Pub Date : 2024-08-08DOI: 10.1101/2024.08.08.607245
Rick M. Searfoss, Xingyu Liu, Benjamin A. Garcia, Zongtao Lin
Arginylation installed by arginyltransferase 1 (ATE1) features an addition of arginine (Arg) to the reactive amino acids (e.g., Glu and Asp) at the protein N-terminus or side chain. Systemic removal of arginylation after ATE1 knockout (KO) in mouse models resulted in heart defects leading to embryonic lethality. The biological importance of arginylation has motivated the discovery of arginylation sites on proteins using bottom-up approaches. While bottom-up proteomics is powerful in localizing peptide arginylation, it lacks the ability to quantify proteoforms at the protein level. Here we developed a top-down proteomics workflow for characterizing and quantifying calreticulin (CALR) arginylation. To generate fully arginylated CALR (R-CALR), we have inserted an R residue after the signaling peptide (AA1-17). Upon overexpression in ATE1 KO cells, CALR and R-CALR were purified by affinity purification and analyzed by LCMS in positive mode. Both proteoforms showed charge states ranging from 27-68 with charge 58 as the most intense charge state. Their MS2 spectra from electron-activated dissociation (EAD) showed preferential fragmentation at the protein N-terminals which yielded sufficient c ions facilitating precise localization of the arginylation sites. The calcium-binding domain (CBD) gave minimum characteristic ions possibly due to the abundant presence of >100 D and E residues. Ultraviolet photodissociation (UVPD) compared with EAD and ETD significantly improved the sequence coverage of CBD. This method can identify and quantify CALR arginylation at absence, endogenous (low), and high levels. To our knowledge, our work is the first application of top-down proteomics in characterizing post-translational arginylation in vitro and in vivo.
精氨酰基转移酶 1（ATE1）的精氨酰化作用是在蛋白质 N 端或侧链的活性氨基酸（如 Glu 和 Asp）上添加精氨酸（Arg）。在小鼠模型中，ATE1 基因敲除（KO）后，全身去除精氨酸化会导致心脏缺陷，从而导致胚胎死亡。精氨酸化的生物学重要性促使人们采用自下而上的方法发现蛋白质上的精氨酸化位点。虽然自下而上的蛋白质组学在定位肽精氨化方面功能强大，但它缺乏在蛋白质水平上量化蛋白质形式的能力。在此，我们开发了一种自上而下的蛋白质组学工作流程，用于表征和量化钙调蛋白（CALR）的精氨酸化。为了生成完全精氨化的 CALR（R-CALR），我们在信号肽（AA1-17）后插入了一个 R 残基。在 ATE1 KO 细胞中过表达后，CALR 和 R-CALR 被亲和纯化，并在正向模式下通过 LCMS 进行分析。两种蛋白形式都显示出 27-68 的电荷状态，其中电荷 58 为最强烈的电荷状态。它们的电子激活解离（EAD）MS2 图谱显示，蛋白质的 N 端优先碎裂，产生了足够的 c 离子，有利于精氨化位点的精确定位。钙结合域（CBD）产生的特征离子最少，这可能是由于存在大量的大于 100 个 D 和 E 残基。紫外光解离（UVPD）与 EAD 和 ETD 相比，大大提高了 CBD 的序列覆盖率。这种方法可以鉴定和量化缺失、内源性（低）和高水平的 CALR 精氨化。据我们所知，我们的工作是首次将自上而下蛋白质组学应用于表征体外和体内翻译后精氨化。
{"title":"Top-down Proteomics for the Characterization and Quantification of Calreticulin Arginylation","authors":"Rick M. Searfoss, Xingyu Liu, Benjamin A. Garcia, Zongtao Lin","doi":"10.1101/2024.08.08.607245","DOIUrl":"https://doi.org/10.1101/2024.08.08.607245","url":null,"abstract":"Arginylation installed by arginyltransferase 1 (ATE1) features an addition of arginine (Arg) to the reactive amino acids (e.g., Glu and Asp) at the protein N-terminus or side chain. Systemic removal of arginylation after ATE1 knockout (KO) in mouse models resulted in heart defects leading to embryonic lethality. The biological importance of arginylation has motivated the discovery of arginylation sites on proteins using bottom-up approaches. While bottom-up proteomics is powerful in localizing peptide arginylation, it lacks the ability to quantify proteoforms at the protein level. Here we developed a top-down proteomics workflow for characterizing and quantifying calreticulin (CALR) arginylation. To generate fully arginylated CALR (R-CALR), we have inserted an R residue after the signaling peptide (AA1-17). Upon overexpression in ATE1 KO cells, CALR and R-CALR were purified by affinity purification and analyzed by LCMS in positive mode. Both proteoforms showed charge states ranging from 27-68 with charge 58 as the most intense charge state. Their MS2 spectra from electron-activated dissociation (EAD) showed preferential fragmentation at the protein N-terminals which yielded sufficient c ions facilitating precise localization of the arginylation sites. The calcium-binding domain (CBD) gave minimum characteristic ions possibly due to the abundant presence of >100 D and E residues. Ultraviolet photodissociation (UVPD) compared with EAD and ETD significantly improved the sequence coverage of CBD. This method can identify and quantify CALR arginylation at absence, endogenous (low), and high levels. To our knowledge, our work is the first application of top-down proteomics in characterizing post-translational arginylation in vitro and in vivo.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.604315
