L1CAMs are immunoglobulin superfamily cell adhesion molecules that ensure proper nervous system development and function. In addition to being associated with the autism and schizophrenia spectrum disorders, mutations in the L1CAM family of genes also underlie distinct developmental syndromes with neurological conditions, such as intellectual disability, spastic paraplegia, hypotonia and congenital hydrocephalus. Studies in both vertebrate and invertebrate model organisms have established conserved neurodevelopmental roles for L1CAMs; these include axon guidance, dendrite morphogenesis, synaptogenesis, and maintenance of neural architecture, among others. In Caenorhabditis elegans, L1CAMs, encoded by the sax-7 gene, are required for coordinated locomotion. We previously uncovered a genetic interaction between sax-7 and components of synaptic vesicle cycle, revealing a non-developmental role for sax-7 in regulating synaptic activity. More recently, we determined that sax-7 also genetically interacts with extracellular signal-related kinase (ERK) signaling in controlling coordinated locomotion. C. elegans ERK, encoded by the mpk-1 gene, is a serine/threonine protein kinase belonging to the mitogen-activated protein kinase (MAPK) family that governs multiple aspects of animal development and cellular homeostasis. Here, we show this genetic interaction between sax-7 and mpk-1 occurs not only in cholinergic neurons for coordinated locomotion, but also extends outside the nervous system, revealing novel roles for SAX-7/L1CAM in non-neuronal processes, including vulval development. Our genetic findings in both the nervous system and developing vulva are consistent with SAX-7/L1CAM acting as an antagonistic modulator of ERK signaling.
{"title":"The L1CAM SAX-7 is an antagonistic modulator of Erk signaling","authors":"Melinda Moseley-Alldredge, Caroline Aragon, Marcus Vargus, Divya Alley, Nirali Somia, Lihsia Chen","doi":"10.1101/2024.09.14.613091","DOIUrl":"https://doi.org/10.1101/2024.09.14.613091","url":null,"abstract":"L1CAMs are immunoglobulin superfamily cell adhesion molecules that ensure proper nervous system development and function. In addition to being associated with the autism and schizophrenia spectrum disorders, mutations in the L1CAM family of genes also underlie distinct developmental syndromes with neurological conditions, such as intellectual disability, spastic paraplegia, hypotonia and congenital hydrocephalus. Studies in both vertebrate and invertebrate model organisms have established conserved neurodevelopmental roles for L1CAMs; these include axon guidance, dendrite morphogenesis, synaptogenesis, and maintenance of neural architecture, among others. In <em>Caenorhabditis elegans</em>, L1CAMs, encoded by the <em>sax-7</em> gene, are required for coordinated locomotion. We previously uncovered a genetic interaction between <em>sax-7</em> and components of synaptic vesicle cycle, revealing a non-developmental role for <em>sax-7</em> in regulating synaptic activity. More recently, we determined that <em>sax-7</em> also genetically interacts with extracellular signal-related kinase (ERK) signaling in controlling coordinated locomotion. <em>C. elegans</em> ERK, encoded by the <em>mpk-1</em> gene, is a serine/threonine protein kinase belonging to the mitogen-activated protein kinase (MAPK) family that governs multiple aspects of animal development and cellular homeostasis. Here, we show this genetic interaction between <em>sax-7</em> and <em>mpk-1</em> occurs not only in cholinergic neurons for coordinated locomotion, but also extends outside the nervous system, revealing novel roles for SAX-7/L1CAM in non-neuronal processes, including vulval development. Our genetic findings in both the nervous system and developing vulva are consistent with SAX-7/L1CAM acting as an antagonistic modulator of ERK signaling.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247560","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 : 2024-09-16DOI: 10.1101/2024.09.12.612591
Youchen Guan, Yong Yu, Shihong Max Gao, Lang Ding, Qian Zhao, Meng Wang
Metabolism is fundamental to organism physiology and pathology. From the intricate network of metabolic reactions, diverse chemical molecules, collectively termed as metabolites, are produced. In multicellular organisms, metabolite communication between different tissues is vital for maintaining homeostasis and adaptation. However, the molecular mechanisms mediating these metabolite communications remain poorly understood. Here, we focus on nucleosides and nucleotides, essential metabolites involved in multiple cellular processes, and report the pivotal role of the SLC29A family of transporters in mediating nucleoside coordination between the soma and the germline. Through genetic analysis, we discovered that two Caenorhabditis elegans homologs of SLC29A transporters, Equilibrative Nucleoside Transporter ENT-1 and ENT-2, act in the germline and the intestine, respectively, to regulate reproduction. Their knockdown synergistically results in sterility. Further single-cell transcriptomic and targeted metabolomic profiling revealed that the ENT double knockdown specifically affects genes in the purine biosynthesis pathway and reduces the ratio of guanosine to adenosine levels. Importantly, guanosine supplementation into the body cavity/pseudocoelom through microinjection rescued the sterility caused by the ENT double knockdown, whereas adenosine microinjection had no effect. Together, these studies support guanosine as a rate limiting factor in the control of reproduction, uncover the previously unknown nucleoside/nucleotide communication between the soma and the germline essential for reproductive success, and highlight the significance of SLC-mediated cell-nonautonomous metabolite coordination in regulating organism physiology.
