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David D, Fino J, Oliveira R, Dória S, Morton CC. Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage. Gene 2023; 887:147737. [PMID: 37625567 DOI: 10.1016/j.gene.2023.147737] [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: 07/18/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Naturally occurring balanced, unbalanced, and complex chromosomal rearrangements have been reported to cause pathogenic genomic or genetic variants leading to infertility and recurrent miscarriage. Therefore, balanced chromosomal rearrangements were used as genomic signposts for identification of candidate genes or genomic loci associated with male infertility due to defects of spermatogenesis, or with recurrent miscarriage. In three male probands, structural chromosomal variants and copy number variants were identified at nucleotide resolution by long-insert genome sequencing approaches and Sanger sequencing. The pathogenic potential of these and affected candidate genes was assessed based on convergent genomic and genotype-phenotype correlation data. Identification of balanced chromosomal rearrangement breakpoints and interpretation in the context of their genomic background of structural and copy number variants led us to conclude that the infertility due to oligoasthenozoospermia and oligozoospermia is most likely associated with a position effect on YIPF5 and SPATC1L, respectively. In a third proband with intellectual disability and recurrent miscarriage, disruption of CAMK2B causing autosomal dominant, intellectual developmental disorder 54 and increased meiotic segregation during gametogenesis of a der(22) are responsible for the reported phenotype. Our data further support the existence of loci at 5q23 and 21q22.3 for these spermatogenesis defects and highlight the importance of the naturally occurring balanced chromosomal rearrangements for assessment of the pathogenic mechanisms. Furthermore, we show comorbidities due to the same balanced chromosomal rearrangement caused by different pathogenic mechanisms.
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Affiliation(s)
- Dezső David
- Department of Human Genetics, National Institute of Health Doctor Ricardo Jorge, 1649-016 Lisbon, Portugal.
| | - Joana Fino
- Department of Human Genetics, National Institute of Health Doctor Ricardo Jorge, 1649-016 Lisbon, Portugal
| | - Renata Oliveira
- Medical Genetics Service, University Hospital Centre of São João, 4200-319 Porto, Portugal
| | - Sofia Dória
- Department of Pathology, Genetics Service, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal; I3S-Health Research and Innovation Institute, University of Porto, 4200-135 Porto, Portugal
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Manchester Centre for Audiology and Deafness (ManCAD), University of Manchester M13 9PL, UK
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2
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Angelotti T. Exploring the eukaryotic Yip and REEP/Yop superfamily of membrane-shaping adapter proteins (MSAPs): A cacophony or harmony of structure and function? Front Mol Biosci 2022; 9:912848. [PMID: 36060263 PMCID: PMC9437294 DOI: 10.3389/fmolb.2022.912848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Polytopic cargo proteins are synthesized and exported along the secretory pathway from the endoplasmic reticulum (ER), through the Golgi apparatus, with eventual insertion into the plasma membrane (PM). While searching for proteins that could enhance cell surface expression of olfactory receptors, a new family of proteins termed “receptor expression-enhancing proteins” or REEPs were identified. These membrane-shaping hairpin proteins serve as adapters, interacting with intracellular transport machinery, to regulate cargo protein trafficking. However, REEPs belong to a larger family of proteins, the Yip (Ypt-interacting protein) family, conserved in yeast and higher eukaryotes. To date, eighteen mammalian Yip family members, divided into four subfamilies (Yipf, REEP, Yif, and PRAF), have been identified. Yeast research has revealed many intriguing aspects of yeast Yip function, functions that have not completely been explored with mammalian Yip family members. This review and analysis will clarify the different Yip family nomenclature that have encumbered prior comparisons between yeast, plants, and eukaryotic family members, to provide a more complete understanding of their interacting proteins, membrane topology, organelle localization, and role as regulators of cargo trafficking and localization. In addition, the biological role of membrane shaping and sensing hairpin and amphipathic helical domains of various Yip proteins and their potential cellular functions will be described. Lastly, this review will discuss the concept of Yip proteins as members of a larger superfamily of membrane-shaping adapter proteins (MSAPs), proteins that both shape membranes via membrane-sensing and hairpin insertion, and well as act as adapters for protein-protein interactions. MSAPs are defined by their localization to specific membranes, ability to alter membrane structure, interactions with other proteins via specific domains, and specific interactions/effects on cargo proteins.
