Acute intermittent porphyria (AIP), an inherited disease of heme biosynthesis, is one of the most common type of the porphyrias. Reduced activity of the enzyme
α-Synuclein accumulation causes synaptic vesicle trafficking defects and may underlie neurodegenerative disorders:Neurodegenerative disorders,such as Parkinson’s disease(PD)and other synucleinopathies,impact the liv...α-Synuclein accumulation causes synaptic vesicle trafficking defects and may underlie neurodegenerative disorders:Neurodegenerative disorders,such as Parkinson’s disease(PD)and other synucleinopathies,impact the lives of millions of patients and their caregivers.Synucleinopathies include PD,dementia with Lewy Bodies(DLB),multiple system atrophy,and several Alzheimer’s Disease variants.They are clinically characterized by intracellular inclusions called Lewy Bodies,which are rich in atypical aggregates of the protein α-synuclein.While dopaminergic neurons in the substantia nigra are particularly susceptible toα-synuclein-induced aggregation and neurodegeneration,glutamatergic neurons in other brain regions(e.g.cortex)are also frequently affected in PD and other synucleinopathies(Schulz-Schaeffer 2010).展开更多
In a recent publication it was shown that homonuclear scalar couplings in directly detected protein NMR spectra can be“decoupled”using deep neural networks,including cases where existing methods fail[1].The work har...In a recent publication it was shown that homonuclear scalar couplings in directly detected protein NMR spectra can be“decoupled”using deep neural networks,including cases where existing methods fail[1].The work harkens back to the introduction of maximum entropy and non-uniform sampling,and it elegantly illustrates how new approaches can be devised in the conceptualization of NMR experiments,freeing researchers from conventional thinking and approaches.The work opens up a new era in biomolecular NMR spectroscopy,where experimental design is tailored towards processing with deep neural networks.(https://doi.org/10.1021/jacs.1c04010).展开更多
Developing an active and stable anode catalyst for the proton exchange membrane water electrolyzer(PEM-WE)is a critical objective to enhance the economic viability of green hydrogen technology.However,the expensive ir...Developing an active and stable anode catalyst for the proton exchange membrane water electrolyzer(PEM-WE)is a critical objective to enhance the economic viability of green hydrogen technology.However,the expensive iridium-based electrocatalyst remains the sole practical material with industrial-level stability for the acidic oxygen evolution reaction(OER)at the anode.Ruthenium-based catalysts have been proposed as more cost-effective alternatives with improved activity,though their stability requires enhancement.The current urgent goal is to reduce costs and noble metal loading of the OER catalyst while maintaining robust activity and stability.In this study,we design a Ru-based OER catalyst incorporating Pb as a supporting element.This electrocatalyst exhibits an OER overpotential of 201 mV at 10 mA·cm^(-2),simultaneously reducing Ru noble metal loading by~40%.Normalization of the electrochemically active surface area unveils improved intrinsic activity compared to the pristine RuO_(2) catalyst.During a practical stability test in a PEM-WE setup,our developed catalyst sustains stable performance over 300 h without notable degradation,underscoring its potential for future applications as a reliable anodic catalyst.展开更多
ALG-2(a gene product of PDCD6) is a 22-kD protein containing five serially repetitive EF-hand structures and belongs to the penta-EF-hand(PEF) family,including the subunits of typical calpains.ALG-2 is the most conser...ALG-2(a gene product of PDCD6) is a 22-kD protein containing five serially repetitive EF-hand structures and belongs to the penta-EF-hand(PEF) family,including the subunits of typical calpains.ALG-2 is the most conserved protein among the PEF family members and its homologs are widely found in eukaryotes.X-ray crystal structures of various PEF proteins including ALG-2 have common features:presence of eightα-helices and dimer formation via paired EF5s that are positioned in anti-parallel orientation.ALG-2 forms a homodimer and a heterodimer with its closest paralog peflin.Like calmodulin,a well-known four-EF-hand protein,ALG-2 interacts with various proteins in a Ca2+-dependent fashion,but the binding motifs are completely different.With some exceptions,ALG-2-interacting proteins commonly contain Pro-rich regions,and ALG-2 recognizes at least two distinct Pro-containing motifs:PPYP(X) nYP(X,variable;n=4 in ALIX and PLSCR3) and PXPGF(represented by Sec31A) .A shorter alternatively spliced isoform,lacking two residues and designated ALG-2 GF122,does not bind ALIX but maintains binding capacity to Sec31A.X-ray crystal structural analyses have revealed that binding of calcium ions induces the configuration of the side chain of R125 so that it opens Pocket 1,which accepts PPYP,but Pocket 1 remains closed in the case of ALG-2 GF122.ALG-2 dimer has two ligand-binding sites,each in a monomer molecule,and appears to function as a Ca2+-dependent adaptor protein to either stabilize a preformed complex or to bridge two proteins on scaffolds in systems of the endosomal sorting complex required for transport(ESCRT) and ER-to-Golgi transport.展开更多