新陈代谢是生物体生理和病理的基础。在错综复杂的代谢反应网络中，会产生各种化学分子，统称为代谢物。在多细胞生物体中，不同组织之间的代谢物交流对于维持平衡和适应至关重要。然而，人们对介导这些代谢物交流的分子机制仍然知之甚少。在这里，我们重点研究了核苷酸和核苷酸这种参与多种细胞过程的重要代谢物，并报告了 SLC29A 转运体家族在介导核苷酸在体细胞和生殖细胞之间的协调中的关键作用。通过遗传分析，我们发现草履虫的两个SLC29A转运体同源物--平衡核苷转运体ENT-1和ENT-2--分别在生殖细胞和肠道中调节生殖。敲除它们会协同导致不育。进一步的单细胞转录组和靶向代谢组分析表明，ENT双基因敲除特异性地影响了嘌呤生物合成途径中的基因，并降低了鸟苷与腺苷的比例。重要的是，通过微量注射向体腔/假肠腔补充鸟苷能挽救 ENT 双基因敲除导致的不育，而微量注射腺苷则没有效果。总之，这些研究支持鸟苷是控制繁殖的限速因子，揭示了之前未知的、对繁殖成功至关重要的体细胞和生殖细胞之间的核苷/核苷酸交流，并强调了 SLC 介导的细胞自主代谢物协调在调节生物体生理方面的重要意义。
{"title":"Cross-Tissue Coordination between SLC Nucleoside Transporters Regulates Reproduction in Caenorhabditis elegans","authors":"Youchen Guan, Yong Yu, Shihong Max Gao, Lang Ding, Qian Zhao, Meng Wang","doi":"10.1101/2024.09.12.612591","DOIUrl":"https://doi.org/10.1101/2024.09.12.612591","url":null,"abstract":"Metabolism is fundamental to organism physiology and pathology. From the intricate network of metabolic reactions, diverse chemical molecules, collectively termed as metabolites, are produced. In multicellular organisms, metabolite communication between different tissues is vital for maintaining homeostasis and adaptation. However, the molecular mechanisms mediating these metabolite communications remain poorly understood. Here, we focus on nucleosides and nucleotides, essential metabolites involved in multiple cellular processes, and report the pivotal role of the SLC29A family of transporters in mediating nucleoside coordination between the soma and the germline. Through genetic analysis, we discovered that two Caenorhabditis elegans homologs of SLC29A transporters, Equilibrative Nucleoside Transporter ENT-1 and ENT-2, act in the germline and the intestine, respectively, to regulate reproduction. Their knockdown synergistically results in sterility. Further single-cell transcriptomic and targeted metabolomic profiling revealed that the ENT double knockdown specifically affects genes in the purine biosynthesis pathway and reduces the ratio of guanosine to adenosine levels. Importantly, guanosine supplementation into the body cavity/pseudocoelom through microinjection rescued the sterility caused by the ENT double knockdown, whereas adenosine microinjection had no effect. Together, these studies support guanosine as a rate limiting factor in the control of reproduction, uncover the previously unknown nucleoside/nucleotide communication between the soma and the germline essential for reproductive success, and highlight the significance of SLC-mediated cell-nonautonomous metabolite coordination in regulating organism physiology.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247558","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 : 2024-09-15DOI: 10.1101/2024.09.14.613027
Deepshikha Ananthaswamy, Kelin Funes, Thiago Borges, Scott P. Roques, Nina Fassnacht, Sereen El Jamal, Paula M. Checchi, Teresa W Lee
Organisms rely on coordinated networks of DNA repair pathways to protect genomes against toxic double-strand breaks (DSBs), particularly in germ cells. All repair mechanisms must successfully negotiate the local chromatin environment in order to access DNA. For example, nucleosomes can be repositioned by the highly conserved Nucleosome Remodeling and Deacetylase (NuRD) complex. In Caenorhabditis elegans, NuRD functions in the germline to repair DSBs - the loss of NuRD's ATPase subunit, LET-418/CHD4, prevents DSB resolution and therefore reduces fertility. In this study, we challenge germlines with exogenous DNA damage to better understand NuRD's role in repairing DSBs. We find that let-418 mutants are hypersensitive to cisplatin and hydroxyurea: exposure to either mutagen impedes DSB repair, generates aneuploid oocytes, and severely reduces fertility and embryonic survival. These defects resemble those seen when the Fanconi anemia (FA) DNA repair pathway is compromised, and we find that LET-418's activity is epistatic to that of the FA component FCD-2/FANCD2. We propose a model in which NuRD is recruited to the site of DNA lesions to remodel chromatin and allow access for FA pathway components. Together, these results implicate NuRD in the repair of both endogenous DSBs and exogenous DNA lesions to preserve genome integrity in developing germ cells.