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3
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Lin CY, Achor D, Levy A. Intracellular Life Cycle of ' Candidatus Liberibacter asiaticus' Inside Psyllid Gut Cells. PHYTOPATHOLOGY 2022; 112:145-153. [PMID: 34689612 DOI: 10.1094/phyto-07-21-0301-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
'Candidatus Liberibacter asiaticus' (CLas), the devastating pathogen related to Huanglongbing (HLB), is a phloem-limited, fastidious, insect-borne bacterium. Rapid spread of HLB disease relies on CLas-efficient propagation in the vector, the Asian citrus psyllid Diaphorina citri, in a circulative manner. Understanding the intracellular lifecycle of CLas in psyllid midgut, the major organ for CLas transmission, is fundamental to improving current management strategies. Using a microscopic approach within CLas-infected insect midgut, we observed the entry of CLas into gut cells inside vesicles, termed Liberibacter-containing vacuoles (LCVs), by endocytosis. Endocytosis is followed by the formation of endoplasmic reticulum-related and replication permissive vacuoles (rLCVs). Additionally, we observed the formation of double membrane autophagosome-like structure, termed autophagy-related vacuole (aLCV). Vesicles containing CLas egress from aLCV and fuse with the cell membrane. Immunolocalization studies showed that CLas uses endocytosis- and exocytosis-like mechanisms that mediates bacterial invasion and egress. Upregulation of autophagy-related genes indicated subversion of host autophagy by CLas in psyllid vector to promote infection. These results indicate that CLas interacts with host cellular machineries to undergo a multistage intracellular cycle through endocytic, secretory, autophagic, and exocytic pathways via complex machineries. Potential tactics for HLB control can be made depending on further investigations on the knowledge of the molecular mechanisms of CLas intracellular cycle.
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Affiliation(s)
- Chun-Yi Lin
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Diann Achor
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Amit Levy
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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4
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De Franco E, Lytrivi M, Ibrahim H, Montaser H, Wakeling MN, Fantuzzi F, Patel K, Demarez C, Cai Y, Igoillo-Esteve M, Cosentino C, Lithovius V, Vihinen H, Jokitalo E, Laver TW, Johnson MB, Sawatani T, Shakeri H, Pachera N, Haliloglu B, Ozbek MN, Unal E, Yıldırım R, Godbole T, Yildiz M, Aydin B, Bilheu A, Suzuki I, Flanagan SE, Vanderhaeghen P, Senée V, Julier C, Marchetti P, Eizirik DL, Ellard S, Saarimäki-Vire J, Otonkoski T, Cnop M, Hattersley AT. YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress. J Clin Invest 2021; 130:6338-6353. [PMID: 33164986 PMCID: PMC7685733 DOI: 10.1172/jci141455] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022] Open
Abstract
Neonatal diabetes is caused by single gene mutations reducing pancreatic β cell number or impairing β cell function. Understanding the genetic basis of rare diabetes subtypes highlights fundamental biological processes in β cells. We identified 6 patients from 5 families with homozygous mutations in the YIPF5 gene, which is involved in trafficking between the endoplasmic reticulum (ER) and the Golgi. All patients had neonatal/early-onset diabetes, severe microcephaly, and epilepsy. YIPF5 is expressed during human brain development, in adult brain and pancreatic islets. We used 3 human β cell models (YIPF5 silencing in EndoC-βH1 cells, YIPF5 knockout and mutation knockin in embryonic stem cells, and patient-derived induced pluripotent stem cells) to investigate the mechanism through which YIPF5 loss of function affects β cells. Loss of YIPF5 function in stem cell–derived islet cells resulted in proinsulin retention in the ER, marked ER stress, and β cell failure. Partial YIPF5 silencing in EndoC-βH1 cells and a patient mutation in stem cells increased the β cell sensitivity to ER stress–induced apoptosis. We report recessive YIPF5 mutations as the genetic cause of a congenital syndrome of microcephaly, epilepsy, and neonatal/early-onset diabetes, highlighting a critical role of YIPF5 in β cells and neurons. We believe this is the first report of mutations disrupting the ER-to-Golgi trafficking, resulting in diabetes.
