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Kalsheker N. PCR Analysis to Identify AAT Gene Promoters and Splice Variants. Methods Mol Biol 2024; 2750:33-39. [PMID: 38108965 DOI: 10.1007/978-1-0716-3605-3_4] [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] [Indexed: 12/19/2023]
Abstract
This chapter explores the methods used for the analysis of alpha1-antitrypsin gene expression. This includes the use of the polymerase chain reaction (PCR), reverse transcriptase-PCR (RT-PCR), and whole transcriptome analysis combined with parallel DNA sequencing to understand the processes involved in AAT expression.
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Lee EJ, Noh SJ, Choi H, Kim MW, Kim SJ, Seo YA, Jeong JE, Shin I, Kim JS, Choi JK, Cho DY, Chang S. Comparative RNA-Seq Analysis Revealed Tissue-Specific Splicing Variations during the Generation of the PDX Model. Int J Mol Sci 2023; 24:17001. [PMID: 38069324 PMCID: PMC10707456 DOI: 10.3390/ijms242317001] [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: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Tissue-specific gene expression generates fundamental differences in the function of each tissue and affects the characteristics of the tumors that are created as a result. However, it is unclear how much the tissue specificity is conserved during grafting of the primary tumor into an immune-compromised mouse model. Here, we performed a comparative RNA-seq analysis of four different primary-patient derived xenograft (PDX) tumors. The analysis revealed a conserved RNA biotype distribution of primary-PDX pairs, as revealed by previous works. Interestingly, we detected significant changes in the splicing pattern of PDX, which was mainly comprised of skipped exons. This was confirmed by splicing variant-specific RT-PCR analysis. On the other hand, the correlation analysis for the tissue-specific genes indicated overall strong positive correlations between the primary and PDX tumor pairs, with the exception of gastric cancer cases, which showed an inverse correlation. These data propose a tissue-specific change in splicing events during PDX formation as a variable factor that affects primary-PDX integrity.
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Affiliation(s)
- Eun Ji Lee
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Seung-Jae Noh
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Huiseon Choi
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Min Woo Kim
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Su Jin Kim
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Yeon Ah Seo
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Ji Eun Jeong
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
| | - Inkyung Shin
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Jong-Seok Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea; (J.-S.K.); (J.-K.C.)
| | - Jong-Kwon Choi
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea; (J.-S.K.); (J.-K.C.)
| | - Dae-Yeon Cho
- PentaMedix Co., Ltd., Seongnam 13449, Republic of Korea; (S.-J.N.); (H.C.); (D.-Y.C.)
| | - Suhwan Chang
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea; (E.J.L.); (M.W.K.); (S.J.K.); (Y.A.S.); (J.E.J.)
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Maslakova AA, Golyshev SA, Potashnikova DM, Moisenovich AM, Orlovsky IV, Smirnova OV, Rubtsov MA. SERPINA1 long transcripts produce non-secretory alpha1-antitrypsin isoform: In vitro translation in living cells. Int J Biol Macromol 2023; 241:124433. [PMID: 37086761 DOI: 10.1016/j.ijbiomac.2023.124433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/24/2023]
Abstract
SERPINA1 is a well-studied serpin gene due to its dramatic impact on human health. Translation initiation at the main SERPINA1 start codon produces the only known alpha1-antitrypsin (AAT) isoform intended for secretion. AAT performs essential functions by inhibiting proteases and modulating immunity. However, SERPINA1 expression at the level of translation is not sufficiently studied. Here we hypothesize that the main SERPINA1 ORF can be alternatively translated, producing a non-secretory AAT isoform by either masking or excluding a signal peptide. We defined SERPINA1 long mRNA isoforms specific for prostate (DU145) and liver (HepG2) cell lines and studied their individual expression by in vitro assay. We found that all long transcripts produce both glycosylated secretory AAT-eGFP fusion protein and non-glycosylated intracellular AAT-eGFP (initiated from an alternative AUG-2 start codon), with the proportion regulated by the SERPINA1 5'-UTR. Both fusion proteins localize to distinct cellular compartments: in contrast to a fusion with the secretory AAT accumulating in the ER, the intracellular one exhibits nuclear-cytoplasmic shuttling. We detected putative endogenous AAT isoform enriching the nuclear speckles. CONCLUSION: Alternative translation initiation might be a mechanism through which SERPINA1 expands the biological diversity of its protein products. Our findings open up new prospects for the study of SERPINA1 gene expression.