生物依靠 DNA 修复途径的协调网络来保护基因组免受有毒双链断裂（DSB）的伤害，尤其是在生殖细胞中。所有修复机制都必须成功地与当地染色质环境进行协商，才能访问 DNA。例如，核糖体可以通过高度保守的核糖体重塑和去乙酰化酶（NuRD）复合物重新定位。在秀丽隐杆线虫（Caenorhabditis elegans）中，NuRD在生殖系中发挥着修复DSB的功能--NuRD的ATP酶亚基LET-418/CHD4的缺失会阻止DSB的修复，从而降低生育能力。在这项研究中，我们用外源DNA损伤挑战种系，以更好地了解NuRD在修复DSB中的作用。我们发现，let-418突变体对顺铂和羟基脲过敏：暴露于这两种诱变剂都会阻碍DSB修复，产生非整倍体卵母细胞，并严重降低生育能力和胚胎存活率。这些缺陷与范可尼贫血症（FA）DNA 修复途径受损时出现的缺陷相似，而且我们发现 LET-418 的活性与 FA 成分 FCD-2/FANCD2 的活性具有外显性。我们提出了一个模型，在该模型中，NuRD被招募到DNA病变部位，以重塑染色质并允许FA通路元件进入。这些结果共同表明，NuRD参与了内源性DSB和外源性DNA病变的修复，以保持发育中生殖细胞基因组的完整性。
{"title":"NuRD chromatin remodeling is required to repair exogenous DSBs in the Caenorhabditis elegans germline","authors":"Deepshikha Ananthaswamy, Kelin Funes, Thiago Borges, Scott P. Roques, Nina Fassnacht, Sereen El Jamal, Paula M. Checchi, Teresa W Lee","doi":"10.1101/2024.09.14.613027","DOIUrl":"https://doi.org/10.1101/2024.09.14.613027","url":null,"abstract":"Organisms rely on coordinated networks of DNA repair pathways to protect genomes against toxic double-strand breaks (DSBs), particularly in germ cells. All repair mechanisms must successfully negotiate the local chromatin environment in order to access DNA. For example, nucleosomes can be repositioned by the highly conserved Nucleosome Remodeling and Deacetylase (NuRD) complex. In Caenorhabditis elegans, NuRD functions in the germline to repair DSBs - the loss of NuRD's ATPase subunit, LET-418/CHD4, prevents DSB resolution and therefore reduces fertility. In this study, we challenge germlines with exogenous DNA damage to better understand NuRD's role in repairing DSBs. We find that let-418 mutants are hypersensitive to cisplatin and hydroxyurea: exposure to either mutagen impedes DSB repair, generates aneuploid oocytes, and severely reduces fertility and embryonic survival. These defects resemble those seen when the Fanconi anemia (FA) DNA repair pathway is compromised, and we find that LET-418's activity is epistatic to that of the FA component FCD-2/FANCD2. We propose a model in which NuRD is recruited to the site of DNA lesions to remodel chromatin and allow access for FA pathway components. Together, these results implicate NuRD in the repair of both endogenous DSBs and exogenous DNA lesions to preserve genome integrity in developing germ cells.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247603","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 : 2024-09-15DOI: 10.1101/2024.09.11.612442
Nataliia D. Kashko, Iuliia Karavaeva, Elena S. Glagoleva, Maria D. Logacheva, Sofya K. Garushyants, Dmitry A. Knorre
Eukaryotic cells contain multiple copies of mitochondrial DNA (mtDNA) molecules that replicate independently. Cell mtDNA content and variability contributes to the overall cell fitness. During sexual reproduction, fungi usually inherit mtDNA from both parents, however, the distribution of the mtDNA in the progeny can be biased toward some mtDNA variants. For example, crossing Saccharomyces cerevisiae strain carrying wild type (rho+) mtDNA with the strain carrying mutant mtDNA variant with large deletion (rho−) can produce up to 99-100% of rho− diploid progeny. Two factors could contribute to this phenomenon. First, rho− cells may accumulate more copies of mtDNA molecules per cell than wild-type cells, making rho− mtDNA a prevalent mtDNA molecule in zygotes. This consequently leads to a high portion of rho− diploid cells in the offspring. Second, rho− mtDNA may have a competitive advantage within heteroplasmic cells, and therefore could displace rho+ mtDNA in a series of generations, regardless of their initial ratio. To assess the contribution of these factors, we investigated the genotypes and phenotypes of twenty two rho− yeast strains. We found that indeed rho− cells have a higher mtDNA copy number per cell than rho+ strains. Using an in silico modelling of mtDNA selection and random drift in heteroplasmic yeast cells, we assessed the intracellular fitness of mutant mtDNA variants. Our model indicates that both higher copy numbers and intracellular fitness advantage of the rho- mtDNA contribute to the biased inheritance of rho− mtDNA.