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Affiliation(s)
- Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Maria Lytrivi
- ULB Center for Diabetes Research and.,Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hossam Montaser
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthew N Wakeling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Federica Fantuzzi
- ULB Center for Diabetes Research and.,Endocrinology and Metabolism, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Kashyap Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | | | - Ying Cai
- ULB Center for Diabetes Research and
| | | | | | - Väinö Lithovius
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Matthew B Johnson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | | | | | | | | | | | - Edip Unal
- Dicle University, Faculty of Medicine, Department of Pediatric Endocrinology, Diyarbakır, Turkey
| | - Ruken Yıldırım
- Dicle University, Faculty of Medicine, Department of Pediatric Endocrinology, Diyarbakır, Turkey
| | | | - Melek Yildiz
- Istanbul University, Istanbul Faculty of Medicine, Department of Pediatric Endocrinology, Istanbul, Turkey
| | - Banu Aydin
- Kanuni Sultan Suleyman Training and Research Hospital, Department of Pediatric Endocrinology, Istanbul, Turkey
| | - Angeline Bilheu
- Institute of Interdisciplinary Research (IRIBHM), ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Ikuo Suzuki
- Institute of Interdisciplinary Research (IRIBHM), ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Sarah E Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Pierre Vanderhaeghen
- Institute of Interdisciplinary Research (IRIBHM), ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.,Welbio, Université Libre de Bruxelles, Brussels, Belgium
| | - Valérie Senée
- Université de Paris, Faculté de Médecine Paris-Diderot, U958, Paris, France
| | - Cécile Julier
- Université de Paris, Faculté de Médecine Paris-Diderot, U958, Paris, France
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Decio L Eizirik
- ULB Center for Diabetes Research and.,Welbio, Université Libre de Bruxelles, Brussels, Belgium.,Indiana Biosciences Research Institute, Indianapolis, Indiana, USA
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Miriam Cnop
- ULB Center for Diabetes Research and.,Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, United Kingdom
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5
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Mareninova OA, Jia W, Gretler SR, Holthaus CL, Thomas DDH, Pimienta M, Dillon DL, Gukovskaya AS, Gukovsky I, Groblewski GE. Transgenic expression of GFP-LC3 perturbs autophagy in exocrine pancreas and acute pancreatitis responses in mice. Autophagy 2020; 16:2084-2097. [PMID: 31942816 PMCID: PMC7595606 DOI: 10.1080/15548627.2020.1715047] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 12/25/2019] [Accepted: 01/08/2020] [Indexed: 12/20/2022] Open
Abstract
Pancreatitis is a common, sometimes fatal, disease of exocrine pancreas, initiated by damaged acinar cells. Recent studies implicate disordered macroautophagy/autophagy in pancreatitis pathogenesis. ATG8/LC3 protein is critical for autophagosome formation and a widely used marker of autophagic vacuoles. Transgenic GFP-LC3 mice are a valuable tool to investigate autophagy ; however, comparison of homeostatic and disease responses between GFP-LC3 and wild-type (WT) mice has not been done. We examined the effects of GFP-LC3 expression on autophagy, acinar cell function, and experimental pancreatitis. Unexpectedly, GFP-LC3 expression markedly increased endogenous LC3-II level in pancreas, caused by downregulation of ATG4B, the protease that deconjugates/delipidates LC3-II. By contrast, GFP-LC3 expression had lesser or no effect on autophagy in liver, lung and spleen. Autophagic flux analysis showed that autophagosome formation in GFP-LC3 acinar cells increased 3-fold but was not fully counterbalanced by increased autophagic degradation. Acinar cell (ex vivo) pancreatitis inhibited autophagic flux in WT and essentially blocked it in GFP-LC3 cells. In vivo pancreatitis caused autophagy impairment in WT mice, manifest by upregulation of LC3-II and SQSTM1/p62, increased number and size of autophagic vacuoles, and decreased level of TFEB, all of which were exacerbated in GFP-LC3 mice. GFP-LC3 expression affected key pancreatitis responses; most dramatically, it worsened increases in serum AMY (amylase), a diagnostic marker of acute pancreatitis, in several mouse models. The results emphasize physiological importance of autophagy for acinar cell function, demonstrate organ-specific effects of GFP-LC3 expression, and indicate that application of GFP-LC3 mice in disease models should be done with caution.Abbreviations: AP: acute pancreatitis; Arg-AP: L-arginine-induced acute pancreatitis; ATG: autophagy-related (protein); AVs: autophagic vacuoles; CCK: cholecystokinin-8; CDE: choline-deficient, D,L-ethionine supplemented diet; CER: caerulein (ortholog of CCK); CTSB: cathepsin B; CTSD: cathepsin D; CTSL: cathepsin L; ER: endoplasmic reticulum; LAMP: lysosomal-associated membrane protein; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; TEM: transmission electron microscopy; TFEB: transcription factor EB; ZG: zymogen granule(s).
