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Nie J, Ma S, Zhang Y, Yu S, Yang J, Li A, Pei D. COPI Vesicle Disruption Inhibits Mineralization via mTORC1-Mediated Autophagy. Int J Mol Sci 2023; 25:339. [PMID: 38203512 PMCID: PMC10779376 DOI: 10.3390/ijms25010339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Bone mineralization is a sophisticated regulated process composed of crystalline calcium phosphate and collagen fibril. Autophagy, an evolutionarily conserved degradation system, whereby double-membrane vesicles deliver intracellular macromolecules and organelles to lysosomes for degradation, has recently been shown to play an essential role in mineralization. However, the formation of autophagosomes in mineralization remains to be determined. Here, we show that Coat Protein Complex I (COPI), responsible for Golgi-to-ER transport, plays a pivotal role in autophagosome formation in mineralization. COPI vesicles were increased after osteoinduction, and COPI vesicle disruption impaired osteogenesis. Mechanistically, COPI regulates autophagy activity via the mTOR complex 1 (mTORC1) pathway, a key regulator of autophagy. Inhibition of mTOR1 rescues the impaired osteogenesis by activating autophagy. Collectively, our study highlights the functional importance of COPI in mineralization and identifies COPI as a potential therapeutic target for treating bone-related diseases.
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Affiliation(s)
| | | | | | | | | | | | - Dandan Pei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China
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Al-Ali AK, Al-Rubaish AM, Alali RA, Almansori MS, Al-Jumaan MA, Alshehri AM, Al-Madan MS, Vatte C, Cherlin T, Young S, Verma SS, Morahan G, Koeleman BPC, Keating BJ. Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts. Sci Rep 2023; 13:21866. [PMID: 38072966 PMCID: PMC10711020 DOI: 10.1038/s41598-023-49105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Genome-wide association studies (GWAS) have yielded significant insights into the genetic architecture of myocardial infarction (MI), although studies in non-European populations are still lacking. Saudi Arabian cohorts offer an opportunity to discover novel genetic variants impacting disease risk due to a high rate of consanguinity. Genome-wide genotyping (GWG), imputation and GWAS followed by meta-analysis were performed based on two independent Saudi Arabian studies comprising 3950 MI patients and 2324 non-MI controls. Meta-analyses were then performed with these two Saudi MI studies and the CardioGRAMplusC4D and UK BioBank GWAS as controls. Meta-analyses of the two Saudi MI studies resulted in 17 SNPs with genome-wide significance. Meta-analyses of all 4 studies revealed 66 loci with genome-wide significance levels of p < 5 × 10-8. All of these variants, except rs2764203, have previously been reported as MI-associated loci or to have high linkage disequilibrium with known loci. One SNP association in Shisa family member 5 (SHISA5) (rs11707229) was evident at a much higher frequency in the Saudi MI populations (> 12% MAF). In conclusion, our results replicated many MI associations, whereas in Saudi-only GWAS (meta-analyses), several new loci were implicated that require future validation and functional analyses.
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Affiliation(s)
- Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, 3144, Dammam, Saudi Arabia.