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Affiliation(s)
- A A Maslakova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia.
| | - S A Golyshev
- A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - D M Potashnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - A M Moisenovich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - I V Orlovsky
- Research Institute of Molecular and Cellular Medicine, Рeoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya, Moscow 117198, Russia
| | - O V Smirnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - M A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya, Moscow 119991, Russia
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4
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Afsharinasab M, Akbari AH, Mirzaei V, Mahmoodi M, Hajizadeh MR, Amri J, Khoshdel A. The investigation of the frequency of the alpha-1-antitrypsin phenotype in patients with liver cirrhosis. Horm Mol Biol Clin Investig 2022; 43:397-403. [PMID: 35973212 DOI: 10.1515/hmbci-2022-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/23/2022] [Indexed: 01/04/2023]
Abstract
OBJECTIVES Alpha-1-antitrypsin (AAT) has different phenotypes. Evidence suggests that the abundance of each of these phenotypes may be associated with a disease. The purpose of this study was to evaluate the frequency of AAT phenotypes in patients with liver cirrhosis as well as in healthy individuals. METHODS In this study, 42 patients with liver cirrhosis were selected. The results of the previous research done by the researcher on healthy individuals were used to construct the control group. After obtaining informed consent, 5 mL of fasting venous blood sample was taken, and phenotypes were analyzed by isoelectric focusing. Data were analyzed using Chi-square and Fisher's exact tests at a significant level of 0.05. RESULTS The results of this study indicated that all 42 healthy subjects had an MM allele (100%). However, among 42 patients, 35 (83.3%) had an MM allele, 5 (11.9%) had an MS allele, and 2 (4.8%) had MZ allele. The difference between the two groups was significant (p=0.02). There was no difference between men and women in the allele type (p=0.557). CONCLUSIONS This study revealed that MS and MZ alleles were observed only in patients with liver cirrhosis, and none of these alleles were found in healthy subjects. Therefore, MS and MZ alleles can be further investigated as risk factors for liver cirrhosis.
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Affiliation(s)
- Mehdi Afsharinasab
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Hossein Akbari
- Molecular Medicine Research Center, Institute of Basic Medical Sciences Research, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Vahid Mirzaei
- Department of Internal Medicine, School of Medicine, and Physiology-Pharmacology Research Center, Ali Ibn Abitaleb Educational and Tretment Hospital, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mehdi Mahmoodi
- Molecular Medicine Research Center, Institute of Basic Medical Sciences Research, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.,Department of Clinical Biochemistry, Afzalipoor Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Reza Hajizadeh
- Molecular Medicine Research Center, Institute of Basic Medical Sciences Research, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.,Department of Clinical Biochemistry, Faculty of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Jamal Amri
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Khoshdel
- Department of Clinical Biochemistry, Nervous System Stem Cells Research Center, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Department of Clinical Biochemistry, Faculty of Medicine, and Pistachio Safety Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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Ghosh AJ, Hobbs BD. Recent advancements in understanding the genetic involvement of alpha-1 antitrypsin deficiency associated lung disease: a look at future precision medicine approaches. Expert Rev Respir Med 2022; 16:173-182. [PMID: 35025710 PMCID: PMC8983484 DOI: 10.1080/17476348.2022.2027755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Alpha-1 antitrypsin deficiency occurs in individuals with deleterious genetic mutations on both chromosomes (maternal and paternal) in SERPINA1, the gene encoding the alpha-1 antitrypsin protein. There has been substantial progress in understanding the genetic variation that underlies the heterogeneous penetrance of lung disease in alpha-1 antitrypsin deficiency. AREAS COVERED This review will cover SERPINA1 gene structure and genetic variation, population genetics, genome-wide genetic modifiers of lung disease, alternative mechanisms of disease, and emerging therapeutics - including gene and cell therapy - related to alpha-1 antitrypsin deficiency-associated lung disease. EXPERT OPINION There remains ample opportunity to employ precision medicine in the diagnosis, prognosis, and therapy of alpha-1 antitrypsin deficiency-associated lung disease. In particular, a genome-wide association study and subsequent polygenic risk score is an important first step in identifying genome-wide genetic modifiers contributing to the variability of lung disease in severe alpha-1 antitrypsin deficiency.
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Affiliation(s)
- Auyon J. Ghosh
- Assistant Professor of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, SUNY Upstate Medical University, 750 E. Adams St, Syracuse, NY, 13210
| | - Brian D. Hobbs
- Assistant Professor of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Boston, MA, 02115,Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital,Harvard Medical School
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Padilla-Godínez FJ, Ramos-Acevedo R, Martínez-Becerril HA, Bernal-Conde LD, Garrido-Figueroa JF, Hiriart M, Hernández-López A, Argüero-Sánchez R, Callea F, Guerra-Crespo M. Protein Misfolding and Aggregation: The Relatedness between Parkinson's Disease and Hepatic Endoplasmic Reticulum Storage Disorders. Int J Mol Sci 2021; 22:ijms222212467. [PMID: 34830348 PMCID: PMC8619695 DOI: 10.3390/ijms222212467] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/21/2022] Open
Abstract
Dysfunction of cellular homeostasis can lead to misfolding of proteins thus acquiring conformations prone to polymerization into pathological aggregates. This process is associated with several disorders, including neurodegenerative diseases, such as Parkinson’s disease (PD), and endoplasmic reticulum storage disorders (ERSDs), like alpha-1-antitrypsin deficiency (AATD) and hereditary hypofibrinogenemia with hepatic storage (HHHS). Given the shared pathophysiological mechanisms involved in such conditions, it is necessary to deepen our understanding of the basic principles of misfolding and aggregation akin to these diseases which, although heterogeneous in symptomatology, present similarities that could lead to potential mutual treatments. Here, we review: (i) the pathological bases leading to misfolding and aggregation of proteins involved in PD, AATD, and HHHS: alpha-synuclein, alpha-1-antitrypsin, and fibrinogen, respectively, (ii) the evidence linking each protein aggregation to the stress mechanisms occurring in the endoplasmic reticulum (ER) of each pathology, (iii) a comparison of the mechanisms related to dysfunction of proteostasis and regulation of homeostasis between the diseases (such as the unfolded protein response and/or autophagy), (iv) and clinical perspectives regarding possible common treatments focused on improving the defensive responses to protein aggregation for diseases as different as PD, and ERSDs.
