Pub Date : 2023-11-14DOI: 10.1101/2023.11.10.566510
Antara Rao, Nuo Chen, Min Joo Kim, Jessica Blumenfeld, Oscar Yip, Yanxia Hao, Zherui Liang, Maxine R Nelson, Nicole Koutsodendris, Brian Grone, Leonardo Ding, Seo Yeon Yoon, Patrick Arriola, Yadong Huang
Despite strong evidence supporting the involvement of both apolipoprotein E4 (APOE4) and microglia in Alzheimer's Disease (AD) pathogenesis, the effects of microglia on neuronal APOE4-driven AD pathogenesis remain elusive. Here, we examined such effects utilizing microglial depletion in a chimeric model with human neurons in mouse hippocampus. Specifically, we transplanted homozygous APOE4, isogenic APOE3, and APOE-knockout (APOE-KO) induced pluripotent stem cell (iPSC)-derived human neurons into the hippocampus of human APOE3 or APOE4 knock-in mice, and depleted microglia in half the chimeric mice. We found that both neuronal APOE and microglial presence were important for the formation of Aβ and tau pathologies in an APOE isoform-dependent manner (APOE4 > APOE3). Single-cell RNA-sequencing analysis identified two pro-inflammatory microglial subtypes with high MHC-II gene expression that are enriched in chimeric mice with human APOE4 neuron transplants. These findings highlight the concerted roles of neuronal APOE, especially APOE4, and microglia in AD pathogenesis.
{"title":"Microglia Depletion Reduces Human Neuronal APOE4-Driven Pathologies in a Chimeric Alzheimer's Disease Model","authors":"Antara Rao, Nuo Chen, Min Joo Kim, Jessica Blumenfeld, Oscar Yip, Yanxia Hao, Zherui Liang, Maxine R Nelson, Nicole Koutsodendris, Brian Grone, Leonardo Ding, Seo Yeon Yoon, Patrick Arriola, Yadong Huang","doi":"10.1101/2023.11.10.566510","DOIUrl":"https://doi.org/10.1101/2023.11.10.566510","url":null,"abstract":"Despite strong evidence supporting the involvement of both apolipoprotein E4 (APOE4) and microglia in Alzheimer's Disease (AD) pathogenesis, the effects of microglia on neuronal APOE4-driven AD pathogenesis remain elusive. Here, we examined such effects utilizing microglial depletion in a chimeric model with human neurons in mouse hippocampus. Specifically, we transplanted homozygous APOE4, isogenic APOE3, and APOE-knockout (APOE-KO) induced pluripotent stem cell (iPSC)-derived human neurons into the hippocampus of human APOE3 or APOE4 knock-in mice, and depleted microglia in half the chimeric mice. We found that both neuronal APOE and microglial presence were important for the formation of Aβ and tau pathologies in an APOE isoform-dependent manner (APOE4 > APOE3). Single-cell RNA-sequencing analysis identified two pro-inflammatory microglial subtypes with high MHC-II gene expression that are enriched in chimeric mice with human APOE4 neuron transplants. These findings highlight the concerted roles of neuronal APOE, especially APOE4, and microglia in AD pathogenesis.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"27 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134957287","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 : 2023-11-14DOI: 10.1101/2023.11.13.566896
Suzhou Yang, Denethi Wijegunawardana, Udit Sheth, Austin Veire, Juliana M. S. Salgado, Manasi Agrawal, Jeffrey Zhou, João D. Pereira, Tania F. Gendron, Junjie U. Guo
A nucleotide repeat expansion (NRE) in the first annotated intron of the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). While C9 NRE-containing RNAs can be translated into several toxic dipeptide repeat proteins, how an intronic NRE can assess the translation machinery in the cytoplasm remains unclear. By capturing and sequencing NRE-containing RNAs from patient-derived cells, we found that C9 NRE was exonized by the usage of downstream 5′ splice sites and exported from the nucleus in a variety of spliced mRNA isoforms. C9ORF72 aberrant splicing was substantially elevated in both C9 NRE+ motor neurons and human brain tissues. Furthermore, NREs above the pathological threshold were sufficient to activate cryptic splice sites in reporter mRNAs. In summary, our results revealed a crucial and potentially widespread role of repeat-induced aberrant splicing in the biogenesis, localization, and translation of NRE-containing RNAs.