The term"circadian rhythms"describes endogenous oscillations with ca.24-h period associated with the earth’s daily rotation and light/dark cycle.Such rhythms reflect the existence of an intrinsic circadian ...The term"circadian rhythms"describes endogenous oscillations with ca.24-h period associated with the earth’s daily rotation and light/dark cycle.Such rhythms reflect the existence of an intrinsic circadian clock that temporally orchestrates physiological processes to adapt the internal environment with the external cues.展开更多
RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA struc- turomes, have been develop...RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA struc- turomes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure-function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes. We emphasize their technological differences especially their unique advantages and caveats. We then summarize the structural insights in RNA functions and regulations obtained from the studies of RNA structuromes. And finally, we propose potential directions for future improvements and studies.展开更多
RNA molecules play crucial roles in various biological processes. Their regulation and function are mediated by interacting with other molecules. Among them RNA-RNA interactions （RRIs） are important in many basic ce...RNA molecules play crucial roles in various biological processes. Their regulation and function are mediated by interacting with other molecules. Among them RNA-RNA interactions （RRIs） are important in many basic cellular activities including transcription, RNA processing, localization, and translation. However, we just start to unveil the complexity of the knowledge and underlying mechanisms of RRIs. Results： In this review, we will summarize approaches for RRI identifications, including both conventional, focused biophysical and biochemical methods and recently developed large scale sequencing-based techniques. We will also discuss discoveries per RRI type revealed by using these technologies, as well as challenges towards a systematic and functional understanding of RRIs. Conclusions： The development of sequencing-based techniques has revolutionized the study of RRIs. Applying these techniques in multiple organisms has identified thousands of RRls, many of which could potentially regulate multiple aspects of gene expression. However, despite the great breakthrough, the RNA-RNA interactome of any species remains far from complete due to intrinsic complex nature of RRI and limitations in current techniques. More efficient experimental methods and computational framework are needed to obtain the full image of RRI networks, and their possible regulatory roles in biology and medicine.展开更多
Background:RNA structure is the crucial basis for RNA function in various cellular processes.Over the last decade,high throughput structure profiling(SP)experiments have brought enormous insight into RNA secondary str...Background:RNA structure is the crucial basis for RNA function in various cellular processes.Over the last decade,high throughput structure profiling(SP)experiments have brought enormous insight into RNA secondary structure.Results:In this review,we first provide an overview of approaches for RNA secondary structure prediction,including free energy-based algorithms and comparative sequence analysis.Then we introduce SP technologies,databases to document SP data,and pipelines/algorithms to normalize and interpret SP data.Computational frameworks that incorporate SP data in RNA secondary structure prediction are also presented.Conclusions:We finally discuss potential directions for improvement in the prediction and differential analysis of RNA secondary structure.展开更多
RNA can interact with RNA-binding proteins(RBPs),mRNA,or other non-coding RNAs(ncRNAs)to form complex regulatory networks.High-throughput CLIP-seq,degradome-seq,and RNA-RNA interactome sequencing methods represent pow...RNA can interact with RNA-binding proteins(RBPs),mRNA,or other non-coding RNAs(ncRNAs)to form complex regulatory networks.High-throughput CLIP-seq,degradome-seq,and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions.However,assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins(RBPs)remains technically challenging.Chemical modifications to mRNA also play important roles in regulating gene expression.Investigation of the functional roles of these modifications relies highly on the detection methods used.RNA structure is also critical at nearly every step of the RNA life cycle.In this review,we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs.We also summarize methods used to detect RNA modifications and to probe RNA structure.展开更多