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Affiliation(s)
- Francisco J. Padilla-Godínez
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Rodrigo Ramos-Acevedo
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Hilda Angélica Martínez-Becerril
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Luis D. Bernal-Conde
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Jerónimo F. Garrido-Figueroa
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Marcia Hiriart
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
| | - Adriana Hernández-López
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Rubén Argüero-Sánchez
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
| | - Francesco Callea
- Department of Histopathology, Bugando Medical Centre, Catholic University of Healthy and Allied Sciences, Mwanza 1464, Tanzania;
| | - Magdalena Guerra-Crespo
- Neurosciences Division, Cell Physiology Institute, National Autonomous University of Mexico, Mexico City 04510, Mexico; (F.J.P.-G.); (R.R.-A.); (H.A.M.-B.); (L.D.B.-C.); (J.F.G.-F.); (M.H.)
- Regenerative Medicine Laboratory, Department of Surgery, Faculty of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico; (A.H.-L.); (R.A.-S.)
- Correspondence:
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Lackey L, Coria A, Ghosh AJ, Grayeski P, Hatfield A, Shankar V, Platig J, Xu Z, Ramos SBV, Silverman EK, Ortega VE, Cho MH, Hersh CP, Hobbs BD, Castaldi P, Laederach A. Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease. PLoS Genet 2021; 17:e1009912. [PMID: 34784346 PMCID: PMC8631626 DOI: 10.1371/journal.pgen.1009912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/30/2021] [Accepted: 10/25/2021] [Indexed: 01/07/2023] Open
Abstract
α1-anti-trypsin (A1AT), encoded by SERPINA1, is a neutrophil elastase inhibitor that controls the inflammatory response in the lung. Severe A1AT deficiency increases risk for Chronic Obstructive Pulmonary Disease (COPD), however, the role of A1AT in COPD in non-deficient individuals is not well known. We identify a 2.1-fold increase (p = 2.5x10-6) in the use of a distal poly-adenylation site in primary lung tissue RNA-seq in 82 COPD cases when compared to 64 controls and replicate this in an independent study of 376 COPD and 267 controls. This alternative polyadenylation event involves two sites, a proximal and distal site, 61 and 1683 nucleotides downstream of the A1AT stop codon. To characterize this event, we measured the distal ratio in human primary tissue short read RNA-seq data and corroborated our results with long read RNA-seq data. Integrating these results with 3' end RNA-seq and nanoluciferase reporter assay experiments we show that use of the distal site yields mRNA transcripts with over 50-fold decreased translation efficiency and A1AT expression. We identified seven RNA binding proteins using enhanced CrossLinking and ImmunoPrecipitation precipitation (eCLIP) with one or more binding sites in the SERPINA1 3' UTR. We combined these data with measurements of the distal ratio in shRNA knockdown experiments, nuclear and cytoplasmic fractionation, and chemical RNA structure probing. We identify Quaking Homolog (QKI) as a modulator of SERPINA1 mRNA translation and confirm the role of QKI in SERPINA1 translation with luciferase reporter assays. Analysis of single-cell RNA-seq showed differences in the distribution of the SERPINA1 distal ratio among hepatocytes, macrophages, αβ-Tcells and plasma cells in the liver. Alveolar Type 1,2, dendritic cells and macrophages also vary in their distal ratio in the lung. Our work reveals a complex post-transcriptional mechanism that regulates alternative polyadenylation and A1AT expression in COPD.