Lucas Prost-Boxoen, Quinten Bafort, Antoine Van de Vloet, Fabrício Almeida-Silva, Yunn Thet Paing, G. Casteleyn, S. D’hondt, O. De Clerck, Yves Van de Peer
Genome merging is a common phenomenon in many organisms, causing a wide range of consequences on phenotype, adaptation, and gene expression, among other effects, yet its broader implications are not well understood. Two consequences of genome merging on gene expression remain poorly understood: dosage effects and evolution of expression. In this study, we employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection (LNS) experiment. Utilizing fitness assays, qPCR, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution over time. Our findings reveal substantial alterations in gene expression, protein homeostasis (proteostasis) and cytonuclear stoichiometry. Notably, gene expression exhibited expression level dominance and transgressivity (i.e., expression level higher or lower than either parent). Ongoing expression level dominance and a pattern of “functional dominance” from the haploid parent was observed, alongside remarkable stability in expression patterns across generations. Despite major nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.
{"title":"Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids","authors":"Lucas Prost-Boxoen, Quinten Bafort, Antoine Van de Vloet, Fabrício Almeida-Silva, Yunn Thet Paing, G. Casteleyn, S. D’hondt, O. De Clerck, Yves Van de Peer","doi":"10.1101/2024.08.06.604315","DOIUrl":"https://doi.org/10.1101/2024.08.06.604315","url":null,"abstract":"Genome merging is a common phenomenon in many organisms, causing a wide range of consequences on phenotype, adaptation, and gene expression, among other effects, yet its broader implications are not well understood. Two consequences of genome merging on gene expression remain poorly understood: dosage effects and evolution of expression. In this study, we employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection (LNS) experiment. Utilizing fitness assays, qPCR, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution over time. Our findings reveal substantial alterations in gene expression, protein homeostasis (proteostasis) and cytonuclear stoichiometry. Notably, gene expression exhibited expression level dominance and transgressivity (i.e., expression level higher or lower than either parent). Ongoing expression level dominance and a pattern of “functional dominance” from the haploid parent was observed, alongside remarkable stability in expression patterns across generations. Despite major nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.07.606946
Patricia Prabutzki, Michele Wölk, J. Böttner, Z. Ni, S. Werner, Holger Thiele, Jürgen Schiller, Petra Büttner, Florian Schlotter, Maria Fedorova
Fibro-calcific aortic valve disease (FCAVD) is the most common valvular heart disease manifesting in pathological fibro-calcific remodeling of the aortic valve (AV) leaflets, ultimately leading to aortic stenosis. Although lipid dysmetabolism is a driver of FCAVD pathogenesis, the molecular details of the AV lipidome remodeling upon fibrosis and calcification remain largely unknown. Here, we employed advanced lipidomics technologies for deep quantitative profiling of metabolic trajectories in human tricuspid and bicuspid AVs at different pathological stages. Specific extrinsic and intrinsic lipid trends, accompanying the development of fibrosis and calcification, were identified. Importantly, significant differences in lipid signatures between male and female individuals were demonstrated and were attributable to altered sphingolipid metabolism. Taken together, deep lipidomics profiling allowed to identify major molecular events and revealed a high extent of sex-dimorphism in lipidomics signatures of human FCAVD.