{"title":"Inheritance bias of deletion-harbouring mtDNA in yeast: the role of copy number and intracellular selection","authors":"Nataliia D. Kashko, Iuliia Karavaeva, Elena S. Glagoleva, Maria D. Logacheva, Sofya K. Garushyants, Dmitry A. Knorre","doi":"10.1101/2024.09.11.612442","DOIUrl":"https://doi.org/10.1101/2024.09.11.612442","url":null,"abstract":"Eukaryotic cells contain multiple copies of mitochondrial DNA (mtDNA) molecules that replicate independently. Cell mtDNA content and variability contributes to the overall cell fitness. During sexual reproduction, fungi usually inherit mtDNA from both parents, however, the distribution of the mtDNA in the progeny can be biased toward some mtDNA variants. For example, crossing Saccharomyces cerevisiae strain carrying wild type (rho+) mtDNA with the strain carrying mutant mtDNA variant with large deletion (rho−) can produce up to 99-100% of rho− diploid progeny. Two factors could contribute to this phenomenon. First, rho− cells may accumulate more copies of mtDNA molecules per cell than wild-type cells, making rho− mtDNA a prevalent mtDNA molecule in zygotes. This consequently leads to a high portion of rho− diploid cells in the offspring. Second, rho− mtDNA may have a competitive advantage within heteroplasmic cells, and therefore could displace rho+ mtDNA in a series of generations, regardless of their initial ratio. To assess the contribution of these factors, we investigated the genotypes and phenotypes of twenty two rho− yeast strains. We found that indeed rho− cells have a higher mtDNA copy number per cell than rho+ strains. Using an in silico modelling of mtDNA selection and random drift in heteroplasmic yeast cells, we assessed the intracellular fitness of mutant mtDNA variants. Our model indicates that both higher copy numbers and intracellular fitness advantage of the rho- mtDNA contribute to the biased inheritance of rho− mtDNA.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247604","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 : 2024-09-15DOI: 10.1101/2024.09.13.612914
Jose Tomas Ahumada Saavedra, Claire Chevalier, Agnes Bloch Zupan, Yann Herault
The most frequent and unique features of Down syndrome (DS) are learning disability and craniofacial (CF) dysmorphism. The DS-specific CF features are an overall reduction in head dimensions (microcephaly), relatively wide neurocranium (brachycephaly), reduced mediolaterally orbital region, reduced bizygomatic breadth, small maxilla, small mandible, and increased individual variability. Until now, the cellular and molecular mechanisms underlying the specific craniofacial phenotype have remained poorly understood. Investigating a new panel of DS mouse models with different segmental duplications on mouse chromosome 16 in the region homologous to human chromosome 21, we identified new regions and the role of two candidate gene for DS-specific CF phenotypes. First, we confirmed the role of Dyrk1a in the neurocranium brachycephaly. Then, we identified the role of the transcription factor Ripply3 overdosage in midface shortening through the downregulation of Tbx1, another transcription factor involved in the CF midface phenotype encountered in DiGeorge syndrome. This last effect occurs during branchial arches development through a reduction in cell proliferation. Our findings define a new dosage-sensitive gene responsible for the DS craniofacial features and propose new models for rescuing all aspects of DS CF phenotypes. This data may also provide insights into specific brain and cardiovascular phenotypes observed in DiGeorge and DS models, opening avenues for potential targeted treatment to soften craniofacial dysmorphism in Down syndrome.