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Affiliation(s)
- Lela Lackey
- Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Aaztli Coria
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Auyon J. Ghosh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Phil Grayeski
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Abigail Hatfield
- Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Vijay Shankar
- Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - John Platig
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zhonghui Xu
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Silvia B. V. Ramos
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Victor E. Ortega
- Department of Internal Medicine, Division of Respiratory Medicine, Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brian D. Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Internal Medicine and Primary Care, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
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8
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Rotondo JC, Aquila G, Oton-Gonzalez L, Selvatici R, Rizzo P, De Mattei M, Pavasini R, Tognon M, Campo GC, Martini F. Methylation of SERPINA1 gene promoter may predict chronic obstructive pulmonary disease in patients affected by acute coronary syndrome. Clin Epigenetics 2021; 13:79. [PMID: 33858475 PMCID: PMC8048251 DOI: 10.1186/s13148-021-01066-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 04/03/2021] [Indexed: 12/16/2022] Open
Abstract
Background Diagnostic biomarkers for detecting chronic obstructive pulmonary disease (COPD) in acute coronary syndrome (ACS) patients are not available. SERPINA1, coding for the most potent circulating anti-inflammatory protein in the lung, has been found to be differentially methylated in blood cells from COPD patients. This study aimed to investigate the methylation profile of SERPINA1 in blood cells from ACS patients, with (COPD+) or without COPD (COPD−). Methods Blood samples were from 115 ACS patients, including 30 COPD+ and 85 COPD− according to lung function phenotype, obtained with spirometry. DNA treated with sodium bisulfite was PCR-amplified at SERPINA1 promoter region. Methylation analysis was carried out by sequencing the PCR products. Lymphocytes count in ACS patients was recorded at hospital admission and discharge. Results SERPINA1 was hypermethylated in 24/30 (80%) COPD+ and 48/85 (56.5%) COPD− (p < 0.05). Interestingly, at hospital discharge, lymphocytes count was higher in COPD− patients carrying SERPINA1 hypermethylated (1.98 × 103 ± 0.6 cell/µl) than in COPD− carrying SERPINA1 hypomethylated (1.7 × 103 ± 0.48 cell/µl) (p < 0.05). Conclusions SERPINA1 is hypermethylated in blood cells from COPD+ patients. COPD− carrying SERPINA1 hypermethylated and high lymphocytes count may be at risk of COPD development. Therefore, SERPINA1 hypermethylation may represent a potential biomarker for predicting COPD development in ACS patients.
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Affiliation(s)
| | - Giorgio Aquila
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | | | - Rita Selvatici
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Paola Rizzo
- Department of Translational Medicine and for Romagna, University of Ferrara, Ferrara, Italy.,Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 70 Eliporto Street, 44121, Ferrara, Italy
| | - Monica De Mattei
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rita Pavasini
- Cardiology Unit, Azienda Ospedaliera Universitaria Di Ferrara, Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | | | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy. .,Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 70 Eliporto Street, 44121, Ferrara, Italy.
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9
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Niemietz C, Bezerra F, Almeida MR, Guo S, Monia BP, Saraiva MJ, Schütz P, Schmidt HHJ, Zibert A. SERPINA1 modulates expression of amyloidogenic transthyretin. Exp Cell Res 2020; 395:112217. [PMID: 32768500 DOI: 10.1016/j.yexcr.2020.112217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022]
Abstract
Hereditary transthyretin amyloidosis (ATTR) is caused by amyloid deposition of misfolded transthyretin (TTR) in various tissues. Recently, reduction of circulating serum TTR, achieved via silencing oligonucleotides, was introduced as therapy of ATTR amyloidosis. We explored the impact of Serpin Family A Member 1 (SERPINA1) on TTR mRNA and protein expression. Oncostatin M (OSM) induced SERPINA1 in hepatoma cells and mice, while concomitantly TTR expression was significantly reduced. SERPINA1 knockdown resulted in specific elevated TTR expression in hepatoma cells; however other genes belonging to the group of acute phase proteins were unaffected. In mice, serum TTR was elevated after mSERPINA1 knockdown throughout antisense treatment. Following SERPINA1 knockdown, TTR deposition in several tissues, including dorsal root ganglia and intestine, was found to be increased, however numbers did not exceed significance levels. The data suggest that SERPINA1 is a co-factor of TTR expression. Our findings provide novel insight in the regulation of TTR and reveal a role of SERPINA1 in the pathogenesis of ATTR amyloidosis.
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Affiliation(s)
- Christoph Niemietz
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
| | - Filipa Bezerra
- i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular,and ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Rosário Almeida
- i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular,and ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | | | | | - Maria João Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, IBMC - Instituto de Biologia Molecular e Celular,and ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Paula Schütz
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
| | - Hartmut H-J Schmidt
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany
| | - Andree Zibert
- Medizinische Klinik B für Gastroenterologie und Hepatologie, Universitätsklinikum Münster, Münster, Germany.
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10
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Melendez QM, Wooten CJ, Krishnaji ST, Knagge K, Kirchner D, Lopez D. Identification of Novel Proteins Interacting with Proprotein Convertase Subtilisin/Kexin 9. INTERNATIONAL JOURNAL OF BIOMEDICAL INVESTIGATION 2020; 3:123. [PMID: 32587953 PMCID: PMC7316369 DOI: 10.31531/2581-4745.1000123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
High levels of cholesterol, especially as low-density lipoprotein (LDL), are a well-known risk factor for atherosclerotic-related diseases. The key atherogenic property of LDL is its ability to form atherosclerotic plaque. Proprotein convertase subtilisin/kexin-9 (PCSK9) is an indirect regulator of plasma LDL levels by controlling the number of LDL receptor molecules expressed at the plasma membrane, especially in the liver. Herein, we performed a combination of affinity chromatography, mass spectrometry analysis and identification, and gene expression studies to identify proteins that interact with PCSK9. Through these studies, we identified three proteins, alpha-1-antitrypsin (A1AT), alpha-1-microglobulin/bikunin precursor (AMBP), and apolipoprotein H (APOH) expressed by C3A cells that interact with PCSK9. The expression levels of A1AT and APOH increased in cells treated with MITO+ medium, a condition previously shown to affect the function of PCSK9, as compared to treating with Regular (control) medium. However, AMBP expression did not change in response to the treatments. Additional studies are required to determine which of these proteins can modulate the expression/function of PCSK9. The identification of endogenous modulators of PCSK9's function could lead to the development of novel diagnostic tests or treatment options for patients suffering hypercholesterolemia in combination with other chronic metabolic diseases.