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Affiliation(s)
- Olga A. Mareninova
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Pancreatic Research Group, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Wenzhuo Jia
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Department of General Surgery, Beijing Hospital, National Centre of Gerontology, Beijing, China
| | - Sophie R. Gretler
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Pancreatic Research Group, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Conner L. Holthaus
- Department of Nutritional Sciences, University of Wisconsin, Madison, WI, USA
| | - Diana D. H. Thomas
- Department of Nutritional Sciences, University of Wisconsin, Madison, WI, USA
| | - Michael Pimienta
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Dustin L. Dillon
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Pancreatic Research Group, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Anna S. Gukovskaya
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Pancreatic Research Group, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Ilya Gukovsky
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Pancreatic Research Group, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Guy E. Groblewski
- Department of Nutritional Sciences, University of Wisconsin, Madison, WI, USA
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6
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Abudurexiti M, Xie H, Jia Z, Zhu Y, Zhu Y, Shi G, Zhang H, Dai B, Wan F, Shen Y, Ye D. Development and External Validation of a Novel 12-Gene Signature for Prediction of Overall Survival in Muscle-Invasive Bladder Cancer. Front Oncol 2019; 9:856. [PMID: 31552180 PMCID: PMC6743371 DOI: 10.3389/fonc.2019.00856] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
Purpose: We aimed to develop and validate a novel gene signature from published data and improve the prediction of survival in muscle-invasive bladder cancer (MIBC). Methods: We searched the published gene signatures associated with the overall survival (OS) of MIBC and compiled all 274 genes to develop a novel gene signature. RNAseq data of TCGA (the Cancer Genome Atlas) bladder cohort were downloaded. All genes were included in a univariate Cox hazard ratio model. We then used a reduced multivariate Cox regression model, which included only genes achieving P < 0.05 in the univariate model. A total of 172 patients at Fudan University Shanghai Cancer Center (FUSCC) and 61 patients from GEO datasets were used as an external validation set. Results: A total of 327 patients in the TCGA cohort were enrolled. We identified 274 genes from eight published papers on the OS of MIBC. Using the TCGA database, we identified 12 genes that correlated with OS (P < 0.05 in both univariate and multivariate analyses). By integrating these genes with the RT-qPCR data in our validation dataset and GEO datasets, we confirmed that the power for predicting OS of the 12-gene panel (AUC of 0.741 and 0.727, respectively) was higher than just clinical data (including gender, age, T stage, grade, and N stage) alone in the TCGA and FUSCC cohort (AUC of 0.667 and 0.631, respectively). Additionally, upon combining the clinical data and 12-gene panel together, the AUC increased to 0.768, 0.757, and 0.88 in the TCGA, FUSCC and GSE13507 cohorts, respectively. Conclusions: Applying published gene signatures and TCGA data, we successfully built and externally validated a novel 12-gene signature for the survival of MIBC.
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Affiliation(s)
- MierXiati Abudurexiti
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Huyang Xie
- Department of Urology, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhongwei Jia
- Department of Medical Oncology, Clinical Medical College of Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, China
| | - Yiping Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yijun Shen
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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7
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Shaik S, Pandey H, Thirumalasetti SK, Nakamura N. Characteristics and Functions of the Yip1 Domain Family (YIPF), Multi-Span Transmembrane Proteins Mainly Localized to the Golgi Apparatus. Front Cell Dev Biol 2019; 7:130. [PMID: 31417902 PMCID: PMC6682643 DOI: 10.3389/fcell.2019.00130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/02/2019] [Indexed: 12/27/2022] Open
Abstract
Yip1 domain family (YIPF) proteins are multi-span, transmembrane proteins mainly localized in the Golgi apparatus. YIPF proteins have been found in virtually all eukaryotes, suggesting that they have essential function(s). Saccharomyces cerevisiae contains four YIPFs: Yip1p, Yif1p, Yip4p, and Yip5p. Early analyses in S. cerevisiae indicated that Yip1p and Yif1p bind to each other and play a role in budding of transport vesicles and/or fusion of vesicles to target membranes. However, the molecular basis of their functions remains unclear. Analysis of YIPF proteins in mammalian cells has yielded significant clues about the function of these proteins. Human cells have nine family members that appear to have overlapping functions. These YIPF proteins are divided into two sub-families: YIPFα/Yip1p and YIPFβ/Yif1p. A YIPFα molecule forms a complex with a specific partner YIPFβ molecule. In the most broadly hypothesized scenario, a basic tetramer complex is formed from two molecules of each partner YIPF protein, and this tetramer forms a higher order oligomer. Three distinct YIPF protein complexes are formed from pairs of YIPFα and YIPFβ proteins. These are differently localized in either the early, middle, or late compartments of the Golgi apparatus and are recycled between adjacent compartments. Because a YIPF protein is predicted to have five transmembrane segments, a YIPF tetramer complex is predicted to have 20 transmembrane segments. This high number of transmembrane segments suggests that YIPF complexes function as channels, transporters, or transmembrane receptors. Here, the evidence from functional studies of YIPF proteins obtained during the last two decades is summarized and discussed.