{"title":"Ripply3 overdosage induces mid-face shortening through Tbx1 downregulation in Down syndrome models.","authors":"Jose Tomas Ahumada Saavedra, Claire Chevalier, Agnes Bloch Zupan, Yann Herault","doi":"10.1101/2024.09.13.612914","DOIUrl":"https://doi.org/10.1101/2024.09.13.612914","url":null,"abstract":"The most frequent and unique features of Down syndrome (DS) are learning disability and craniofacial (CF) dysmorphism. The DS-specific CF features are an overall reduction in head dimensions (microcephaly), relatively wide neurocranium (brachycephaly), reduced mediolaterally orbital region, reduced bizygomatic breadth, small maxilla, small mandible, and increased individual variability. Until now, the cellular and molecular mechanisms underlying the specific craniofacial phenotype have remained poorly understood. Investigating a new panel of DS mouse models with different segmental duplications on mouse chromosome 16 in the region homologous to human chromosome 21, we identified new regions and the role of two candidate gene for DS-specific CF phenotypes. First, we confirmed the role of Dyrk1a in the neurocranium brachycephaly. Then, we identified the role of the transcription factor Ripply3 overdosage in midface shortening through the downregulation of Tbx1, another transcription factor involved in the CF midface phenotype encountered in DiGeorge syndrome. This last effect occurs during branchial arches development through a reduction in cell proliferation. Our findings define a new dosage-sensitive gene responsible for the DS craniofacial features and propose new models for rescuing all aspects of DS CF phenotypes. This data may also provide insights into specific brain and cardiovascular phenotypes observed in DiGeorge and DS models, opening avenues for potential targeted treatment to soften craniofacial dysmorphism in Down syndrome.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247600","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 : 2024-09-15DOI: 10.1101/2024.09.13.612837
Tom Snelling, Leo Olory-Garnotel, Isabella Jeru, Maud Tusseau, Laurence Cuisset, Antoinette Perlat, Geoffrey Minard, Thibaut Benquey, Yann Maucourant, Nicola T Wood, Philip Cohen, Alban Ziegler
ROSAH syndrome is an autosomal dominant autoinflammatory disorder characterised by visual disturbance caused by pathogenic variation in the protein kinase ALPK1. Only two such variants have been reported to cause ROSAH syndrome to date: 66 out of 67 patients harbour the Thr237Met variant, while a single patient carries a Tyr254Cys variant. Here we identify a family in which ROSAH syndrome is caused by a Ser277Phe variant in ALPK1. The phenotypic variability in this family is high, with four of the seven individuals legally blind. Hypohidrosis, splenomegaly and arthritis were present in several family members. In contrast to wildtype ALPK1, which is activated specifically by the bacterial metabolite ADP-heptose during bacterial infection, ALPK1[Ser277Phe] was also activated by the human metabolites UDP-mannose and ADP-ribose, even more strongly than the ALPK1[Thr237Met] variant. However, unlike ALPK1[Thr237Met], ALPK1[Ser277Phe] could additionally be activated by GDP-mannose. These observations can explain why these ALPK1 variants are active in cells in the absence of ADP-heptose and hence why patients have episodes of autoinflammation. Examination of the three-dimensional structure of ALPK1 revealed that the sidechains of Ser277 and Tyr254 interact but mutational analysis established that this interaction is not critical for the integrity of the ADP-heptose binding site. Instead, it is the replacement of Ser277 by a large hydrophobic phenylalanine residue or the replacement of Tyr254 by a much smaller cysteine residue that is responsible for altering the specificity of the ADP-heptose-binding pocket. The characterisation of ALPK1 variants that cause ROSAH syndrome suggests ways in which drugs that inhibit these disease- causing variants selectively can be developed.
{"title":"Discovery and functional analysis of a novel ALPK1 variant causing ROSAH syndrome","authors":"Tom Snelling, Leo Olory-Garnotel, Isabella Jeru, Maud Tusseau, Laurence Cuisset, Antoinette Perlat, Geoffrey Minard, Thibaut Benquey, Yann Maucourant, Nicola T Wood, Philip Cohen, Alban Ziegler","doi":"10.1101/2024.09.13.612837","DOIUrl":"https://doi.org/10.1101/2024.09.13.612837","url":null,"abstract":"ROSAH syndrome is an autosomal dominant autoinflammatory disorder characterised by visual disturbance caused by pathogenic variation in the protein kinase ALPK1. Only two such variants have been reported to cause ROSAH syndrome to date: 66 out of 67 patients harbour the Thr237Met variant, while a single patient carries a Tyr254Cys variant. Here we identify a family in which ROSAH syndrome is caused by a Ser277Phe variant in ALPK1. The phenotypic variability in this family is high, with four of the seven individuals legally blind. Hypohidrosis, splenomegaly and arthritis were present in several family members. In contrast to wildtype ALPK1, which is activated specifically by the bacterial metabolite ADP-heptose during bacterial infection, ALPK1[Ser277Phe] was also activated by the human metabolites UDP-mannose and ADP-ribose, even more strongly than the ALPK1[Thr237Met] variant. However, unlike ALPK1[Thr237Met], ALPK1[Ser277Phe] could additionally be activated by GDP-mannose. These observations can explain why these ALPK1 variants are active in cells in the absence of ADP-heptose and hence why patients have episodes of autoinflammation. Examination of the three-dimensional structure of ALPK1 revealed that the sidechains of Ser277 and Tyr254 interact but mutational analysis established that this interaction is not critical for the integrity of the ADP-heptose binding site. Instead, it is the replacement of Ser277 by a large hydrophobic phenylalanine residue or the replacement of Tyr254 by a much smaller cysteine residue that is responsible for altering the specificity of the ADP-heptose-binding pocket. The characterisation of ALPK1 variants that cause ROSAH syndrome suggests ways in which drugs that inhibit these disease- causing variants selectively can be developed.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247602","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 : 2024-09-15DOI: 10.1101/2024.09.12.612675