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Affiliation(s)
- Quantil M. Melendez
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), College of Arts and Sciences, North Carolina Central University, Durham, USA
| | - Catherine J. Wooten
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), College of Arts and Sciences, North Carolina Central University, Durham, USA
| | | | - Kevin Knagge
- David H Murdock Research Institute, Kannapolis, USA
| | | | - Dayami Lopez
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise (BRITE), College of Arts and Sciences, North Carolina Central University, Durham, USA
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11
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Gómez-Mariano G, Matamala N, Martínez S, Justo I, Marcacuzco A, Jimenez C, Monzón S, Cuesta I, Garfia C, Martínez MT, Huch M, Pérez de Castro I, Posada M, Janciauskiene S, Martínez-Delgado B. Liver organoids reproduce alpha-1 antitrypsin deficiency-related liver disease. Hepatol Int 2019; 14:127-137. [PMID: 31832977 PMCID: PMC6994530 DOI: 10.1007/s12072-019-10007-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/26/2019] [Indexed: 01/12/2023]
Abstract
BACKGROUND AND AIMS Alpha-1 antitrypsin (AAT) is a product of SERPINA1 gene mainly expressed by hepatocytes. Clinically relevant mutations in the SERPINA1 gene, such as Z (Glu342Lys), results in an expression of misfolded AAT protein having high propensity to polymerize, accumulate in hepatocytes and thus to enhance a risk for hepatocyte damage and subsequent liver disease. So far, the relationship between the Z-AAT accumulation and liver cell damage remains not completely understood. We present three-dimensional organoid culture systems, as a novel tool for modeling Z-AAT-related liver diseases. METHODS We have established liver organoids from liver biopsies of patients with homozygous (ZZ) and heterozygous (MZ) deficiency and normal (MM) genotypes of AAT. The features of these organoid models were characterized by analyzing AAT protein secretion and intracellular aggregation in MZ and ZZ genotypes as well as SERPINA1 expression in differentiated cultures. RESULTS Transcriptional analysis of differentiated organoid cultures by RNA-Seq showed hepatocyte-specific gene expression profile. Genes, such as ALB, APOB, CYP3A4 and SERPINA1, were validated and confirmed through quantitative-PCR analysis. The organoids from MZ and ZZ cases showed intracellular aggregation and lower secretion of AAT protein, and lower expression of ALB and APOB, as typically seen in hepatocytes from Z-AAT deficiency patients. Furthermore, organoids responded to external stimulus. Treatment with oncostatin M, a well-known inducer of SERPINA1, increased expression of the full-length transcripts (AAT-1C) as well as the short transcript of AAT (AAT-ST1C4). CONCLUSIONS Liver organoid model recapitulates the key features of Z-AAT deficiency and provides a useful tool for disease modeling.
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Affiliation(s)
- Gema Gómez-Mariano
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
| | - Nerea Matamala
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
| | - Selene Martínez
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
| | - Iago Justo
- General and Digestive Surgery Department, Hospital Doce de Octubre, Madrid, Spain
| | - Alberto Marcacuzco
- General and Digestive Surgery Department, Hospital Doce de Octubre, Madrid, Spain
| | - Carlos Jimenez
- General and Digestive Surgery Department, Hospital Doce de Octubre, Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Cristina Garfia
- Digestive Department, Hospital Doce de Octubre, Madrid, Spain
| | | | - Meritxell Huch
- Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ignacio Pérez de Castro
- Gene Therapy Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Manuel Posada
- Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Centre for Biomedical Network Research on Rare Diseases, CIBERER, Madrid, Spain
| | - Sabina Janciauskiene
- Department of Respiratory Medicine, German Centre for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Beatriz Martínez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Ctra. Majadahonda-Pozuelo Km2,200, 28220 Madrid, Spain
- Institute of Rare Diseases Research, Institute of Health Carlos III (ISCIII), Centre for Biomedical Network Research on Rare Diseases, CIBERER, Madrid, Spain
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12
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Periconceptional undernutrition affects the levels of DNA methylation in the peri-implantation pig endometrium and in embryos. Theriogenology 2018; 123:185-193. [PMID: 30312936 DOI: 10.1016/j.theriogenology.2018.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