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Affiliation(s)
- Shaheena Shaik
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Himani Pandey
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Satish Kumar Thirumalasetti
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Department of Biotechnology, Vignan's University, Guntur, India
| | - Nobuhiro Nakamura
- Graduate School of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
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8
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Vasileiou T, Foresti D, Bayram A, Poulikakos D, Ferrari A. Toward Contactless Biology: Acoustophoretic DNA Transfection. Sci Rep 2016; 6:20023. [PMID: 26828312 PMCID: PMC4734324 DOI: 10.1038/srep20023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/21/2015] [Indexed: 01/02/2023] Open
Abstract
Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors.
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Affiliation(s)
- Thomas Vasileiou
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, CH-8092 Zurich, Switzerland
| | - Daniele Foresti
- Harvard University, School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Northwest Labs, B146.40, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Adem Bayram
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, CH-8092 Zurich, Switzerland
| | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, CH-8092 Zurich, Switzerland
| | - Aldo Ferrari
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, CH-8092 Zurich, Switzerland
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9
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Alterio J, Masson J, Diaz J, Chachlaki K, Salman H, Areias J, Al Awabdh S, Emerit MB, Darmon M. Yif1B Is Involved in the Anterograde Traffic Pathway and the Golgi Architecture. Traffic 2015; 16:978-93. [DOI: 10.1111/tra.12306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/03/2015] [Accepted: 06/08/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Jeanine Alterio
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Justine Masson
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Jorge Diaz
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Konstantina Chachlaki
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Haysam Salman
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Julie Areias
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Sana Al Awabdh
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Michel Boris Emerit
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
| | - Michèle Darmon
- INSERM U894; Centre de Psychiatrie et Neurosciences; Paris F-75014 France
- Université Paris Descartes; Sorbonne Paris Cité - Paris 5; UMR U894 Paris F-75014 France
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Yip1B isoform is localized at ER-Golgi intermediate and cis-Golgi compartments and is not required for maintenance of the Golgi structure in skeletal muscle. Histochem Cell Biol 2014; 143:235-43. [PMID: 25208654 DOI: 10.1007/s00418-014-1277-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2014] [Indexed: 10/24/2022]
Abstract
The mechanism of endoplasmic reticulum (ER)-Golgi complex (GC) traffic is conserved from yeast to higher animals, but the architectures and the dynamics of vesicles' traffic between ER and GC vary across cell types and species. Skeletal muscle is a unique tissue in which ER and GC undergo a structural reorganization during differentiation that completely remodels the secretory pathway. In mature skeletal muscle, the ER is turned into sarcoplasmic reticulum, which is composed of junctional and longitudinal regions specialized, respectively, in calcium release and uptake during contraction. During skeletal muscle differentiation, GC acquires a particular fragmented organization as it appears as spots both at the nuclear poles and along the fibers. The ubiquitary-expressed Yip1A isoform has been proposed to be involved in anterograde trafficking from the ER exit sites to the cis-side of the GC and in ER and GC architecture organization. We investigated the role of Yip1 in skeletal muscle. Here we report that, following skeletal muscle development, the expression of the Yip1A decreases and is replaced by the muscle-specific Yip1B isoform. Confocal microscope analysis revealed that in adult skeletal muscle the Yip1B isoform is localized in the ER-Golgi intermediate and cis-Golgi compartments. Finally, skeletal muscle knockdown experiments in vitro and in vivo suggested that Yip1B is not involved in GC structure maintenance.
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