了一个最大的多脑区批量转录数据集,并描述了性别差异基因表达模式,以研究该物种对性别差异神经疾病的可转化性。我们发现了与人类相似的模式,这些模式与包括自闭症在内的人类性别偏向性疾病的重叠调控机制、生物过程和相关基因有关。我们还发现,性别偏向基因在表达方面表现出更大的遗传变异和更多的组织特异性表达模式,这可能会促进性别偏向基因的快速进化。我们的研究结果为性别偏见疾病的生物学机制提供了见解,并支持将猕猴模型用于这些疾病的转化研究。
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引用次数: 0
Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. 无论植物寄主或基质特异性如何,真菌的蘑菇基因组总体都在极度扩张。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-27 DOI: 10.1016/j.xgen.2024.100586
Christoffer Bugge Harder, Shingo Miyauchi, Máté Virágh, Alan Kuo, Ella Thoen, Bill Andreopoulos, Dabao Lu, Inger Skrede, Elodie Drula, Bernard Henrissat, Emmanuelle Morin, Annegret Kohler, Kerrie Barry, Kurt LaButti, Asaf Salamov, Anna Lipzen, Zsolt Merényi, Botond Hegedüs, Petr Baldrian, Martina Stursova, Hedda Weitz, Andy Taylor, Maxim Koriabine, Emily Savage, Igor V Grigoriev, László G Nagy, Francis Martin, Håvard Kauserud

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

真菌属(Mycena s.s.)是一种无处不在的蘑菇属,其成员能降解多种死亡植物基质,并伺机侵入活植物根部。在对 24 个真菌属物种的核基因组进行测序后,我们发现它们打破了人们对真菌的预期模式,这种预期模式是基于真菌传统的食腐生态学和基质特化。在新基因家族出现、基因复制、编码多糖降解酶的分泌体增大、转座元件(TE)扩散和水平基因转移的驱动下,真菌的基因组整体上出现了大规模扩张,影响到所有基因家族。主要由于转座元件(TE)的增殖,北极真菌的基因组高达 502 Mbp(是温带真菌的 2 至 8 倍),是形成蘑菇的姬松茸真菌中最大的基因组,这表明在进化过程中可能会出现北极植物基因组扩张的现象。总之,真菌表现出非常不寻常的、多变的、类似马赛克的基因组结构,可适应多种生活方式,为人们日益认识到真菌的生态位适应可能比传统认为的更多变提供了基因组说明。
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引用次数: 0
SpRY-mediated screens facilitate functional dissection of non-coding sequences at single-base resolution. SpRY 介导的筛选有助于以单碱基分辨率对非编码序列进行功能分析。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-17 DOI: 10.1016/j.xgen.2024.100583
Yao Yao, Zhiwei Zhou, Xiaoling Wang, Zhirui Liu, Yixin Zhai, Xiaolin Chi, Jingyi Du, Liheng Luo, Zhigang Zhao, Xiaoyue Wang, Chaoyou Xue, Shuquan Rao

CRISPR mutagenesis screens conducted with SpCas9 and other nucleases have identified certain cis-regulatory elements and genetic variants but at a limited resolution due to the absence of protospacer adjacent motif (PAM) sequences. Here, leveraging the broad targeting scope of the near-PAMless SpRY variant, we have demonstrated that saturated SpRY mutagenesis and base editing screens can faithfully identify functional regulatory elements and essential genetic variants for target gene expression at single-base resolution. We further extended this methodology to investigate a genome-wide association study (GWAS) locus at 10q22.1 associated with a red blood cell trait, where we identified potential enhancers regulating HK1 gene expression, despite not all of these enhancers exhibiting typical chromatin signatures. More importantly, our saturated base editing screens pinpoint multiple causal variants within this locus that would otherwise be missed by Bayesian statistical fine-mapping. Our approach is generally applicable to functional interrogation of all non-coding genomic elements while complementing other high-coverage CRISPR screens.