Maternal undernutrition during the periconceptional period alters the transcriptomic profile of pig endometrium and embryos. Herein, we tested the hypothesis that restricted maternal consumption by females during the periconceptional period impairs the pattern of DNA methylation in both the endometrium and embryos during the peri-implantation period (Day 15-16 of gestation). Affected genes in restricted-diet-fed pig endometrium and embryos were identified using quantitative methylation-specific PCR and comprised those genes which are known to be important in reproductive, metabolic and epigenetic function, thereby exhibiting altered transcriptomic expression in endometrium and embryos of restricted-diet-fed gilts. Specifically, levels of DNA methylation of selected genes with altered expression in the endometrium included acid phosphatase type 2C (PPAP2C), salivary lipocalin (SAL1), endothelin receptor type B (EDNRB), regulator of G-protein signalling 12 (RGS12), type 4 17β-hydroxysteroid dehydrogenase (HSD17B4), toll-like receptor 3 (TLR3), and adiponectin receptor 1 (ADIPOR1). In embryos, adiponectin receptor 2 (ADIPOR2), prostaglandin-endoperoxide synthase 2 (PTGS2), arachidonate 12-lipoxygenase (ALOX12), progestin and adipoQ receptor family member 7 (PAQR7), progesterone receptor membrane component 2 (PGRMC2), steroidogenic acute regulatory protein (STAR), and serpin family A member 1 (SERPINA1) were altered. Finally, 5 acid phosphatase tartrate resistant (ACP5), high mobility group box 2 (HMGB2), and DNA (cytosine-5)-methyltransferase 1 (DNMT1) were altered in both the endometrium and in embryos. In the endometrium, the methylation levels of ACP5 (regulation of endometrial-conceptus iron transport), RGS12 (protein-coupled receptor signalling), and TLR3 (immune response) were increased, while that of EDNRB (corpus luteum maintenance) was decreased. In embryos, the methylation levels of ADIPOR2 (metabolic homeostasis) and DNMT1 (DNA methylation maintenance) were increased. The levels of methylation in other studied endometrial and embryonic genes were unchanged. DNA methylation levels in both the peri-implantation pig endometrium and embryos may be altered in response to female nutritional restriction.
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13
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Franczak A, Zglejc-Waszak K, Martyniak M, Waszkiewicz EM, Kotwica G. Peri-conceptional nutritional restriction alters transcriptomic profile in the peri-implantation pig embryos. Anim Reprod Sci 2018; 197:305-316. [PMID: 30197056 DOI: 10.1016/j.anireprosci.2018.08.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/17/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022]
Abstract
Restricted nutritional consumption during the peri-conceptional period affects the potential for DNA methylation and alters endometrial transcriptomic profile during the peri-implantation period. The restricted diet fed to females during the peri-conceptional period may affect the transcriptomic profile in peri-implantation embryos. In the present study, the transcriptome of embryos of normal-diet-fed gilts was determined and compared with that in embryos of restricted-diet-fed gilts during the peri-implantation period. The restricted-diet-fed gilts were fed forage, in which the dose of proteins and energy had been reduced by 30% compared to the normal diet (Polish Norms of Nutrition). To clarify the issue Agilent's Porcine (V2) Two-Color Gene Expression Microarray 4 × 44 was used. Analysis of the microarray data revealed that the expression of 787 genes with known biological function were consistently altered (496 up- and 291 down-regulated) in embryos. The accurately annotated genes were organized into five categories and 18 subcategories containing 62 biological pathways. The qPCR analysis of ten selected genes [i.e., 5 acid phosphatase, tartrate resistant (ACP5), high mobility group box 2 (HMGB2), prostaglandin-endoperoxide synthase 2 (PTGS2), arachidonate 12-lipoxygenase (ALOX12), adiponectin receptor 2 (ADIPOR2), DNA (cytosine-5)-methyltransferase 1 (DNMT1), steroidogenic acute regulatory protein (STAR), progesterone receptor membrane component 2 (PGRMC2), progestin and adipoQ receptor family member 7 (PAQR7) and serpin family A member 1 (SERPINA1)] confirmed altered gene expression in embryos of restricted-diet-fed gilts. The insight into embryonic transcriptome indicates that female under-nutrition during the peri-conceptional period may create alterations in the pattern of genes expressed in the peri-implantation embryos.
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Affiliation(s)
- Anita Franczak
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Kamila Zglejc-Waszak
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Marcin Martyniak
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Ewa Monika Waszkiewicz
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
| | - Genowefa Kotwica
- Department of Anatomy and Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowski 1A, 10-719, Olsztyn, Poland.