{"title":"Deep lipidomic profiling reveals sex dimorphism of lipid metabolism in fibro-calcific aortic valve disease","authors":"Patricia Prabutzki, Michele Wölk, J. Böttner, Z. Ni, S. Werner, Holger Thiele, Jürgen Schiller, Petra Büttner, Florian Schlotter, Maria Fedorova","doi":"10.1101/2024.08.07.606946","DOIUrl":"https://doi.org/10.1101/2024.08.07.606946","url":null,"abstract":"Fibro-calcific aortic valve disease (FCAVD) is the most common valvular heart disease manifesting in pathological fibro-calcific remodeling of the aortic valve (AV) leaflets, ultimately leading to aortic stenosis. Although lipid dysmetabolism is a driver of FCAVD pathogenesis, the molecular details of the AV lipidome remodeling upon fibrosis and calcification remain largely unknown. Here, we employed advanced lipidomics technologies for deep quantitative profiling of metabolic trajectories in human tricuspid and bicuspid AVs at different pathological stages. Specific extrinsic and intrinsic lipid trends, accompanying the development of fibrosis and calcification, were identified. Importantly, significant differences in lipid signatures between male and female individuals were demonstrated and were attributable to altered sphingolipid metabolism. Taken together, deep lipidomics profiling allowed to identify major molecular events and revealed a high extent of sex-dimorphism in lipidomics signatures of human FCAVD.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141928766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.07.606501
Xiang Cui, Hongda Zheng, Haoming Li, Fang Zhang, Liao Yang, Jiayu Ni, Dengfeng Wang, Huali Zhang, Pan Tang, Ru Li, Qi Zhang, Min Cui
Paraptosis is a novel form of programmed cell death characterized by distinct morphological features such as swelling of the endoplasmic reticulum and mitochondria, and cytoplasmic vacuolation. Unlike apoptosis, paraptosis does not involve the activation of caspases or DNA fragmentation. These unique features make paraptosis an intriguing target for cancer therapy, particularly against apoptosis-resistant cells. Here, we report a novel morphological feature of paraptosis: the formation of high-density spherical structure, which we tentatively term “paraptosome.” We found that these putative paraptosomes originate from the Golgi apparatus, appearing as high-density formations under light microscopy and colocalizing with the trans-Golgi marker β4GALT1-RFP. Time-lapse confocal microscopy and immunostaining demonstrated that putative paraptosomes form due to Golgi stress or disintegration, leading to severe disruption of Golgi function. Furthermore, we show that paraptosis inducers such as glabridin, morusin, and honokiol can cause significant alterations in the endoplasmic reticulum, mitochondria, autophagosomes, and lysosomes in U251MG glioblastoma cells; however, the formation of putative paraptosomes is not induced by isolated stress inducers. Collectively, these findings suggest that the putative paraptosome may be a novel characteristic structure of paraptosis. The discovery of paraptosomes provides a unique marker for defining paraptotic cell death and offers new insights into the characteristic pathological phenomena associated with multiple organelle dysfunction. This finding broadens the scope of cell biology research by introducing a new structural paradigm linked to paraptosis and may have implications for developing targeted therapies against apoptosis-resistant cancers.