使用 SpCas9 和其他核酸酶进行的 CRISPR 诱变筛选已经鉴定出了某些顺式调控元件和遗传变异,但由于缺乏原间隔邻接基序(PAM),分辨率有限。在这里,我们利用近乎无 PAM 的 SpRY 变体的广泛靶向范围,证明了饱和 SpRY 诱变和碱基编辑筛选能以单碱基分辨率忠实地鉴定功能调控元件和靶基因表达的基本遗传变异。我们进一步扩展了这一方法,研究了与红细胞性状相关的 10q22.1 全基因组关联研究(GWAS)位点,发现了调控 HK1 基因表达的潜在增强子,尽管这些增强子并非都表现出典型的染色质特征。更重要的是,我们的饱和碱基编辑筛选确定了该基因座中的多个因果变异,否则贝叶斯统计精细作图就会漏掉这些变异。我们的方法普遍适用于所有非编码基因组元件的功能检测,同时也是对其他高覆盖率 CRISPR 筛选的补充。
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引用次数: 0
eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis. eQTLs 确定了个体对败血症反应的调控网络和变异驱动因素。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-18 DOI: 10.1016/j.xgen.2024.100587
Katie L Burnham, Nikhil Milind, Wanseon Lee, Andrew J Kwok, Kiki Cano-Gamez, Yuxin Mi, Cyndi G Geoghegan, Ping Zhang, Stuart McKechnie, Nicole Soranzo, Charles J Hinds, Julian C Knight, Emma E Davenport

Sepsis is a clinical syndrome of life-threatening organ dysfunction caused by a dysregulated response to infection, for which disease heterogeneity is a major obstacle to developing targeted treatments. We have previously identified gene-expression-based patient subgroups (sepsis response signatures [SRS]) informative for outcome and underlying pathophysiology. Here, we aimed to investigate the role of genetic variation in determining the host transcriptomic response and to delineate regulatory networks underlying SRS. Using genotyping and RNA-sequencing data on 638 adult sepsis patients, we report 16,049 independent expression (eQTLs) and 32 co-expression module (modQTLs) quantitative trait loci in this disease context. We identified significant interactions between SRS and genotype for 1,578 SNP-gene pairs and combined transcription factor (TF) binding site information (SNP2TFBS) and predicted regulon activity (DoRothEA) to identify candidate upstream regulators. Overall, these approaches identified putative mechanistic links between host genetic variation, cell subtypes, and the individual transcriptomic response to infection.

败血症是一种由感染反应失调引起的危及生命的器官功能障碍临床综合征,其疾病异质性是开发靶向治疗的主要障碍。我们之前已经确定了基于基因表达的患者亚群(脓毒症反应特征 [SRS]),这些亚群对预后和潜在的病理生理学具有参考价值。在此,我们旨在研究基因变异在决定宿主转录组反应中的作用,并勾勒出 SRS 的基础调控网络。利用对 638 名成年败血症患者的基因分型和 RNA 测序数据,我们报告了这种疾病背景下的 16,049 个独立表达(eQTLs)和 32 个共表达模块(modQTLs)定量性状位点。我们确定了 1,578 个 SNP 基因对的 SRS 与基因型之间的显着交互作用,并结合转录因子 (TF) 结合位点信息(SNP2TFBS)和预测调控子活性(DoRothEA)确定了候选上游调控因子。总之,这些方法确定了宿主遗传变异、细胞亚型和个体转录组对感染的反应之间的潜在机理联系。
{"title":"eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis.","authors":"Katie L Burnham, Nikhil Milind, Wanseon Lee, Andrew J Kwok, Kiki Cano-Gamez, Yuxin Mi, Cyndi G Geoghegan, Ping Zhang, Stuart McKechnie, Nicole Soranzo, Charles J Hinds, Julian C Knight, Emma E Davenport","doi":"10.1016/j.xgen.2024.100587","DOIUrl":"10.1016/j.xgen.2024.100587","url":null,"abstract":"<p><p>Sepsis is a clinical syndrome of life-threatening organ dysfunction caused by a dysregulated response to infection, for which disease heterogeneity is a major obstacle to developing targeted treatments. We have previously identified gene-expression-based patient subgroups (sepsis response signatures [SRS]) informative for outcome and underlying pathophysiology. Here, we aimed to investigate the role of genetic variation in determining the host transcriptomic response and to delineate regulatory networks underlying SRS. Using genotyping and RNA-sequencing data on 638 adult sepsis patients, we report 16,049 independent expression (eQTLs) and 32 co-expression module (modQTLs) quantitative trait loci in this disease context. We identified significant interactions between SRS and genotype for 1,578 SNP-gene pairs and combined transcription factor (TF) binding site information (SNP2TFBS) and predicted regulon activity (DoRothEA) to identify candidate upstream regulators. Overall, these approaches identified putative mechanistic links between host genetic variation, cell subtypes, and the individual transcriptomic response to infection.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100587"},"PeriodicalIF":11.1,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11293594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428438","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}
引用次数: 0
Lineage-specific splicing regulation of MAPT gene in the primate brain. 灵长类动物大脑中 MAPT 基因的特异性剪接调控。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-06-12 Epub Date: 2024-05-20 DOI: 10.1016/j.xgen.2024.100563
Yocelyn Recinos, Suying Bao, Xiaojian Wang, Brittany L Phillips, Yow-Tyng Yeh, Sebastien M Weyn-Vanhentenryck, Maurice S Swanson, Chaolin Zhang