shiyou wei, Kuang Du, Hongbin Lan, Zhenyu Yang, Yulan Deng, Zhi Wei, Dennie T Frederick, Jinho Lee, Marilyne Labrie, Tian Tian, Tabea Moll, Yeqing Chen, Ryan J. Sullivan, Gordon B Mills, Genevieve M Boland, Keith Flaherty, lunxu liu, Meenhard Herlyn, Gao Zhang
While a subset of patients with metastatic melanoma achieves durable responses to immune checkpoint blockade (ICB) therapies, the majority ultimately exhibit either innate or acquired resistance to these treatments. However, the molecular mechanisms underlying resistance to ICB therapies remain elusive and are warranted to elucidate. Here, we comprehensively investigated the tumor and tumor immune microenvironment (TIME) of paired pre- and post-treatment tumor specimens from metastatic melanoma patients who were primary or secondary resistance to anti-CTLA-4 and/or anti-PD-1/PD-L1 therapies. Differentially expressed gene (DEG) analysis and single-sample gene set enrichment analysis (ssGSEA) with transcriptomic data identified cell cycle and c-MYC signaling as pathway-based resistance signatures. And weighted gene co-expression network analysis (WGCNA) revealed the activation of a cross-resistance meta-program involving key signaling pathways related to tumor progression in ICB resistant melanoma. Moreover, spatially-resolved, image-based immune monitoring analysis by using NanoString digital spatial profiling (DSP) and Cyclic Immunofluorescence (CyCIF) showed infiltration of suppressive immune cells in the tumor microenvironment of melanoma with resistance to ICB therapies. Our study reveals the molecular mechanisms underlying resistance to ICB therapies in patients with metastatic melanoma by conducting such integrated analyses of multi-dimensional data, and provides rationale for salvage therapies that will potentially overcome resistance to ICB therapies.
{"title":"A Comprehensive Proteogenomic and Spatial Analysis of Innate and Acquired Resistance of Metastatic Melanoma to Immune Checkpoint Blockade Therapies","authors":"shiyou wei, Kuang Du, Hongbin Lan, Zhenyu Yang, Yulan Deng, Zhi Wei, Dennie T Frederick, Jinho Lee, Marilyne Labrie, Tian Tian, Tabea Moll, Yeqing Chen, Ryan J. Sullivan, Gordon B Mills, Genevieve M Boland, Keith Flaherty, lunxu liu, Meenhard Herlyn, Gao Zhang","doi":"10.1101/2024.09.12.612675","DOIUrl":"https://doi.org/10.1101/2024.09.12.612675","url":null,"abstract":"While a subset of patients with metastatic melanoma achieves durable responses to immune checkpoint blockade (ICB) therapies, the majority ultimately exhibit either innate or acquired resistance to these treatments. However, the molecular mechanisms underlying resistance to ICB therapies remain elusive and are warranted to elucidate. Here, we comprehensively investigated the tumor and tumor immune microenvironment (TIME) of paired pre- and post-treatment tumor specimens from metastatic melanoma patients who were primary or secondary resistance to anti-CTLA-4 and/or anti-PD-1/PD-L1 therapies. Differentially expressed gene (DEG) analysis and single-sample gene set enrichment analysis (ssGSEA) with transcriptomic data identified cell cycle and c-MYC signaling as pathway-based resistance signatures. And weighted gene co-expression network analysis (WGCNA) revealed the activation of a cross-resistance meta-program involving key signaling pathways related to tumor progression in ICB resistant melanoma. Moreover, spatially-resolved, image-based immune monitoring analysis by using NanoString digital spatial profiling (DSP) and Cyclic Immunofluorescence (CyCIF) showed infiltration of suppressive immune cells in the tumor microenvironment of melanoma with resistance to ICB therapies. Our study reveals the molecular mechanisms underlying resistance to ICB therapies in patients with metastatic melanoma by conducting such integrated analyses of multi-dimensional data, and provides rationale for salvage therapies that will potentially overcome resistance to ICB therapies.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247598","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 : 2024-09-15DOI: 10.1101/2024.09.12.612680
Zhen Fan, Aaron Liston, Douglas Soltis, Pamela Sue Soltis, Tia-Lynn Ashman, Vance M Whitaker
The identity of the diploid progenitors of octoploid cultivated strawberry (Fragaria × ananassa) has been subject to much debate. Past work identified four subgenomes and consistent evidence for F. californica (previously named F. vesca subsp. bracteata) and F. iinumae as donors for subgenomes A and B, respectively, with conflicting results for the origins of subgenomes C and D. Here, reticulate phylogeny and admixture analysis support hybridization between F. viridis and F. vesca in the ancestry of subgenome A, and between F. nipponica and F. iinumae in the ancestry of subgenome B. Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports of F. viridis and F. nipponica as donors of the C and D subgenomes and unify conflicting hypotheses about the evolutionary origin of octoploid Fragaria.