{"title":"Aberrant splicing exonizes C9ORF72 repeat expansion in ALS/FTD","authors":"Suzhou Yang, Denethi Wijegunawardana, Udit Sheth, Austin Veire, Juliana M. S. Salgado, Manasi Agrawal, Jeffrey Zhou, João D. Pereira, Tania F. Gendron, Junjie U. Guo","doi":"10.1101/2023.11.13.566896","DOIUrl":"https://doi.org/10.1101/2023.11.13.566896","url":null,"abstract":"A nucleotide repeat expansion (NRE) in the first annotated intron of the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). While C9 NRE-containing RNAs can be translated into several toxic dipeptide repeat proteins, how an intronic NRE can assess the translation machinery in the cytoplasm remains unclear. By capturing and sequencing NRE-containing RNAs from patient-derived cells, we found that C9 NRE was exonized by the usage of downstream 5′ splice sites and exported from the nucleus in a variety of spliced mRNA isoforms. C9ORF72 aberrant splicing was substantially elevated in both C9 NRE+ motor neurons and human brain tissues. Furthermore, NREs above the pathological threshold were sufficient to activate cryptic splice sites in reporter mRNAs. In summary, our results revealed a crucial and potentially widespread role of repeat-induced aberrant splicing in the biogenesis, localization, and translation of NRE-containing RNAs.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"27 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134957289","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 : 2023-11-14DOI: 10.1101/2023.11.13.566931
Alexander Crits-Christoph, Shinyoung Clair Kang, Henry H Lee, Nili Ostrov
Bacteria and archaea use restriction-modification (R-M) systems to distinguish self from foreign DNA by methylating their genomes with DNA methyltransferases with diverse sequence specificities, and these immunity systems often vary at the strain level. Identifying active methylation patterns and R-M systems can reveal barriers to the introduction of recombinant DNA or phage infection. Here, we present the computational MicrobeMod toolkit for identifying 5mC and 6mA methylation sequence motifs and R-M systems in bacterial genomes using nanopore sequencing of native DNA. We benchmark this approach on a set of reference E. coli strains expressing methyltransferases with known specificities. We then applied these analyses to 31 diverse bacterial and archaeal organisms to reveal the methylation patterns of strains with previously unexplored epigenetics, finding that prokaryotic 5-methylcytosine may be more common than previously reported. In summary, MicrobeMod can rapidly reveal new epigenetics within a prokaryotic genome sequenced with Oxford Nanopore R10.4.1 flow cells at sequencing depths as low as 10x and only requires native DNA. This toolkit can be used to advance fundamental knowledge of bacterial methylation and guide strategies to overcome R-M barriers of genetic tractability in non-model microbes.