Divergence of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is widespread in mammals, including primates, but the underlying mechanisms and functional impact are poorly understood. Here, we modeled cassette exon inclusion in primate brains as a quantitative trait and identified 1,170 (∼3%) exons with lineage-specific splicing shifts under stabilizing selection. Among them, microtubule-associated protein tau (MAPT) exons 2 and 10 underwent anticorrelated, two-step evolutionary shifts in the catarrhine and hominoid lineages, leading to their present inclusion levels in humans. The developmental-stage-specific divergence of exon 10 splicing, whose dysregulation can cause frontotemporal lobar degeneration (FTLD), is mediated by divergent distal intronic MBNL-binding sites. Competitive binding of these sites by CRISPR-dCas13d/gRNAs effectively reduces exon 10 inclusion, potentially providing a therapeutically compatible approach to modulate tau isoform expression. Our data suggest adaptation of MAPT function and, more generally, a role for AS in the evolutionary expansion of the primate brain.

前体信使 RNA(pre-mRNA)替代剪接(AS)的分化在哺乳动物(包括灵长类动物)中很普遍,但对其潜在机制和功能影响却知之甚少。在这里,我们将灵长类动物大脑中的盒式外显子包含作为一种数量性状建模,并鉴定出1170个(∼3%)外显子在稳定选择下具有品系特异性剪接转变。其中,微管相关蛋白 tau(MAPT)外显子 2 和 10 在猫科动物和同系动物中经历了反相关的两步进化转变,导致了它们在人类中目前的内含水平。第 10 号外显子剪接的发育阶段特异性分化(其失调可导致额颞叶变性(FTLD))是由不同的远端内含子 MBNL 结合位点介导的。CRISPR-dCas13d/gRNA 与这些位点的竞争性结合可有效减少第 10 号外显子的包含,从而为调节 tau 异构体的表达提供了一种潜在的治疗方法。我们的数据表明了 MAPT 功能的适应性,更广泛地说,AS 在灵长类动物大脑的进化扩张中扮演着重要角色。
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引用次数: 0
Complete spatially resolved gene expression is not necessary for identifying spatial domains. 完整的空间解析基因表达并不是识别空间域的必要条件。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-06-12 Epub Date: 2024-05-22 DOI: 10.1016/j.xgen.2024.100565
Senlin Lin, Yan Cui, Fangyuan Zhao, Zhidong Yang, Jiangning Song, Jianhua Yao, Yu Zhao, Bin-Zhi Qian, Yi Zhao, Zhiyuan Yuan

Spatially resolved transcriptomics (SRT) technologies have revolutionized the study of tissue organization. We introduce a graph convolutional network with an attention and positive emphasis mechanism, termed BINARY, relying exclusively on binarized SRT data to accurately delineate spatial domains. BINARY outperforms existing methods across various SRT data types while using significantly less input information. Our study suggests that precise gene expression quantification may not always be essential, inspiring further exploration of the broader applications of spatially resolved binarized gene expression data.