八倍体栽培草莓（Fragaria × ananassa）的二倍体祖先的身份一直备受争议。过去的工作确定了四个亚基因组，并有一致证据表明 F. californica（以前名为 F. vesca subsp.使用基于 LTR 年龄分布的方法，我们估计八倍体及其中间的六倍体和四倍体祖先分别出现于大约 80 万年前、200 万年前和 300 万年前。这些结果解释了之前关于 F. viridis 和 F. nipponica 是 C 和 D 亚基因组捐赠者的报道，并统一了关于八倍体 Fragaria 进化起源的相互冲突的假说。
{"title":"Homoploid Hybridization Resolves the Origin of Octoploid Strawberries","authors":"Zhen Fan, Aaron Liston, Douglas Soltis, Pamela Sue Soltis, Tia-Lynn Ashman, Vance M Whitaker","doi":"10.1101/2024.09.12.612680","DOIUrl":"https://doi.org/10.1101/2024.09.12.612680","url":null,"abstract":"The identity of the diploid progenitors of octoploid cultivated strawberry (Fragaria × ananassa) has been subject to much debate. Past work identified four subgenomes and consistent evidence for F. californica (previously named F. vesca subsp. bracteata) and F. iinumae as donors for subgenomes A and B, respectively, with conflicting results for the origins of subgenomes C and D. Here, reticulate phylogeny and admixture analysis support hybridization between F. viridis and F. vesca in the ancestry of subgenome A, and between F. nipponica and F. iinumae in the ancestry of subgenome B. Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports of F. viridis and F. nipponica as donors of the C and D subgenomes and unify conflicting hypotheses about the evolutionary origin of octoploid Fragaria.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247601","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 : 2024-09-15DOI: 10.1101/2024.09.13.612941
Sidrit Uruci, Nicole M Hoitsma, Maria E. Soler-Oliva, Aleix Bayona-Feliu, Vincent Gaggioli, Maria L. Garcia Rubio, Calvin S.Y. Lo, Collin Bakker, Jessica Marinello, Eleni Maria Manolika, Giovanni Capranico, Martijn S. Luijsterburg, Karolin Luger, Andres Aguilera, Nitika Taneja
DNA replication often encounters obstacles like the stalled transcription machinery and R-loops. While ribonucleases and DNA-RNA helicases can resolve these structures, the role of chromatin remodelers remains understudied. Through a series of in vitro and in vivo experiments, we show that the chromatin remodeler SMARCAD1, which associates with active replication forks, is crucial for resolving nearby R-loops to maintain fork stability. SMARCAD1 directly binds R-loops via its ATPase domain and associates with the replisome through its N-terminus region. Both interactions are critical for resolving R-loops within cells. Genome-wide assays reveal that cells expressing mutant SMARCAD1 accumulate significantly more R-loops than wild-type cells, particularly in regions distinct from known fork blockage-prone sites. These R-loop-enriched regions in SMARCAD1 mutants also exhibit increased mutagenesis in germline tumors, suggesting they are mutation hotspots in cancer. Therefore, SMARCAD1 acts as an R-loop sensor and resolvase at actively progressing forks, maintaining genome stability and preventing tumorigenesis.
DNA 复制经常会遇到转录机制停滞和 R 环等障碍。核糖核酸酶和DNA-RNA螺旋酶可以解决这些结构，但染色质重塑者的作用仍未得到充分研究。通过一系列体外和体内实验，我们发现染色质重塑器 SMARCAD1 与活跃的复制叉相关联，对于解决附近的 R 环以维持复制叉的稳定性至关重要。SMARCAD1通过其ATPase结构域直接结合R环，并通过其N端区域与复制体结合。这两种相互作用对于解决细胞内的 R 环至关重要。全基因组检测显示，表达突变体 SMARCAD1 的细胞比野生型细胞积累了更多的 R-环，尤其是在与已知叉阻断易发位点不同的区域。在种系肿瘤中，SMARCAD1突变体中的这些R环富集区也表现出更多的突变，表明它们是癌症突变的热点。因此，SMARCAD1 在积极进展的分叉中充当 R 环传感器和解旋酶，维持基因组稳定并防止肿瘤发生。
{"title":"SMARCAD1 Regulates R-Loops at Active Replication Forks Linked to Cancer Mutation Hotspots","authors":"Sidrit Uruci, Nicole M Hoitsma, Maria E. Soler-Oliva, Aleix Bayona-Feliu, Vincent Gaggioli, Maria L. Garcia Rubio, Calvin S.Y. Lo, Collin Bakker, Jessica Marinello, Eleni Maria Manolika, Giovanni Capranico, Martijn S. Luijsterburg, Karolin Luger, Andres Aguilera, Nitika Taneja","doi":"10.1101/2024.09.13.612941","DOIUrl":"https://doi.org/10.1101/2024.09.13.612941","url":null,"abstract":"DNA replication often encounters obstacles like the stalled transcription machinery and R-loops. While ribonucleases and DNA-RNA helicases can resolve these structures, the role of chromatin remodelers remains understudied. Through a series of in vitro and in vivo experiments, we show that the chromatin remodeler SMARCAD1, which associates with active replication forks, is crucial for resolving nearby R-loops to maintain fork stability. SMARCAD1 directly binds R-loops via its ATPase domain and associates with the replisome through its N-terminus region. Both interactions are critical for resolving R-loops within cells. Genome-wide assays reveal that cells expressing mutant SMARCAD1 accumulate significantly more R-loops than wild-type cells, particularly in regions distinct from known fork blockage-prone sites. These R-loop-enriched regions in SMARCAD1 mutants also exhibit increased mutagenesis in germline tumors, suggesting they are mutation hotspots in cancer. Therefore, SMARCAD1 acts as an R-loop sensor and resolvase at actively progressing forks, maintaining genome stability and preventing tumorigenesis.