Ovarian carcinoma is one of the most common causes for cancer death in women;lack of early diagnosis and acquired resistance to platinum-based chemotherapy account for its poor prognosis and high mortality rate.As wit...Ovarian carcinoma is one of the most common causes for cancer death in women;lack of early diagnosis and acquired resistance to platinum-based chemotherapy account for its poor prognosis and high mortality rate.As with other cancer types,ovarian cancer is characterized by dysregulated signaling pathways and protein synthesis,which together contribute to rapid cellular growth and invasiveness.The mechanistic/mammalian target of rapamycin(mTOR)pathway represents the core of different signaling pathways regulating a number of essential steps in the cell,among which protein synthesis and the eukaryotic initiation factor 4E(eIF4E),the mRNA cap binding protein,is one of its downstream effectors.eIF4E is a limiting factor in translation initiation and its overexpression is a hallmark in many cancers.Because its action is regulated by a number of factors that compete for the same binding site,eIF4E is an ideal target for developing novel antineoplastic drugs.Several inhibitors targeting the mTOR signaling pathway have been designed thus far,however most of these molecules show poor stability and high toxicity in vivo.This minireview explores the possibility of targeting mTOR and eIF4E proteins,thus impacting on translation initiation in ovarian cancer,describing the most promising experimental strategies and specific inhibitors that have been shown to have an effect on other kinds of cancers.展开更多
Calcium signaling is essential for lymphocyte activation, with genetic disruptions of store-operated calcium (Ca^(2+)) entry resulting in severe immunodeficiency. The inositol 1,4,5-trisphosphate receptor (IP_(3)R), a...Calcium signaling is essential for lymphocyte activation, with genetic disruptions of store-operated calcium (Ca^(2+)) entry resulting in severe immunodeficiency. The inositol 1,4,5-trisphosphate receptor (IP_(3)R), a homo- or heterotetramer of the IP_(3)R1-3 isoforms, amplifies lymphocyte signaling by releasing Ca^(2+) from endoplasmic reticulum stores following antigen stimulation. Although knockout of all IP_(3)R isoforms in mice causes immunodeficiency, the seeming redundancy of the isoforms is thought to explain the absence of variants in human immunodeficiency. In this study, we identified compound heterozygous variants of ITPR3 (a gene encoding IP_(3)R subtype 3) in two unrelated Caucasian patients presenting with immunodeficiency. To determine whether ITPR3 variants act in a nonredundant manner and disrupt human immune responses, we characterized the Ca^(2+) signaling capacity, the lymphocyte response, and the clinical phenotype of these patients. We observed disrupted Ca^(2+) signaling in patient-derived fibroblasts and immune cells, with abnormal proliferation and activation responses following T-cell receptor stimulation. Reconstitution of IP_(3)R3 in IP_(3)R knockout cell lines led to the identification of variants as functional hypomorphs that showed reduced ability to discriminate between homeostatic and induced states, validating a genotype–phenotype link. These results demonstrate a functional link between defective endoplasmic reticulum Ca^(2+) channels and immunodeficiency and identify IP_(3)Rs as diagnostic targets for patients with specific inborn errors of immunity. These results also extend the known cause of Ca^(2+)-associated immunodeficiency from store-operated entry to impaired Ca^(2+) mobilization from the endoplasmic reticulum, revealing a broad sensitivity of lymphocytes to genetic defects in Ca^(2+) signaling.展开更多
Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain enigmatic.PARIS(Psoralen Analysis of RNA Inter...Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain enigmatic.PARIS(Psoralen Analysis of RNA Interactions and Structures)is a recently developed high-throughput sequencing-based approach that enables direct capture of RNA duplex structures in vivo.However,the existence of incompatible,fuzzy pairing information obstructs the integration of PARIS data with the existing tools for reconstructing RNA secondary structure models at the single-base resolution.Methods:We introduce IRIS,a method for predicting RNA secondary structure ensembles based on PARIS data.IRIS generates a large set of candidate RNA secondary structure models under the guidance of redistributed PARIS reads and then uses a Bayesian model to identify the optimal ensemble,according to both thermodynamic principles and PARIS data.Results:The predicted RNA structure ensembles by IRIS have been verified based on evolutionary conservation information and consistency with other experimental RNA structural data.HIS is implemented in Python and freely available at http://iris.zhanglab.net.Conclusion:IRIS capitalizes upon PARIS data to improve the prediction of in vivo RNA secondary structure ensembles.We expect that IRIS will enhance the application of the PARIS technology and shed more insight on in vivo RNA secondary structures.展开更多
文摘Acute intermittent porphyria (AIP), an inherited disease of heme biosynthesis, is one of the most common type of the porphyrias. Reduced activity of the enzyme
基金supported by a grant from the National Institutes of Health National Institute of Neurological Disorders and Stroke/National Institute on Aging(NIH NINDS/NIA R01NS078165 to JRM)National Institute of General Medical Sciences(NIH/NIGMS Grant R01GM118933 to EML and RS).