副凋亡是一种新型的程序性细胞死亡，其特点是具有明显的形态特征，如内质网和线粒体肿胀以及细胞质空泡化。与细胞凋亡不同，副凋亡不涉及 Caspases 激活或 DNA 断裂。这些独特的特征使副凋亡成为癌症治疗的一个令人感兴趣的靶点，尤其是针对抗凋亡细胞的治疗。在这里，我们报告了一种新的副凋亡形态学特征：高密度球形结构的形成，我们暂且称之为 "副凋亡体"。我们发现，这些假定的paraptosome源自高尔基体，在光镜下表现为高密度形成，并与跨高尔基体标记β4GALT1-RFP共聚焦。延时共聚焦显微镜和免疫染色表明，假定的副aptosomes 的形成是由于高尔基体受压或解体，从而导致高尔基体功能的严重破坏。此外，我们还发现，副aptosis诱导剂（如格拉布林、吗啉和霍诺克醇）可导致 U251MG胶质母细胞瘤细胞的内质网、线粒体、自噬体和溶酶体发生显著变化；然而，孤立的应激诱导剂并不能诱导推测性副aptosom的形成。总之，这些研究结果表明，推定副aptosome可能是副aptosis的一种新型特征结构。副aptosomes的发现为定义凋亡细胞提供了一个独特的标记，并为了解与多细胞器功能障碍相关的特征性病理现象提供了新的视角。这一发现拓宽了细胞生物学研究的范围，引入了一种与凋亡相关的新结构范式，并可能对开发针对抗凋亡癌症的靶向疗法产生影响。
{"title":"Paraptosome: A Novel Pathological Feature in Paraptotic Cell Death","authors":"Xiang Cui, Hongda Zheng, Haoming Li, Fang Zhang, Liao Yang, Jiayu Ni, Dengfeng Wang, Huali Zhang, Pan Tang, Ru Li, Qi Zhang, Min Cui","doi":"10.1101/2024.08.07.606501","DOIUrl":"https://doi.org/10.1101/2024.08.07.606501","url":null,"abstract":"Paraptosis is a novel form of programmed cell death characterized by distinct morphological features such as swelling of the endoplasmic reticulum and mitochondria, and cytoplasmic vacuolation. Unlike apoptosis, paraptosis does not involve the activation of caspases or DNA fragmentation. These unique features make paraptosis an intriguing target for cancer therapy, particularly against apoptosis-resistant cells. Here, we report a novel morphological feature of paraptosis: the formation of high-density spherical structure, which we tentatively term “paraptosome.” We found that these putative paraptosomes originate from the Golgi apparatus, appearing as high-density formations under light microscopy and colocalizing with the trans-Golgi marker β4GALT1-RFP. Time-lapse confocal microscopy and immunostaining demonstrated that putative paraptosomes form due to Golgi stress or disintegration, leading to severe disruption of Golgi function. Furthermore, we show that paraptosis inducers such as glabridin, morusin, and honokiol can cause significant alterations in the endoplasmic reticulum, mitochondria, autophagosomes, and lysosomes in U251MG glioblastoma cells; however, the formation of putative paraptosomes is not induced by isolated stress inducers. Collectively, these findings suggest that the putative paraptosome may be a novel characteristic structure of paraptosis. The discovery of paraptosomes provides a unique marker for defining paraptotic cell death and offers new insights into the characteristic pathological phenomena associated with multiple organelle dysfunction. This finding broadens the scope of cell biology research by introducing a new structural paradigm linked to paraptosis and may have implications for developing targeted therapies against apoptosis-resistant cancers.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.08.607131
Matthew W. Funk, J. Kidd
Canines are an important model system for genetics and evolution. Recent advances in sequencing technologies have enabled the creation of large databases of genetic variation in canines, but analysis of allele sharing among canine groups has been limited. We applied GeoVar, an approach originally developed to study the sharing of single nucleotide polymorphisms across human populations, to assess the sharing of genetic variation among groups of wolves, village dogs, and breed dogs. Our analysis shows that wolves differ from each other at an average of approximately 2.3 million sites while dogs from the same breed differ at nearly 1 million sites. We find that 22% of variants are common across wolves, village dogs, and breed dogs, that ∼16% of variable sites are common across breed dogs, and that nearly half of the differences between two dogs of different breeds are due to sites that are common in all clades. These analyses represent a succinct summary of allele sharing across canines and illustrate the effects of canine history on the apportionment of genetic variation.