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14
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Aggarwal N, Koepke J, Matamala N, Martinez-Delgado B, Martinez MT, Golpon H, Stolk J, Janciauskiene S, Koczulla R. Alpha-1 Antitrypsin Regulates Transcriptional Levels of Serine Proteases in Blood Mononuclear Cells. Am J Respir Crit Care Med 2017; 193:1065-7. [PMID: 27128707 DOI: 10.1164/rccm.201510-2062le] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
| | | | | | | | | | | | - Jan Stolk
- 5 Leiden University Medical Center Leiden, the Netherlands
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15
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An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. Proc Natl Acad Sci U S A 2017; 114:E10244-E10253. [PMID: 29109288 PMCID: PMC5703279 DOI: 10.1073/pnas.1706539114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Protein and mRNA expression are in most cases poorly correlated, which suggests that the posttranscriptional regulatory program of a cell is an important component of gene expression. This regulatory network is still poorly understood, including how RNA structure quantitatively contributes to translational control. We present here a series of structural and functional experiments that together allow us to derive a quantitative, structure-dependent model of translation that accurately predicts translation efficiency in reporter assays and primary human tissue for a complex and medically important protein, α-1-antitrypsin. Our model demonstrates the importance of accurate, experimentally derived RNA structural models partnered with Kozak sequence information to explain protein expression and suggests a strategy by which α-1-antitrypsin expression may be increased in diseased individuals. Chronic obstructive pulmonary disease (COPD) affects over 65 million individuals worldwide, where α-1-antitrypsin deficiency is a major genetic cause of the disease. The α-1-antitrypsin gene, SERPINA1, expresses an exceptional number of mRNA isoforms generated entirely by alternative splicing in the 5′-untranslated region (5′-UTR). Although all SERPINA1 mRNAs encode exactly the same protein, expression levels of the individual mRNAs vary substantially in different human tissues. We hypothesize that these transcripts behave unequally due to a posttranscriptional regulatory program governed by their distinct 5′-UTRs and that this regulation ultimately determines α-1-antitrypsin expression. Using whole-transcript selective 2′-hydroxyl acylation by primer extension (SHAPE) chemical probing, we show that splicing yields distinct local 5′-UTR secondary structures in SERPINA1 transcripts. Splicing in the 5′-UTR also changes the inclusion of long upstream ORFs (uORFs). We demonstrate that disrupting the uORFs results in markedly increased translation efficiencies in luciferase reporter assays. These uORF-dependent changes suggest that α-1-antitrypsin protein expression levels are controlled at the posttranscriptional level. A leaky-scanning model of translation based on Kozak translation initiation sequences alone does not adequately explain our quantitative expression data. However, when we incorporate the experimentally derived RNA structure data, the model accurately predicts translation efficiencies in reporter assays and improves α-1-antitrypsin expression prediction in primary human tissues. Our results reveal that RNA structure governs a complex posttranscriptional regulatory program of α-1-antitrypsin expression. Crucially, these findings describe a mechanism by which genetic alterations in noncoding gene regions may result in α-1-antitrypsin deficiency.
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16
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Ni K, Umair Mukhtar Mian M, Meador C, Gill A, Barwinska D, Cao D, Justice MJ, Jiang D, Schaefer N, Schweitzer KS, Chu HW, March KL, Petrache I. Oncostatin M and TNF-α Induce Alpha-1 Antitrypsin Production in Undifferentiated Adipose Stromal Cells. Stem Cells Dev 2017; 26:1468-1476. [PMID: 28825379 DOI: 10.1089/scd.2017.0099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Alpha-1 antitrypsin (A1AT), a circulating acute-phase reactant antiprotease, is produced and secreted by cells of endodermal epithelial origin, primarily hepatocytes, and by immune cells. Deficiency of A1AT is associated with increased risk of excessive lung inflammation and injury, especially following chronic cigarette smoke (CS) exposure. Exogenous administration of mesenchymal progenitor cells, including adipose tissue-derived stromal/stem cells (ASC), alleviates CS-induced lung injury through paracrine effectors such as growth factors. It is unknown, however, if mesodermal ASC can secrete functional A1AT and if CS exposure affects their A1AT production. Human ASC collected via liposuction from nonsmoking or smoking donors were stimulated by inflammatory cytokines tumor necrosis alpha (TNFα), oncostatin M (OSM), and/or dexamethasone (DEX) or were exposed to sublethal concentrations of ambient air control or CS extract (0.5%-2%). We detected minimal expression and secretion of A1AT by cultured ASC during unstimulated conditions, which significantly increased following stimulation with TNFα or OSM. Furthermore, TNFα and OSM synergistically enhanced A1AT expression and secretion, which were further increased by DEX. The A1AT transcript variant produced by stimulated ASC resembled that produced by bronchial epithelial cells rather than the variant produced by monocytes/macrophages. While the cigarette smoking status of the ASC donor had no measurable effect on the ability of ASC to induce A1AT expression, active exposure to CS extract markedly reduced A1AT expression and secretion by cultured ASC, as well as human tracheobronchial epithelial cells. ASC-secreted A1AT covalently complexed with neutrophil elastase in control ASC, but not in cells transfected with A1AT siRNA. Undifferentiated ASC may require priming to secrete functional A1AT, a potent antiprotease that may be relevant to stem cell therapeutic effects.