空间分辨转录组学(SRT)技术彻底改变了对组织结构的研究。我们介绍了一种具有注意力和正向强调机制的图卷积网络,称为 "BINARY",它完全依靠二值化的 SRT 数据来精确划分空间域。在各种 SRT 数据类型中,BINARY 的表现优于现有的方法,同时使用的输入信息也少得多。我们的研究表明,精确的基因表达量化并不总是必要的,这激励我们进一步探索空间分辨二值化基因表达数据的更广泛应用。
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引用次数: 0
A gene with a thousand alleles: The hyper-variable effectors of plant-parasitic nematodes. 千变万化的基因:植物寄生线虫的超变异效应因子。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-06-12 Epub Date: 2024-05-29 DOI: 10.1016/j.xgen.2024.100580
Unnati Sonawala, Helen Beasley, Peter Thorpe, Kyriakos Varypatakis, Beatrice Senatori, John T Jones, Lida Derevnina, Sebastian Eves-van den Akker

Pathogens are engaged in a fierce evolutionary arms race with their host. The genes at the forefront of the engagement between kingdoms are often part of diverse and highly mutable gene families. Even in this context, we discovered unprecedented variation in the hyper-variable (HYP) effectors of plant-parasitic nematodes. HYP effectors are single-gene loci that potentially harbor thousands of alleles. Alleles vary in the organization, as well as the number, of motifs within a central hyper-variable domain (HVD). We dramatically expand the HYP repertoire of two plant-parasitic nematodes and define distinct species-specific "rules" underlying the apparently flawless genetic rearrangements. Finally, by analyzing the HYPs in 68 individual nematodes, we unexpectedly found that despite the huge number of alleles, most individuals are germline homozygous. These data support a mechanism of programmed genetic variation, termed HVD editing, where alterations are locus specific, strictly governed by rules, and theoretically produce thousands of variants without errors.

病原体与其宿主进行着激烈的进化军备竞赛。处于王国间交战最前沿的基因往往是多样化和高度变异基因家族的一部分。即使在这种情况下,我们也在植物寄生线虫的超变异(HYP)效应因子中发现了前所未有的变异。HYP 效应子是单基因位点,可能包含数千个等位基因。等位基因在中心超变异结构域(HVD)内的基序组织和数量上各不相同。我们极大地扩展了两种植物寄生线虫的 HYP 基因库,并确定了表面上完美无瑕的基因重排所依据的不同物种特异性 "规则"。最后,通过分析 68 条线虫个体的 HYPs,我们意外地发现,尽管等位基因数量巨大,但大多数个体都是种系同源的。这些数据支持一种被称为 HVD 编辑的程序化基因变异机制,在这种机制下,基因改变是特定位点的,严格受规则约束,理论上可以无差错地产生成千上万个变体。
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引用次数: 0
SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. SIMS:用于单细胞 RNA 测序分析的深度学习标签转移工具。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-06-12 Epub Date: 2024-05-31 DOI: 10.1016/j.xgen.2024.100581
Jesus Gonzalez-Ferrer, Julian Lehrer, Ash O'Farrell, Benedict Paten, Mircea Teodorescu, David Haussler, Vanessa D Jonsson, Mohammed A Mostajo-Radji

Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.

细胞图谱是对新样本进行自动细胞标记的重要参考,但现有的分类算法在准确性方面却举步维艰。在此,我们介绍 SIMS(用于单细胞的可扩展、可解释的机器学习),这是一种用于单细胞 RNA 分类的低代码数据高效管道。我们针对不同组织和物种的数据集对 SIMS 进行了基准测试。我们证明了 SIMS 在大脑细胞分类中的功效,即使使用较小的训练集也能达到很高的准确率(见图 1)。
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引用次数: 0
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Cell genomics
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