文摘α-Synuclein accumulation causes synaptic vesicle trafficking defects and may underlie neurodegenerative disorders:Neurodegenerative disorders,such as Parkinson’s disease(PD)and other synucleinopathies,impact the lives of millions of patients and their caregivers.Synucleinopathies include PD,dementia with Lewy Bodies(DLB),multiple system atrophy,and several Alzheimer’s Disease variants.They are clinically characterized by intracellular inclusions called Lewy Bodies,which are rich in atypical aggregates of the protein α-synuclein.While dopaminergic neurons in the substantia nigra are particularly susceptible toα-synuclein-induced aggregation and neurodegeneration,glutamatergic neurons in other brain regions(e.g.cortex)are also frequently affected in PD and other synucleinopathies(Schulz-Schaeffer 2010).
基金the Intramural Research Program of the National Cancer Institute,National Institutes of Health,and this work falls under Project ZIA BC 011132。
文摘In a recent publication it was shown that homonuclear scalar couplings in directly detected protein NMR spectra can be“decoupled”using deep neural networks,including cases where existing methods fail[1].The work harkens back to the introduction of maximum entropy and non-uniform sampling,and it elegantly illustrates how new approaches can be devised in the conceptualization of NMR experiments,freeing researchers from conventional thinking and approaches.The work opens up a new era in biomolecular NMR spectroscopy,where experimental design is tailored towards processing with deep neural networks.(https://doi.org/10.1021/jacs.1c04010).
基金supported by the Robert A.Welch Foundation(No.C-2051-20230405)the David and Lucile Packard Foundation(No.2020-71371)the Alfred P.Sloan Foundation(No.FG-2021-15638).
文摘Developing an active and stable anode catalyst for the proton exchange membrane water electrolyzer(PEM-WE)is a critical objective to enhance the economic viability of green hydrogen technology.However,the expensive iridium-based electrocatalyst remains the sole practical material with industrial-level stability for the acidic oxygen evolution reaction(OER)at the anode.Ruthenium-based catalysts have been proposed as more cost-effective alternatives with improved activity,though their stability requires enhancement.The current urgent goal is to reduce costs and noble metal loading of the OER catalyst while maintaining robust activity and stability.In this study,we design a Ru-based OER catalyst incorporating Pb as a supporting element.This electrocatalyst exhibits an OER overpotential of 201 mV at 10 mA·cm^(-2),simultaneously reducing Ru noble metal loading by~40%.Normalization of the electrochemically active surface area unveils improved intrinsic activity compared to the pristine RuO_(2) catalyst.During a practical stability test in a PEM-WE setup,our developed catalyst sustains stable performance over 300 h without notable degradation,underscoring its potential for future applications as a reliable anodic catalyst.
文摘ALG-2(a gene product of PDCD6) is a 22-kD protein containing five serially repetitive EF-hand structures and belongs to the penta-EF-hand(PEF) family,including the subunits of typical calpains.ALG-2 is the most conserved protein among the PEF family members and its homologs are widely found in eukaryotes.X-ray crystal structures of various PEF proteins including ALG-2 have common features:presence of eightα-helices and dimer formation via paired EF5s that are positioned in anti-parallel orientation.ALG-2 forms a homodimer and a heterodimer with its closest paralog peflin.Like calmodulin,a well-known four-EF-hand protein,ALG-2 interacts with various proteins in a Ca2+-dependent fashion,but the binding motifs are completely different.With some exceptions,ALG-2-interacting proteins commonly contain Pro-rich regions,and ALG-2 recognizes at least two distinct Pro-containing motifs:PPYP(X) nYP(X,variable;n=4 in ALIX and PLSCR3) and PXPGF(represented by Sec31A) .A shorter alternatively spliced isoform,lacking two residues and designated ALG-2 GF122,does not bind ALIX but maintains binding capacity to Sec31A.X-ray crystal structural analyses have revealed that binding of calcium ions induces the configuration of the side chain of R125 so that it opens Pocket 1,which accepts PPYP,but Pocket 1 remains closed in the case of ALG-2 GF122.ALG-2 dimer has two ligand-binding sites,each in a monomer molecule,and appears to function as a Ca2+-dependent adaptor protein to either stabilize a preformed complex or to bridge two proteins on scaffolds in systems of the endosomal sorting complex required for transport(ESCRT) and ER-to-Golgi transport.