{"title":"A variant centric analysis of allele sharing in dogs and wolves","authors":"Matthew W. Funk, J. Kidd","doi":"10.1101/2024.08.08.607131","DOIUrl":"https://doi.org/10.1101/2024.08.08.607131","url":null,"abstract":"Canines are an important model system for genetics and evolution. Recent advances in sequencing technologies have enabled the creation of large databases of genetic variation in canines, but analysis of allele sharing among canine groups has been limited. We applied GeoVar, an approach originally developed to study the sharing of single nucleotide polymorphisms across human populations, to assess the sharing of genetic variation among groups of wolves, village dogs, and breed dogs. Our analysis shows that wolves differ from each other at an average of approximately 2.3 million sites while dogs from the same breed differ at nearly 1 million sites. We find that 22% of variants are common across wolves, village dogs, and breed dogs, that ∼16% of variable sites are common across breed dogs, and that nearly half of the differences between two dogs of different breeds are due to sites that are common in all clades. These analyses represent a succinct summary of allele sharing across canines and illustrate the effects of canine history on the apportionment of genetic variation.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141926662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.07.605876
Ignacio L Ibarra, Johanna Schneeberger, Ege Erdogan, Lennart Redl, Laura Martens, Dominik Klein, H. Aliee, Fabian J. Theis
Epigenomics assays, such as chromatin accessibility, can identify DNA-sequence-specific regulatory factors. Models that predict read counts from sequence features can explain cell-based readouts using specific DNA patterns (genomic motifs) but do not encode the changes in genomic regulation over time, which is crucial for understanding biological events during cell transitions. To bridge this gap, we present muBind, a deep learning model that accurately predicts genomic counts of single-cell datasets based on DNA sequence features, their cell-based activities, and cell relationships (graphs) in a single architecture, enhancing the interpretability of cell transitions due to the possibility of inspecting motif activities weighted by nearest neighbors. MuBind shows competitive performance in bulk and single-cell genomics. When complemented with graphs learned from RNA-based dynamical models used as injected priors in our model, muBind enhances through motif-graph interactions the identification of transcriptional regulators explaining cell transition events, including Sox9 in pancreatic endocrinogenesis scATAC-seq, and Gli3/Prdm16 in mouse neurogenesis and human organoids scRNA-seq, both supported by independent evidence, including associations between chromatin and motif activities over pseudotime, TF-gene expression patterns, and biological knowledge of these regulators. muBind advances our understanding of cell transitions by revealing regulatory motifs and their interactions, providing valuable insights for genomic research and gene regulatory network dynamics. It is available at https://github.com/theislab/mubind.
染色质可及性等表观基因组学检测可以识别 DNA 序列特异性调控因子。根据序列特征预测读数的模型可以利用特定的DNA模式（基因组图案）解释基于细胞的读数，但不能编码基因组调控随时间的变化，而这对于理解细胞转换过程中的生物事件至关重要。为了弥合这一差距，我们提出了一种深度学习模型--muBind，它能在单一架构中根据 DNA 序列特征、基于细胞的活动和细胞关系（图谱）准确预测单细胞数据集的基因组计数，由于可以通过近邻加权检查图案活动，从而提高了细胞转换的可解释性。MuBind 在大块基因组学和单细胞基因组学中表现出极具竞争力的性能。在我们的模型中，muBind 将基于 RNA 的动力学模型作为注入先验，与从这些模型中学习到的图互补，通过主题图与主题图之间的相互作用，提高了对解释细胞转换事件的转录调控因子的识别能力，包括胰腺内分泌发生 scATAC-seq 中的 Sox9 和小鼠神经发生及人类器官组织 scRNA-seq 中的 Gli3/Prdm16，两者都得到了独立证据的支持，包括染色质与主题活动在伪时间上的关联、TF 基因表达模式以及这些调控因子的生物学知识。muBind 通过揭示调控基团及其相互作用，为基因组研究和基因调控网络动态提供有价值的见解，从而推进我们对细胞转换的理解。它可在 https://github.com/theislab/mubind 上获取。
{"title":"Learning sequence-based regulatory dynamics in single-cell genomics","authors":"Ignacio L Ibarra, Johanna Schneeberger, Ege Erdogan, Lennart Redl, Laura Martens, Dominik Klein, H. Aliee, Fabian J. Theis","doi":"10.1101/2024.08.07.605876","DOIUrl":"https://doi.org/10.1101/2024.08.07.605876","url":null,"abstract":"Epigenomics assays, such as chromatin accessibility, can identify DNA-sequence-specific regulatory factors. Models that predict read counts from sequence features can explain cell-based readouts using specific DNA patterns (genomic motifs) but do not encode the changes in genomic regulation over time, which is crucial for understanding biological events during cell transitions. To bridge this gap, we present muBind, a deep learning model that accurately predicts genomic counts of single-cell datasets based on DNA sequence features, their cell-based activities, and cell relationships (graphs) in a single architecture, enhancing the interpretability of cell transitions due to the possibility of inspecting motif activities weighted by nearest neighbors. MuBind shows competitive performance in bulk and single-cell genomics. When complemented with graphs learned from RNA-based dynamical models used as injected priors in our model, muBind enhances through motif-graph interactions the identification of transcriptional regulators explaining cell transition events, including Sox9 in pancreatic endocrinogenesis scATAC-seq, and Gli3/Prdm16 in mouse neurogenesis and human organoids scRNA-seq, both supported by independent evidence, including associations between chromatin and motif activities over pseudotime, TF-gene expression patterns, and biological knowledge of these regulators. muBind advances our understanding of cell transitions by revealing regulatory motifs and their interactions, providing valuable insights for genomic research and gene regulatory network dynamics. It is available at https://github.com/theislab/mubind.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606842
Andrew P. Latham, Jeremy O. B. Tempkin, S. Otsuka, Wanlu Zhang, J. Ellenberg, Andrej Šali
Dynamic processes involving biomolecules are essential for the function of the cell. Here, we introduce an integrative method for computing models of these processes based on multiple heterogeneous sources of information, including time-resolved experimental data and physical models of dynamic processes. We first compute integrative structure models at fixed time points and then optimally select and connect these snapshots into a series of trajectories that optimize the likelihood of both the snapshots and transitions between them. The method is demonstrated by application to the assembly process of the human Nuclear Pore Complex in the context of the reforming nuclear envelope during mitotic cell division, based on live-cell correlated electron tomography, bulk fluorescence correlation spectroscopy-calibrated quantitative live imaging, and a structural model of the fully-assembled Nuclear Pore Complex. Modeling of the assembly process improves the model precision over static integrative structure modeling alone. The method is applicable to a wide range of time-dependent systems in cell biology, and is available to the broader scientific community through an implementation in the open source Integrative Modeling Platform software.