{"title":"MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing","authors":"Alexander Crits-Christoph, Shinyoung Clair Kang, Henry H Lee, Nili Ostrov","doi":"10.1101/2023.11.13.566931","DOIUrl":"https://doi.org/10.1101/2023.11.13.566931","url":null,"abstract":"Bacteria and archaea use restriction-modification (R-M) systems to distinguish self from foreign DNA by methylating their genomes with DNA methyltransferases with diverse sequence specificities, and these immunity systems often vary at the strain level. Identifying active methylation patterns and R-M systems can reveal barriers to the introduction of recombinant DNA or phage infection. Here, we present the computational MicrobeMod toolkit for identifying 5mC and 6mA methylation sequence motifs and R-M systems in bacterial genomes using nanopore sequencing of native DNA. We benchmark this approach on a set of reference E. coli strains expressing methyltransferases with known specificities. We then applied these analyses to 31 diverse bacterial and archaeal organisms to reveal the methylation patterns of strains with previously unexplored epigenetics, finding that prokaryotic 5-methylcytosine may be more common than previously reported. In summary, MicrobeMod can rapidly reveal new epigenetics within a prokaryotic genome sequenced with Oxford Nanopore R10.4.1 flow cells at sequencing depths as low as 10x and only requires native DNA. This toolkit can be used to advance fundamental knowledge of bacterial methylation and guide strategies to overcome R-M barriers of genetic tractability in non-model microbes.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"48 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992191","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 : 2023-11-14DOI: 10.1101/2023.11.10.566575
Blake Morton, Dominic Charles Henri, Kristy A Adaway, Charlotte Hopkins
Biodiversity loss is inextricably linked to declining human-nature "connectedness", particularly in terms of how people form attitudes and beliefs about the natural world. Anthropomorphism, or attributing human-like qualities to non-human beings, is an increasingly common conservation strategy to encourage human connectedness to wildlife, but such strategies may also contribute to species' persecution (e.g., "bold" and "cunning" predators). The public often ascribes psychological abilities to wildlife, but there have been limited efforts to link public wildlife attitudes to actual animal psychology research. Through a national level survey (n = 1, 373), we used a controlled experimental approach to test whether providing information on the boldness and problem-solving abilities of a wild carnivore, the red fox (Vulpes vulpes), changed people's tolerance of them. Half of participants were given information on fox psychology (video or a press release about fox boldness and problem-solving), the other half were given content unrelated to animal psychology (video or a press release about fox habitat use). While attitudes and beliefs related to overall tolerance were unaffected, our findings suggest that providing the public with information about animal psychology research, particularly through videos, may have a role in shaping human-wildlife connectedness by changing, either positively or negatively, other facets to people's attitudes (e.g., interest factor), and that such effects may be more impactful than information about an animal's basic ecology. If harnessed correctly, animal psychology research could offer a useful and unique platform for generating greater public awareness and engagement with the biodiversity crisis.
{"title":"Animal psychology research changes public attitudes, but not tolerance, towards a wild carnivore beyond non-psychological information","authors":"Blake Morton, Dominic Charles Henri, Kristy A Adaway, Charlotte Hopkins","doi":"10.1101/2023.11.10.566575","DOIUrl":"https://doi.org/10.1101/2023.11.10.566575","url":null,"abstract":"Biodiversity loss is inextricably linked to declining human-nature \"connectedness\", particularly in terms of how people form attitudes and beliefs about the natural world. Anthropomorphism, or attributing human-like qualities to non-human beings, is an increasingly common conservation strategy to encourage human connectedness to wildlife, but such strategies may also contribute to species' persecution (e.g., \"bold\" and \"cunning\" predators). The public often ascribes psychological abilities to wildlife, but there have been limited efforts to link public wildlife attitudes to actual animal psychology research. Through a national level survey (n = 1, 373), we used a controlled experimental approach to test whether providing information on the boldness and problem-solving abilities of a wild carnivore, the red fox (Vulpes vulpes), changed people's tolerance of them. Half of participants were given information on fox psychology (video or a press release about fox boldness and problem-solving), the other half were given content unrelated to animal psychology (video or a press release about fox habitat use). While attitudes and beliefs related to overall tolerance were unaffected, our findings suggest that providing the public with information about animal psychology research, particularly through videos, may have a role in shaping human-wildlife connectedness by changing, either positively or negatively, other facets to people's attitudes (e.g., interest factor), and that such effects may be more impactful than information about an animal's basic ecology. If harnessed correctly, animal psychology research could offer a useful and unique platform for generating greater public awareness and engagement with the biodiversity crisis.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992988","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 : 2023-11-14DOI: 10.1101/2023.11.14.567076
Alex A Bigger-Allen, Ali Hashemi Ghenani, Rosalyn M Adam
Injury to contractile organs such as the heart, vasculature, urinary bladder and gut can stimulate a pathological response that results in loss of normal contractility. PDGF and TGF are among the most well studied initiators of the injury response and have been shown to induce aberrant contraction in mechanically active cells of hollow organs including smooth muscle cells (SMC) and fibroblasts. However the mechanisms driving contractile alterations downstream of PDGF and TGF in SMC and fibroblasts are incompletely understood, limiting therapeutic interventions. To identify potential molecular targets, we have leveraged the analysis of publicly available data, comparing transcriptomic changes in mechanically active cells stimulated with PDGF and TGF and identified a shared molecular profile regulated by MYC and members of the AP-1 transcription factor complex. We also analyzed data sets from SMC and fibroblasts treated in the presence or absence of the MYC inhibitor JQ1. This analysis revealed a unique set of cytoskeleton-associated genes that were sensitive to MYC inhibition. JQ1 was also able to attenuate TGF and PDGF induced changes to the cytoskeleton and contraction of smooth muscle cells and fibroblasts in vitro. These findings identify MYC as a key driver of aberrant cytoskeletal and contractile changes in fibroblasts and SMC, and suggest that JQ1 could be used to restore normal contractile function in hollow organs.