文摘The term"circadian rhythms"describes endogenous oscillations with ca.24-h period associated with the earth’s daily rotation and light/dark cycle.Such rhythms reflect the existence of an intrinsic circadian clock that temporally orchestrates physiological processes to adapt the internal environment with the external cues.
基金supported by the National Natural Science Foundation of China(Grant No.31671355)the National Thousand Young Talents Program of China to QCZ
文摘RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA struc- turomes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure-function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes. We emphasize their technological differences especially their unique advantages and caveats. We then summarize the structural insights in RNA functions and regulations obtained from the studies of RNA structuromes. And finally, we propose potential directions for future improvements and studies.
文摘RNA molecules play crucial roles in various biological processes. Their regulation and function are mediated by interacting with other molecules. Among them RNA-RNA interactions （RRIs） are important in many basic cellular activities including transcription, RNA processing, localization, and translation. However, we just start to unveil the complexity of the knowledge and underlying mechanisms of RRIs. Results： In this review, we will summarize approaches for RRI identifications, including both conventional, focused biophysical and biochemical methods and recently developed large scale sequencing-based techniques. We will also discuss discoveries per RRI type revealed by using these technologies, as well as challenges towards a systematic and functional understanding of RRIs. Conclusions： The development of sequencing-based techniques has revolutionized the study of RRIs. Applying these techniques in multiple organisms has identified thousands of RRls, many of which could potentially regulate multiple aspects of gene expression. However, despite the great breakthrough, the RNA-RNA interactome of any species remains far from complete due to intrinsic complex nature of RRI and limitations in current techniques. More efficient experimental methods and computational framework are needed to obtain the full image of RRI networks, and their possible regulatory roles in biology and medicine.
基金the National Natural Science Foundation of China(No.11601259)Shanghai Municipal Science and Technology Major Project(No.2017SHZDZX01).
文摘Background:RNA structure is the crucial basis for RNA function in various cellular processes.Over the last decade,high throughput structure profiling(SP)experiments have brought enormous insight into RNA secondary structure.Results:In this review,we first provide an overview of approaches for RNA secondary structure prediction,including free energy-based algorithms and comparative sequence analysis.Then we introduce SP technologies,databases to document SP data,and pipelines/algorithms to normalize and interpret SP data.Computational frameworks that incorporate SP data in RNA secondary structure prediction are also presented.Conclusions:We finally discuss potential directions for improvement in the prediction and differential analysis of RNA secondary structure.
文摘RNA can interact with RNA-binding proteins(RBPs),mRNA,or other non-coding RNAs(ncRNAs)to form complex regulatory networks.High-throughput CLIP-seq,degradome-seq,and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions.However,assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins(RBPs)remains technically challenging.Chemical modifications to mRNA also play important roles in regulating gene expression.Investigation of the functional roles of these modifications relies highly on the detection methods used.RNA structure is also critical at nearly every step of the RNA life cycle.In this review,we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs.We also summarize methods used to detect RNA modifications and to probe RNA structure.
文摘Ovarian carcinoma is one of the most common causes for cancer death in women;lack of early diagnosis and acquired resistance to platinum-based chemotherapy account for its poor prognosis and high mortality rate.As with other cancer types,ovarian cancer is characterized by dysregulated signaling pathways and protein synthesis,which together contribute to rapid cellular growth and invasiveness.The mechanistic/mammalian target of rapamycin(mTOR)pathway represents the core of different signaling pathways regulating a number of essential steps in the cell,among which protein synthesis and the eukaryotic initiation factor 4E(eIF4E),the mRNA cap binding protein,is one of its downstream effectors.eIF4E is a limiting factor in translation initiation and its overexpression is a hallmark in many cancers.Because its action is regulated by a number of factors that compete for the same binding site,eIF4E is an ideal target for developing novel antineoplastic drugs.Several inhibitors targeting the mTOR signaling pathway have been designed thus far,however most of these molecules show poor stability and high toxicity in vivo.This minireview explores the possibility of targeting mTOR and eIF4E proteins,thus impacting on translation initiation in ovarian cancer,describing the most promising experimental strategies and specific inhibitors that have been shown to have an effect on other kinds of cancers.