| | - Abdullah M Al-Rubaish
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Rudaynah A Alali
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed S Almansori
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed A Al-Jumaan
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
- Department of Emergency Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
| | - Abdullah M Alshehri
- Department of Internal Medicine, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Mohammed S Al-Madan
- College of Medicine, Imam Abdulrahman bin Faisal University, 31441, Dammam, Saudi Arabia
- Department of Pediatrics, King Fahd Hospital of the University, 34445, Al-Khobar, Saudi Arabia
| | - ChittiBabu Vatte
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman bin Faisal University, 3144, Dammam, Saudi Arabia
| | - Tess Cherlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sylvia Young
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, 6009, Australia
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, 6009, Australia
| | - Bobby P C Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, 85500/3508 GA, The Netherlands
| | - Brendan J Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Kim N, Kim TH, Kim C, Lee JE, Kang MG, Shin S, Jung M, Kim JS, Mun JY, Rhee HW, Park SY, Shin Y, Yoo JY. Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport. Dev Cell 2023; 58:1950-1966.e8. [PMID: 37816329 DOI: 10.1016/j.devcel.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023]
Abstract
Newly synthesized proteins in the endoplasmic reticulum (ER) are sorted by coat protein complex II (COPII) at the ER exit site en route to the Golgi. Under cellular stresses, COPII proteins become targets of regulation to control the transport. Here, we show that the COPII outer coat proteins Sec31 and Sec13 are selectively sequestered into the biomolecular condensate of SCOTIN/SHISA-5, which interferes with COPII vesicle formation and inhibits ER-to-Golgi transport. SCOTIN is an ER transmembrane protein with a cytosolic intrinsically disordered region (IDR), which is required and essential for the formation of condensates. Upon IFN-γ stimulation, which is a cellular condition that induces SCOTIN expression and condensation, ER-to-Golgi transport was inhibited in a SCOTIN-dependent manner. Furthermore, cancer-associated mutations of SCOTIN perturb its ability to form condensates and control transport. Together, we propose that SCOTIN impedes the ER-to-Golgi transport through its ability to form biomolecular condensates at the ER membrane.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| | - Tae-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jee-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghee Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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Tuerdimaimaiti D, Abuduaini B, Kang S, Jiao J, Li M, Madeniyati W, Tuerdi B, Aili G, Tuerhong R, Kulaxi A. Genome-wide identification and functional analysis of dysregulated alternative splicing profiles in sepsis. J Inflamm (Lond) 2023; 20:31. [PMID: 37749550 PMCID: PMC10521395 DOI: 10.1186/s12950-023-00355-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 08/10/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND An increasing body of evidence now shows that the long-term mortality of patients with sepsis are associated with various sepsis-related immune cell defects. Alternative splicing (AS), as a sepsis-related immune cell defect, is considered as a potential immunomodulatory therapy target to improve patient outcomes. However, our understanding of the role AS plays in sepsis is currently insufficient. AIM This study investigated possible associations between AS and the gene regulatory networks affecting immune cells. We also investigated apoptosis and AS functionality in sepsis pathophysiology. METHODS In this study, we assessed publicly available mRNA-seq data that was obtained from the NCBI GEO dataset (GSE154918), which included a healthy group (HLTY), a mild infection group (INF1), asepsis group (Seps), and a septic shock group (Shock). A total of 79 samples (excluding significant outliers) were identified by a poly-A capture method to generate RNA-seq data. The variable splicing events and highly correlated RNA binding protein (RBP) genes in each group were then systematically analyzed. RESULTS For the first time, we used systematic RNA-seq analysis of sepsis-related AS and identified 1505 variable AS events that differed significantly (p <= 0.01) across the four groups. In the sepsis group, the genes related to significant AS events, such as, SHISA5 and IFI27, were mostly enriched in the cell apoptosis pathway. Furthermore, we identified differential splicing patterns within each of the four groups. Significant differences in the expression of RNA Binding Protein(RBP) genes were observed between the control group and the sepsis group. RBP gene expression was highly correlated with variant splicing events in sepsis, as determined by co-expression analysis; The expression of DDX24, CBFA2T2, NOP, ILF3, DNMT1, FTO, PPRC1, NOLC1 RBPs were significant reduced in sepsis compared to the healthy group. Finally, we constructed an RBP-AS functional network. CONCLUSION Analysis indicated that the RBP-AS functional network serves as a critical post-transcriptional mechanism that regulates the development of sepsis. AS dysregulation is associated with alterations in the regulatory gene expression network that is involved in sepsis. Therefore, the RBP-AS expression network could be useful in refining biomarker predictions in the development of new therapeutic targets for the pathogenesis of sepsis.
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Affiliation(s)
- Dilixiati Tuerdimaimaiti
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Buzukela Abuduaini
- The Intensive Care Unit, The First Affiliated Hospital of Xinjiang Medical University, Wulumuqi, Xinjiang, 830054, China
| | - Shaotao Kang
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Jinliang Jiao
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Mengchen Li
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Wolazihan Madeniyati
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Baihetinisha Tuerdi
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China.