{"title":"Investigation of the impact of bromodomain inhibition on cytoskeleton stability and contraction","authors":"Alex A Bigger-Allen, Ali Hashemi Ghenani, Rosalyn M Adam","doi":"10.1101/2023.11.14.567076","DOIUrl":"https://doi.org/10.1101/2023.11.14.567076","url":null,"abstract":"Injury to contractile organs such as the heart, vasculature, urinary bladder and gut can stimulate a pathological response that results in loss of normal contractility. PDGF and TGF are among the most well studied initiators of the injury response and have been shown to induce aberrant contraction in mechanically active cells of hollow organs including smooth muscle cells (SMC) and fibroblasts. However the mechanisms driving contractile alterations downstream of PDGF and TGF in SMC and fibroblasts are incompletely understood, limiting therapeutic interventions. To identify potential molecular targets, we have leveraged the analysis of publicly available data, comparing transcriptomic changes in mechanically active cells stimulated with PDGF and TGF and identified a shared molecular profile regulated by MYC and members of the AP-1 transcription factor complex. We also analyzed data sets from SMC and fibroblasts treated in the presence or absence of the MYC inhibitor JQ1. This analysis revealed a unique set of cytoskeleton-associated genes that were sensitive to MYC inhibition. JQ1 was also able to attenuate TGF and PDGF induced changes to the cytoskeleton and contraction of smooth muscle cells and fibroblasts in vitro. These findings identify MYC as a key driver of aberrant cytoskeletal and contractile changes in fibroblasts and SMC, and suggest that JQ1 could be used to restore normal contractile function in hollow organs.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"27 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134954380","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 : 2023-11-14DOI: 10.1101/2023.11.10.566528
Jean Jacques Walker, Estelle Meunier, Samuel Garcia, Belkacem Messaoudi, Anne-Marie Mouly, Alexandra Veyrac, Nathalie Buonviso, Emmanuelle Courtiol
Parkinson disease (PD) is the second most frequent neurodegenerative disorder. Besides major deficits in motor coordination, patients may also display sensory and cognitive impairments, which are often overlooked despite being inherently part of the PD symptomatology. Amongst those symptoms, respiration, a key mechanism involved in the regulation of multiple physiological and neuronal processes, appears to be altered. Importantly, breathing patterns are highly correlated with the animal's behavioral states, and although respiration has been investigated in different models of PD, no study has yet taken into consideration the potential impact of behavioral state on respiration deficits in these models. To explore this variable, we first characterized the respiratory parameters in a neurotoxin-induced rat model of PD (6-OHDA) across different vigilance states: sleep, quiet waking and exploration. We noted a significantly higher respiratory frequency in 6-OHDA rats during quiet waking compared to Sham rats. A higher respiratory amplitude was also observed in 6-OHDA rats during both quiet waking and exploration. No effect of the treatment was noted during sleep. Given the relation between respiration and olfaction and the presence of olfactory deficits in PD patients, we then investigated the odor-evoked sniffing response in PD rats, using an odor habituation/cross-habituation paradigm. No substantial differences were observed in olfactory abilities between the two groups, as assessed through sniffing frequency. These results corroborate the hypothesis that respiratory impairments in 6-OHDA rats are vigilance-dependent. Our results also shed light on the importance of considering the behavioral state as an impacting factor when analyzing respiration.