{"title":"Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex","authors":"Andrew P. Latham, Jeremy O. B. Tempkin, S. Otsuka, Wanlu Zhang, J. Ellenberg, Andrej Šali","doi":"10.1101/2024.08.06.606842","DOIUrl":"https://doi.org/10.1101/2024.08.06.606842","url":null,"abstract":"Dynamic processes involving biomolecules are essential for the function of the cell. Here, we introduce an integrative method for computing models of these processes based on multiple heterogeneous sources of information, including time-resolved experimental data and physical models of dynamic processes. We first compute integrative structure models at fixed time points and then optimally select and connect these snapshots into a series of trajectories that optimize the likelihood of both the snapshots and transitions between them. The method is demonstrated by application to the assembly process of the human Nuclear Pore Complex in the context of the reforming nuclear envelope during mitotic cell division, based on live-cell correlated electron tomography, bulk fluorescence correlation spectroscopy-calibrated quantitative live imaging, and a structural model of the fully-assembled Nuclear Pore Complex. Modeling of the assembly process improves the model precision over static integrative structure modeling alone. The method is applicable to a wide range of time-dependent systems in cell biology, and is available to the broader scientific community through an implementation in the open source Integrative Modeling Platform software.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606937
A. S. Ben Geoffrey, Deepak Agrawal, Nagaraj M Kulkarni, G. Manonmani
Protein function modulation using small molecule binding is an important therapeutic strategy for many diseases. However, many proteins remain undruggable due to lack of suitable binding pockets for small molecule binding. Proximity induced protein degradation using molecular glues has recently been identified as an important strategy to target undruggable proteins. Molecular glues were discovered serendipitously and as such currently lack an established approach for in-silico driven rationale design. In this work, we aim to establish an in-silico method for designing molecular glues. To achieve this, we leverage known molecular glue-mediated ternary complexes and derive a rationale for in-silico design of molecular glues. Establishing an in-silico rationale for molecular glue design would significantly contribute to the literature and accelerate the discovery of molecular glues for targeting previously undruggable proteins. Our work presented here and named as Molecular Glue-Designer-Evaluator (MOLDE) contributes to the growing literature of in-silico approaches to drug design in-silico literature.