基金supported by the VIB Grand Challenges Program,the KU Leuven C1 program,the European Union’s Horizon 2020 research and innovation program under grant agreement No 779295(to AL)the Biotechnology and Biological Sciences Research Council(BBSRC)through Institute Strategic Program Grant funding BBS/E/B/000C0427 and BBS/E/B/000C0428 and the KU Leuven BOFZAP start-up grant(to SH-B)+7 种基金Work in the Bultynck team was supported by grants from the Research Council of the KU Leuven(C14/19/99 and AKUL/19/34)Research Foundation-Flanders(G.0818.21NG.0945.22N)DIY is supported by the National Institutes of Health(NIH)R01-DE0014756 grant.MRB and IIS are supported by the NIH R01GM072804 grant(to IIS)the Welch Foundation Research Grant AU-2014-20190331(to IIS)the American Heart Association grant 18CDA34110086(to MRB)IIS,DIY,and GB are in the FWO Scientific Research Network CaSign(W0.019.17N)IM and RS are FWO senior clinical investigator fellows.IM and RS are members of the European Reference Network for Rare Immunodeficiency,Autoinflammatory and Autoimmune Diseases(project ID No.739543).
文摘Calcium signaling is essential for lymphocyte activation, with genetic disruptions of store-operated calcium (Ca^(2+)) entry resulting in severe immunodeficiency. The inositol 1,4,5-trisphosphate receptor (IP_(3)R), a homo- or heterotetramer of the IP_(3)R1-3 isoforms, amplifies lymphocyte signaling by releasing Ca^(2+) from endoplasmic reticulum stores following antigen stimulation. Although knockout of all IP_(3)R isoforms in mice causes immunodeficiency, the seeming redundancy of the isoforms is thought to explain the absence of variants in human immunodeficiency. In this study, we identified compound heterozygous variants of ITPR3 (a gene encoding IP_(3)R subtype 3) in two unrelated Caucasian patients presenting with immunodeficiency. To determine whether ITPR3 variants act in a nonredundant manner and disrupt human immune responses, we characterized the Ca^(2+) signaling capacity, the lymphocyte response, and the clinical phenotype of these patients. We observed disrupted Ca^(2+) signaling in patient-derived fibroblasts and immune cells, with abnormal proliferation and activation responses following T-cell receptor stimulation. Reconstitution of IP_(3)R3 in IP_(3)R knockout cell lines led to the identification of variants as functional hypomorphs that showed reduced ability to discriminate between homeostatic and induced states, validating a genotype–phenotype link. These results demonstrate a functional link between defective endoplasmic reticulum Ca^(2+) channels and immunodeficiency and identify IP_(3)Rs as diagnostic targets for patients with specific inborn errors of immunity. These results also extend the known cause of Ca^(2+)-associated immunodeficiency from store-operated entry to impaired Ca^(2+) mobilization from the endoplasmic reticulum, revealing a broad sensitivity of lymphocytes to genetic defects in Ca^(2+) signaling.
基金the Chinese Ministry of Science and Technology(No.2018YFA0107603 to Q.C.Z.)the National Natural Science Foundation ofChina(Nos.91740204 and 31761163007 to Q.C.Z.)+1 种基金the National Natural Science Foundation of China(No.61772197 to T.J.)the National Key Research and Development Program of China(No.2018YFC0910404 to T.J.)。
文摘Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain enigmatic.PARIS(Psoralen Analysis of RNA Interactions and Structures)is a recently developed high-throughput sequencing-based approach that enables direct capture of RNA duplex structures in vivo.However,the existence of incompatible,fuzzy pairing information obstructs the integration of PARIS data with the existing tools for reconstructing RNA secondary structure models at the single-base resolution.Methods:We introduce IRIS,a method for predicting RNA secondary structure ensembles based on PARIS data.IRIS generates a large set of candidate RNA secondary structure models under the guidance of redistributed PARIS reads and then uses a Bayesian model to identify the optimal ensemble,according to both thermodynamic principles and PARIS data.Results:The predicted RNA structure ensembles by IRIS have been verified based on evolutionary conservation information and consistency with other experimental RNA structural data.HIS is implemented in Python and freely available at http://iris.zhanglab.net.Conclusion:IRIS capitalizes upon PARIS data to improve the prediction of in vivo RNA secondary structure ensembles.We expect that IRIS will enhance the application of the PARIS technology and shed more insight on in vivo RNA secondary structures.