{"title":"State-dependent alteration of respiration in a rat model of Parkinson disease","authors":"Jean Jacques Walker, Estelle Meunier, Samuel Garcia, Belkacem Messaoudi, Anne-Marie Mouly, Alexandra Veyrac, Nathalie Buonviso, Emmanuelle Courtiol","doi":"10.1101/2023.11.10.566528","DOIUrl":"https://doi.org/10.1101/2023.11.10.566528","url":null,"abstract":"Parkinson disease (PD) is the second most frequent neurodegenerative disorder. Besides major deficits in motor coordination, patients may also display sensory and cognitive impairments, which are often overlooked despite being inherently part of the PD symptomatology. Amongst those symptoms, respiration, a key mechanism involved in the regulation of multiple physiological and neuronal processes, appears to be altered. Importantly, breathing patterns are highly correlated with the animal's behavioral states, and although respiration has been investigated in different models of PD, no study has yet taken into consideration the potential impact of behavioral state on respiration deficits in these models. To explore this variable, we first characterized the respiratory parameters in a neurotoxin-induced rat model of PD (6-OHDA) across different vigilance states: sleep, quiet waking and exploration. We noted a significantly higher respiratory frequency in 6-OHDA rats during quiet waking compared to Sham rats. A higher respiratory amplitude was also observed in 6-OHDA rats during both quiet waking and exploration. No effect of the treatment was noted during sleep. Given the relation between respiration and olfaction and the presence of olfactory deficits in PD patients, we then investigated the odor-evoked sniffing response in PD rats, using an odor habituation/cross-habituation paradigm. No substantial differences were observed in olfactory abilities between the two groups, as assessed through sniffing frequency. These results corroborate the hypothesis that respiratory impairments in 6-OHDA rats are vigilance-dependent. Our results also shed light on the importance of considering the behavioral state as an impacting factor when analyzing respiration.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134957441","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 : 2023-11-14DOI: 10.1101/2023.11.13.566337
Jui Wan Loh, John F Ouyang
Single-cell transcriptomics (scRNA-seq) is extensively applied in uncovering biological heterogeneity. There are different dimensionality reduction techniques, but it is unclear which method works best in preserving biological information when creating a two-dimensional embedding. Therefore, we implemented cellstruct, which calculates three metrics scores to quantify the global or local biological similarity between a two-dimensional and its corresponding higher-dimensional PCA embeddings at either single-cell or cluster level. These scores pinpoint cell populations with low biological information preservation, in addition to visualizing the cell-cell or cluster-cluster relationships in the PCA embedding. Two study cases illustrate the usefulness of cellstruct in exploratory data analysis.
{"title":"cellstruct: Metrics scores to quantify the biological preservation between two embeddings","authors":"Jui Wan Loh, John F Ouyang","doi":"10.1101/2023.11.13.566337","DOIUrl":"https://doi.org/10.1101/2023.11.13.566337","url":null,"abstract":"Single-cell transcriptomics (scRNA-seq) is extensively applied in uncovering biological heterogeneity. There are different dimensionality reduction techniques, but it is unclear which method works best in preserving biological information when creating a two-dimensional embedding. Therefore, we implemented cellstruct, which calculates three metrics scores to quantify the global or local biological similarity between a two-dimensional and its corresponding higher-dimensional PCA embeddings at either single-cell or cluster level. These scores pinpoint cell populations with low biological information preservation, in addition to visualizing the cell-cell or cluster-cluster relationships in the PCA embedding. Two study cases illustrate the usefulness of cellstruct in exploratory data analysis.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"45 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991603","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}
The mechanistic bases of complex traits are consequences of activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. We built prediction models using genomic, transcriptomic, and methylomic data for six Arabidopsis traits. Single data-based models performed similarly but identified different benchmark genes. In addition, distinct genes contributed to trait prediction in different genetic backgrounds. Models integrating multi-omics data performed best and revealed gene interactions, extending knowledge about regulatory networks. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.