{"title":"Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design","authors":"A. S. Ben Geoffrey, Deepak Agrawal, Nagaraj M Kulkarni, G. Manonmani","doi":"10.1101/2024.08.06.606937","DOIUrl":"https://doi.org/10.1101/2024.08.06.606937","url":null,"abstract":"Protein function modulation using small molecule binding is an important therapeutic strategy for many diseases. However, many proteins remain undruggable due to lack of suitable binding pockets for small molecule binding. Proximity induced protein degradation using molecular glues has recently been identified as an important strategy to target undruggable proteins. Molecular glues were discovered serendipitously and as such currently lack an established approach for in-silico driven rationale design. In this work, we aim to establish an in-silico method for designing molecular glues. To achieve this, we leverage known molecular glue-mediated ternary complexes and derive a rationale for in-silico design of molecular glues. Establishing an in-silico rationale for molecular glue design would significantly contribute to the literature and accelerate the discovery of molecular glues for targeting previously undruggable proteins. Our work presented here and named as Molecular Glue-Designer-Evaluator (MOLDE) contributes to the growing literature of in-silico approaches to drug design in-silico literature.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.605120
Emily Roberts, Aishwarya V Bhurke, Sornakala Ganeshkumar, S. Gunewardena, R. Arora, Vargheese M Chennthukuzhi
Successful embryo implantation requires coordinated changes in the uterine luminal epithelium, including structural adaptations, apical-basal polarity shifts, intrauterine fluid resorption, and cellular communication. Planar cell polarity (PCP) proteins, essential for cell organization, are understudied in the context of uterine physiology and implantation. PRICKLE proteins, components of PCP, are suggested to play critical roles in epithelial polarization and tissue morphogenesis. However, their function in the polarized unicellular layer of endometrial epithelium, which supports embryo implantation, is unknown. We developed an endometrial epithelial-specific knockout (cKO) of mouse Prickle1 using Lactoferrin-iCre to investigate its’s role in uterine physiology. Prickle1 ablation in the endometrial epithelium of mice resulted in decreased embryo implantation by gestational day 4.5 leading to lower fertility. Three-dimensional imaging of the uterus revealed abnormal luminal folding, impaired luminal closure, and altered glandular length in mutant uteri. Additionally, we observed decreased aquaporin-2 expression, disrupted cellular architecture, and altered E-Cadherin expression and localization in the mutant uterine epithelium. Evidence of epithelial-mesenchymal transition (EMT) was found within luminal epithelial cells, further linking PRICKLE1 loss to uterine pathologies. Furthermore, altered polarity of cell division leading to incomplete cytokinesis and increase in binuclear or multinucleated cells suggests a crucial role for PRICKLE1 in the maintenance of epithelial architecture. Our findings highlight PRICKLE1’s critical role in the PCP pathway within the uterus, revealing its importance in the molecular and cellular responses essential for successful pregnancy and fertility. Graphical Abstract Conditional ablation of Prickle1, a crucial Wnt/ PCP gene, in mouse uterine epithelium results in altered plane of cell division and incomplete cytokinesis leading to binucleated/multinucleated cells, epithelial – mesenchymal transition, altered gland length, and defective implantation. Some images adapted from BioRender.com (2024). Significance Statement Conservative cell division is essential to maintain apical-basal polarity and proper epithelial function in the uterus. Wnt/ Planar cell polarity signaling molecules are hypothesized to provide the spatial cues to organize unicellular, 2-dimensional sheet of epithelium in a plane orthogonal to the apical-basal polarity. Conditional ablation of Prickle1, a crucial Wnt/ PCP gene, in mouse uterine epithelium results in aberrant expression of epithelial cadherin, altered plane of cell division, incomplete cytokinesis leading to binucleated/ multinucleated cells, epithelial – mesenchymal transition, and defective implantation. Role of Prickle1 in maintaining symmetric uterine epithelial cell division and tissue architecture is unique among Wnt/PCP genes, including previously described mouse models for Va
{"title":"Loss of PRICKLE1 leads to abnormal endometrial epithelial architecture, decreased embryo implantation, and reduced fertility in mice","authors":"Emily Roberts, Aishwarya V Bhurke, Sornakala Ganeshkumar, S. Gunewardena, R. Arora, Vargheese M Chennthukuzhi","doi":"10.1101/2024.08.06.605120","DOIUrl":"https://doi.org/10.1101/2024.08.06.605120","url":null,"abstract":"Successful embryo implantation requires coordinated changes in the uterine luminal epithelium, including structural adaptations, apical-basal polarity shifts, intrauterine fluid resorption, and cellular communication. Planar cell polarity (PCP) proteins, essential for cell organization, are understudied in the context of uterine physiology and implantation. PRICKLE proteins, components of PCP, are suggested to play critical roles in epithelial polarization and tissue morphogenesis. However, their function in the polarized unicellular layer of endometrial epithelium, which supports embryo implantation, is unknown. We developed an