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247562","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 : 2024-09-15DOI: 10.1101/2024.09.13.612919
Shih-Hsun Hung, Yuan Liang, Wolf Dietrich Heyer
Repairing DNA double-strand breaks is crucial for maintaining genome integrity, which occurs primarily through homologous recombination (HR) in S. cerevisiae. Nucleosomes, composed of DNA wrapped around a histone octamer, present a natural barrier to end-resection to initiate HR, but the impact on the downstream HR steps of homology search, DNA strand invasion and repair synthesis remain to be determined. Displacement loops (D-loops) play a pivotal role in HR, yet the influence of chromatin dynamics on D-loop metabolism remains unclear. Using the physical D-loop capture (DLC) and D-loop extension (DLE) assays to track HR intermediates, we employed genetic analysis to reveal that H2B mono-ubiquitylation (H2Bubi) affects multiple steps during HR repair. We infer that H2Bubi modulates chromatin structure, not only promoting histone degradation for nascent D-loop formation but also stabilizing extended D-loops through nucleosome assembly. Furthermore, H2Bubi regulates DNA resection via Rad9 recruitment to suppress a feedback control mechanism that dampens D-loop formation and extension at hyper-resected ends. Through physical and genetic assays to determine repair outcomes, we demonstrate that H2Bubi plays a crucial role in preventing break-induced replication and thus promoting genomic stability.
DNA 双链断裂的修复对于维持基因组的完整性至关重要，这主要是通过同源重组（HR）来实现的。核小体由包裹在组蛋白八聚体周围的 DNA 组成，为启动 HR 的末端重组提供了天然屏障，但其对同源搜索、DNA 链侵入和修复合成等下游 HR 步骤的影响仍有待确定。位移环（D-loop）在HR中起着关键作用，但染色质动力学对D-loop代谢的影响仍不清楚。我们利用物理 D-loop 捕获（DLC）和 D-loop 延伸（DLE）试验追踪 HR 中间体，并通过遗传分析揭示了 H2B 单泛素化（H2Bubi）影响 HR 修复过程中的多个步骤。我们推断，H2Bubi 调节染色质结构，不仅促进组蛋白降解以形成新生 D 环，还通过核小体组装稳定扩展的 D 环。此外，H2Bubi 还通过 Rad9 招募调节 DNA 切除，抑制反馈控制机制，从而抑制 D 环在超切除末端的形成和延伸。通过物理和遗传实验来确定修复结果，我们证明了 H2Bubi 在防止断裂诱导复制从而促进基因组稳定性方面起着至关重要的作用。
{"title":"Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair","authors":"Shih-Hsun Hung, Yuan Liang, Wolf Dietrich Heyer","doi":"10.1101/2024.09.13.612919","DOIUrl":"https://doi.org/10.1101/2024.09.13.612919","url":null,"abstract":"Repairing DNA double-strand breaks is crucial for maintaining genome integrity, which occurs primarily through homologous recombination (HR) in S. cerevisiae. Nucleosomes, composed of DNA wrapped around a histone octamer, present a natural barrier to end-resection to initiate HR, but the impact on the downstream HR steps of homology search, DNA strand invasion and repair synthesis remain to be determined. Displacement loops (D-loops) play a pivotal role in HR, yet the influence of chromatin dynamics on D-loop metabolism remains unclear. Using the physical D-loop capture (DLC) and D-loop extension (DLE) assays to track HR intermediates, we employed genetic analysis to reveal that H2B mono-ubiquitylation (H2Bubi) affects multiple steps during HR repair. We infer that H2Bubi modulates chromatin structure, not only promoting histone degradation for nascent D-loop formation but also stabilizing extended D-loops through nucleosome assembly. Furthermore, H2Bubi regulates DNA resection via Rad9 recruitment to suppress a feedback control mechanism that dampens D-loop formation and extension at hyper-resected ends. Through physical and genetic assays to determine repair outcomes, we demonstrate that H2Bubi plays a crucial role in preventing break-induced replication and thus promoting genomic stability.","PeriodicalId":501246,"journal":{"name":"bioRxiv - Genetics","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142247599","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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