{"title":"Prediction of plant complex traits via integration of multi-omics data","authors":"Peipei Wang, Melissa D Lehti-Shiu, Serena Lotreck, Kenia Segura Aba, Shin-Han Shiu","doi":"10.1101/2023.11.14.566971","DOIUrl":"https://doi.org/10.1101/2023.11.14.566971","url":null,"abstract":"The mechanistic bases of complex traits are consequences of activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. We built prediction models using genomic, transcriptomic, and methylomic data for six Arabidopsis traits. Single data-based models performed similarly but identified different benchmark genes. In addition, distinct genes contributed to trait prediction in different genetic backgrounds. Models integrating multi-omics data performed best and revealed gene interactions, extending knowledge about regulatory networks. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"45 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991607","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 : 2023-11-14DOI: 10.1101/2023.11.11.566649
Patrick H. Kennedy, Amin Alborzian Deh Sheikh, Matthew Balakar, Alexander C. Jones, Meagan E. Olive, Mudra Hedge, Maria I. Matias, Natan Pirete, Rajan Burt, Jonathan Levy, Tamia Little, Patrick G. Hogan, David R. Liu, John G. Doench, Alexandra C. Newton, Rachel A. Gottschalk, Carl de Boer, Suzie Alarcon, Gregory Newby, Samuel A. Myers
Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe "signaling-to-transcription network" mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
{"title":"Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput","authors":"Patrick H. Kennedy, Amin Alborzian Deh Sheikh, Matthew Balakar, Alexander C. Jones, Meagan E. Olive, Mudra Hedge, Maria I. Matias, Natan Pirete, Rajan Burt, Jonathan Levy, Tamia Little, Patrick G. Hogan, David R. Liu, John G. Doench, Alexandra C. Newton, Rachel A. Gottschalk, Carl de Boer, Suzie Alarcon, Gregory Newby, Samuel A. Myers","doi":"10.1101/2023.11.11.566649","DOIUrl":"https://doi.org/10.1101/2023.11.11.566649","url":null,"abstract":"Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe \"signaling-to-transcription network\" mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"52 10","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991736","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 : 2023-11-14DOI: 10.1101/2023.11.10.566574
Charles P Burton, Evgeny J Chumin, Alyssa Y Collins, Ravi S Pandey, Scott A Persohn, Sara K Quinney, Ravi S Pandey, Kristen D Onos, Paul R Territo
INTRODUCTION: Subcritical epileptiform activity is associated with impaired cognitive function and is commonly seen in patients with Alzheimer's disease (AD). The anti-convulsant, levetiracetam (LEV), is currently being evaluated in clinical trials for its ability to reduce epileptiform activity and improve cognitive function in AD. The purpose of the current study was to apply pharmacokinetics (PK), network analysis of medical imaging, gene transcriptomics, and PK/PD modeling to a cohort of amyloidogenic mice to establish how LEV restores or drives alterations in the brain networks of mice in a dose-dependent basis using the rigorous preclinical pipeline of the MODEL-AD Preclinical Testing Core. METHODS: Chronic LEV was administered to 5XFAD mice of both sexes for 3 months based on allometrically scaled clinical dose levels from PK models. Data collection and analysis consisted of a multi-modal approach utilizing 18F-FDG PET/MRI imaging and analysis, transcriptomic analyses, and PK/PD modeling. RESULTS: Pharmacokinetics of LEV showed a sex and dose dependence in Cmax, CL/F, and AUC(0-inf);, with simulations used to estimate dose regimens. Chronic dosing at 10, 30, and 56 mg/kg, showed 18F-FDG specific regional differences in brain uptake, and in whole brain covariance measures such as clustering coefficient, degree, network density, and connection strength (i.e. positive and negative). In addition, transcriptomic analysis via nanoString showed dose-dependent changes in gene expression in pathways