| | - Gulisitan Aili
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Reyila Tuerhong
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
| | - Ajiguli Kulaxi
- Department of RICU, The First Affiliated Hospital of Xinjiang Medical University, 393 South Li Yu Shan Road, Wulumuqi, Xinjiang, 830054, China
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Thi My Nhung T, Phuoc Long N, Diem Nghi T, Suh Y, Hoang Anh N, Jung CW, Minh Triet H, Jung M, Woo Y, Yoo J, Noh S, Kim SJ, Lee SB, Park S, Thomas G, Simmen T, Mun J, Rhee HW, Kwon SW, Park SK. Genome-wide kinase-MAM interactome screening reveals the role of CK2A1 in MAM Ca 2+ dynamics linked to DEE66. Proc Natl Acad Sci U S A 2023; 120:e2303402120. [PMID: 37523531 PMCID: PMC10410754 DOI: 10.1073/pnas.2303402120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/15/2023] [Indexed: 08/02/2023] Open
Abstract
The endoplasmic reticulum (ER) and mitochondria form a unique subcellular compartment called mitochondria-associated ER membranes (MAMs). Disruption of MAMs impairs Ca2+ homeostasis, triggering pleiotropic effects in the neuronal system. Genome-wide kinase-MAM interactome screening identifies casein kinase 2 alpha 1 (CK2A1) as a regulator of composition and Ca2+ transport of MAMs. CK2A1-mediated phosphorylation of PACS2 at Ser207/208/213 facilitates MAM localization of the CK2A1-PACS2-PKD2 complex, regulating PKD2-dependent mitochondrial Ca2+ influx. We further reveal that mutations of PACS2 (E209K and E211K) associated with developmental and epileptic encephalopathy-66 (DEE66) impair MAM integrity through the disturbance of PACS2 phosphorylation at Ser207/208/213. This, in turn, causes the reduction of mitochondrial Ca2+ uptake and the dramatic increase of the cytosolic Ca2+ level, thereby, inducing neurotransmitter release at the axon boutons of glutamatergic neurons. In conclusion, our findings suggest a molecular mechanism that MAM alterations induced by pathological PACS2 mutations modulate Ca2+-dependent neurotransmitter release.
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Affiliation(s)
- Truong Thi My Nhung
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan47392, Republic of Korea
| | - Tran Diem Nghi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Yeongjun Suh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Nguyen Hoang Anh
- College of Pharmacy, Seoul National University, Seoul08826, Republic of Korea
| | - Cheol Woon Jung
- College of Pharmacy, Seoul National University, Seoul08826, Republic of Korea
| | - Hong Minh Triet
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu41062, Republic of Korea
| | - Youngsik Woo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Jinyeong Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Sujin Noh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Soo Jeong Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Su Been Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
| | - Seongoh Park
- School of Mathematics, Statistics and Data Science, Sungshin Women’s University, Seoul02844, Republic of Korea
| | - Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, PA15219
| | - Thomas Simmen
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, ABT6G 2H7, Canada
| | - Jiyoung Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu41062, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul08826, Korea
| | - Sung Won Kwon
- College of Pharmacy, Seoul National University, Seoul08826, Republic of Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang37673, Republic of Korea
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Yun H, Jung M, Lee H, Jung S, Kim T, Kim N, Park SY, Kim WJ, Mun JY, Yoo JY. Homotypic SCOTIN assemblies form ER-endosome membrane contacts and regulate endosome dynamics. EMBO Rep 2023:e56538. [PMID: 37377038 PMCID: PMC10398665 DOI: 10.15252/embr.202256538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
The ER regulates the spatiotemporal organization of endolysosomal systems by membrane contact. In addition to tethering via heterotypic interactions on both organelles, we present a novel ER-endosome tethering mechanism mediated by homotypic interactions. The single-pass transmembrane protein SCOTIN is detected in the membrane of the ER and endosomes. In SCOTIN-knockout (KO) cells, the ER-late endosome contacts are reduced, and the perinuclear positioning of endosomes is disturbed. The cytosolic proline-rich domain (PRD) of SCOTIN forms homotypic assemblies in vitro and is necessary for ER-endosome membrane tethering in cells. A region of 28 amino acids spanning 150-177 within the SCOTIN PRD is essential to elicit membrane tethering and endosomal dynamics, as verified by reconstitution in SCOTIN-KO cells. The assembly of SCOTIN (PRD) is sufficient to mediate membrane tethering, as purified SCOTIN (PRD), but not SCOTIN (PRDΔ150-177), brings two different liposomes closer in vitro. Using organelle-specific targeting of a chimeric PRD domain shows that only the presence on both organellar membranes enables the ER-endosome membrane contact, indicating that the assembly of SCOTIN on heterologous membranes mediates organelle tethering.
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Affiliation(s)
- Hyeri Yun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hojin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Taehyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Won Jong Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
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