endometrial epithelial-specific knockout (cKO) of mouse Prickle1 using Lactoferrin-iCre to investigate its’s role in uterine physiology. Prickle1 ablation in the endometrial epithelium of mice resulted in decreased embryo implantation by gestational day 4.5 leading to lower fertility. Three-dimensional imaging of the uterus revealed abnormal luminal folding, impaired luminal closure, and altered glandular length in mutant uteri. Additionally, we observed decreased aquaporin-2 expression, disrupted cellular architecture, and altered E-Cadherin expression and localization in the mutant uterine epithelium. Evidence of epithelial-mesenchymal transition (EMT) was found within luminal epithelial cells, further linking PRICKLE1 loss to uterine pathologies. Furthermore, altered polarity of cell division leading to incomplete cytokinesis and increase in binuclear or multinucleated cells suggests a crucial role for PRICKLE1 in the maintenance of epithelial architecture. Our findings highlight PRICKLE1’s critical role in the PCP pathway within the uterus, revealing its importance in the molecular and cellular responses essential for successful pregnancy and fertility. Graphical Abstract Conditional ablation of Prickle1, a crucial Wnt/ PCP gene, in mouse uterine epithelium results in altered plane of cell division and incomplete cytokinesis leading to binucleated/multinucleated cells, epithelial – mesenchymal transition, altered gland length, and defective implantation. Some images adapted from BioRender.com (2024). Significance Statement Conservative cell division is essential to maintain apical-basal polarity and proper epithelial function in the uterus. Wnt/ Planar cell polarity signaling molecules are hypothesized to provide the spatial cues to organize unicellular, 2-dimensional sheet of epithelium in a plane orthogonal to the apical-basal polarity. Conditional ablation of Prickle1, a crucial Wnt/ PCP gene, in mouse uterine epithelium results in aberrant expression of epithelial cadherin, altered plane of cell division, incomplete cytokinesis leading to binucleated/ multinucleated cells, epithelial – mesenchymal transition, and defective implantation. Role of Prickle1 in maintaining symmetric uterine epithelial cell division and tissue architecture is unique among Wnt/PCP genes, including previously described mouse models for Va","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141926592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.03.606469
Emin Serin, Kerstin Ritter, Gunter Schumann, Tobias Banaschewski, A. Marquand, H. Walter
Task-based functional magnetic resonance imaging (tb-fMRI) provides valuable insights into individual differences in the neural basis of cognitive functions because it links specific cognitive tasks to their evoked neural responses. Yet, it is challenging to scale to population-level data due to its cognitive demands, variations in task design across studies, and a limited number of tasks acquired in typical large-scale studies. Here, we present DeepTaskGen, a convolutional neural network (CNN) approach that enables us to generate synthetic task-based contrast maps from resting-state fMRI (rs-fMRI) data. Our method outperforms several benchmarks, exhibiting superior reconstruction performance while retaining inter-individual variation essential for biomarker development. We showcase DeepTaskGen by generating synthetic task images from the UK Biobank cohort, achieving competitive or greater performance compared to actual task contrast maps and resting-state connectomes for predicting a wide range of demographic, cognitive, and clinical variables. This approach will facilitate the study of individual differences and the generation of task-related biomarkers by enabling the generation of arbitrary functional cognitive tasks from readily available rs-fMRI data.
{"title":"Generating Synthetic Task-based Brain Fingerprints for Population Neuroscience Using Deep Learning","authors":"Emin Serin, Kerstin Ritter, Gunter Schumann, Tobias Banaschewski, A. Marquand, H. Walter","doi":"10.1101/2024.08.03.606469","DOIUrl":"https://doi.org/10.1101/2024.08.03.606469","url":null,"abstract":"Task-based functional magnetic resonance imaging (tb-fMRI) provides valuable insights into individual differences in the neural basis of cognitive functions because it links specific cognitive tasks to their evoked neural responses. Yet, it is challenging to scale to population-level data due to its cognitive demands, variations in task design across studies, and a limited number of tasks acquired in typical large-scale studies. Here, we present DeepTaskGen, a convolutional neural network (CNN) approach that enables us to generate synthetic task-based contrast maps from resting-state fMRI (rs-fMRI) data. Our method outperforms several benchmarks, exhibiting superior reconstruction performance while retaining inter-individual variation essential for biomarker development. We showcase DeepTaskGen by generating synthetic task images from the UK Biobank cohort, achieving competitive or greater performance compared to actual task contrast maps and resting-state connectomes for predicting a wide range of demographic, cognitive, and clinical variables. This approach will facilitate the study of individual differences and the generation of task-related biomarkers by enabling the generation of arbitrary functional cognitive tasks from readily available rs-fMRI data.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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