consistent 18F-FDG uptake and network changes, and PK/PD modeling showed a concentration dependence for key genes, but not for network covariance modeling. DISCUSSION: This study represents the first report detailing the relationships of metabolic covariance and transcriptomic network changes resulting from LEV administration in 5XFAD mice. Overall, our results highlight non-linear kinetics based on dose and sex, where gene expression analysis demonstrated LEV dose- and concentration- dependent changes, along with cerebral metabolism, and/or cerebral homeostatic mechanisms relevant to human AD, which aligned closely with network covariance analysis of 18F-FDG images. Collectively, this study show cases the value of a multimodal connectomic, transcriptomic, and pharmacokinetic approach to further investigate dose dependent relationships in preclinical studies, with translational value towards informing clinical study design.
{"title":"Levetiracetam Modulates Brain Metabolic Networks and Transcriptomic Signatures in the 5XFAD Mouse Model of Alzheimer's disease.","authors":"Charles P Burton, Evgeny J Chumin, Alyssa Y Collins, Ravi S Pandey, Scott A Persohn, Sara K Quinney, Ravi S Pandey, Kristen D Onos, Paul R Territo","doi":"10.1101/2023.11.10.566574","DOIUrl":"https://doi.org/10.1101/2023.11.10.566574","url":null,"abstract":"INTRODUCTION: Subcritical epileptiform activity is associated with impaired cognitive function and is commonly seen in patients with Alzheimer's disease (AD). The anti-convulsant, levetiracetam (LEV), is currently being evaluated in clinical trials for its ability to reduce epileptiform activity and improve cognitive function in AD. The purpose of the current study was to apply pharmacokinetics (PK), network analysis of medical imaging, gene transcriptomics, and PK/PD modeling to a cohort of amyloidogenic mice to establish how LEV restores or drives alterations in the brain networks of mice in a dose-dependent basis using the rigorous preclinical pipeline of the MODEL-AD Preclinical Testing Core. METHODS: Chronic LEV was administered to 5XFAD mice of both sexes for 3 months based on allometrically scaled clinical dose levels from PK models. Data collection and analysis consisted of a multi-modal approach utilizing 18F-FDG PET/MRI imaging and analysis, transcriptomic analyses, and PK/PD modeling. RESULTS: Pharmacokinetics of LEV showed a sex and dose dependence in Cmax, CL/F, and AUC(0-inf);, with simulations used to estimate dose regimens. Chronic dosing at 10, 30, and 56 mg/kg, showed 18F-FDG specific regional differences in brain uptake, and in whole brain covariance measures such as clustering coefficient, degree, network density, and connection strength (i.e. positive and negative). In addition, transcriptomic analysis via nanoString showed dose-dependent changes in gene expression in pathways consistent 18F-FDG uptake and network changes, and PK/PD modeling showed a concentration dependence for key genes, but not for network covariance modeling. DISCUSSION: This study represents the first report detailing the relationships of metabolic covariance and transcriptomic network changes resulting from LEV administration in 5XFAD mice. Overall, our results highlight non-linear kinetics based on dose and sex, where gene expression analysis demonstrated LEV dose- and concentration- dependent changes, along with cerebral metabolism, and/or cerebral homeostatic mechanisms relevant to human AD, which aligned closely with network covariance analysis of 18F-FDG images. Collectively, this study show cases the value of a multimodal connectomic, transcriptomic, and pharmacokinetic approach to further investigate dose dependent relationships in preclinical studies, with translational value towards informing clinical study design.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"32 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134993447","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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