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Affiliation(s)
- Kevin Ni
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado.,2 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana
| | | | - Catherine Meador
- 2 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana
| | - Amar Gill
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado
| | - Daria Barwinska
- 2 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana
| | - Danting Cao
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado
| | - Matthew J Justice
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado.,3 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Di Jiang
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado
| | - Niccolette Schaefer
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado
| | - Kelly S Schweitzer
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado.,2 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana
| | - Hong Wei Chu
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado
| | - Keith L March
- 2 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana.,4 Department of Cellular and Integrative Physiology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Irina Petrache
- 1 Department of Medicine, National Jewish Health, University of Colorado School of Medicine , Denver, Colorado.,2 Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana.,3 Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana
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17
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Sarabhai T, Peter C, Bär AK, Windolf J, Relja B, Wesselborg S, Wahlers T, Paunel-Görgülü A. Serum α-1 Antitrypsin (AAT) antagonizes intrinsic apoptosis induction in neutrophils from patients with systemic inflammatory response syndrome. PLoS One 2017; 12:e0177450. [PMID: 28493974 PMCID: PMC5426753 DOI: 10.1371/journal.pone.0177450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 12/23/2022] Open
Abstract
Excessive neutrophil activation accompanied by delayed apoptotic cell death in inflammatory conditions causes progressive damage of cells and tissues, leading to life-threatening multiple organ dysfunction syndrome. Previous work suggested that circulating serum factors during inflammation are critically involved in the suppression of neutrophil cell death although the identity of these antiapoptotic mediators remained elusive. In this study, we identified the acute phase protein α-1 Antitrypsin (AAT) as a potent suppressor of staurosporine (STS)-induced apoptosis in human neutrophils through a mechanism implicating caspases-independent pathways. We show here that serum levels of AAT, potentially in part released by stimulated neutrophils, are markedly elevated in major trauma patients suffering from systemic inflammatory response syndrome (SIRS). Notably, AAT depletion from serum increased sensitivity of human neutrophils for STS-induced cell death. In fact, AAT was demonstrated to confer intrinsic apoptosis resistance by preventing PKC/Akt inactivation and subsequent proteasomal degradation of antiapoptotic Mcl-1 protein in response to STS treatment. Neither MAP kinase ERK1/2 nor caspases were found to be involved in AAT-triggered antiapoptotic pathways in neutrophils. In summary, these results establish a novel pivotal role of circulating AAT in mediating survival by antagonizing the proapoptotic action of the PKC inhibitor STS and should be considered for AAT augmentation therapies in future.
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Affiliation(s)
- Theresia Sarabhai
- Department of Trauma and Hand Surgery, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Christoph Peter
- Institute for Molecular Medicine I, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Anne-Kathrin Bär
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
| | - Joachim Windolf
- Department of Trauma and Hand Surgery, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Borna Relja
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Sebastian Wesselborg
- Institute for Molecular Medicine I, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Thorsten Wahlers
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
| | - Adnana Paunel-Görgülü
- Department of Cardiothoracic Surgery, Heart Center of the University of Cologne, Cologne, Germany
- * E-mail:
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18
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Li W, Wang Q, Li S, Jiang A, Sun W. Molecular cloning, genomic structure, polymorphism analysis and recombinant expression of a α1-antitrypsin like gene from swamp eel, Monopterus albus. FISH & SHELLFISH IMMUNOLOGY 2017; 62:124-138. [PMID: 28108341 DOI: 10.1016/j.fsi.2017.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/23/2016] [Accepted: 01/13/2017] [Indexed: 06/06/2023]
Abstract
Alpha-1-antitrypsin (AAT) is a highly polymorphic glycoprotein antiprotease, involved in the regulation of human immune response. Beyond some genomic characterization and a few protein characterizations, the function of teleost AAT remains uncertain. In this study we cloned an AAT-like gene from a swamp eel liver identifying four exons and three introns, and the full-length cDNA. The elucidated swamp eel AAT amino acid sequence showed high homology with known AATs from other teleosts. The swamp eel AAT was examined both in ten healthy tissues and in four bacterially-stimulated tissues resulting in up-regulation of swamp eel AAT at different times. Swamp eel AAT transcripts were ubiquitously but unevenly expressed in ten tissues. Further, the mature peptide sequence of swamp eel AAT was subcloned and transformed into E. coli with the recombinant proteins successfully inhibiting bovine trypsin activity. Analysis of recombinant AAT showed equimolar formation of irreversible complexes with proteinases, high stability at pH 7.0-10.0 and temperatures below 55 °C. Serum AAT protein level significantly increased in response to inflammation with AAT anti-sera, and, NF-κB, apolipoprotein A1 and transferrin gene expression were dramatically decreased over 72 h post recombinant AAT injection. Lastly, examination of swamp eel AAT allelic polymorphism identified all alleles in both healthy and diseased stock except allele*g, found only in diseased stock, but without statistical difference between the distribution frequency of allele*g in the two stocks. These results are crucial to our ongoing study of the role of teleost AAT in the innate immune system.
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Affiliation(s)
- Wei Li
- Engineering Research Center of Ecology and Agriculture Use of Wetland, Ministry of Education, Jingzhou 434025, PR China; College of Life Science, Yangtze University, Jingzhou 434025, PR China
| | - Quanhe Wang
- College of Life Science, Yangtze University, Jingzhou 434025, PR China
| | - Shaobin Li
- College of Life Science, Yangtze University, Jingzhou 434025, PR China
| | - Ao Jiang
- College of Life Science, Yangtze University, Jingzhou 434025, PR China
| | - Wenxiu Sun
- Engineering Research Center of Ecology and Agriculture Use of Wetland, Ministry of Education, Jingzhou 434025, PR China; College of Life Science, Yangtze University, Jingzhou 434025, PR China.
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19
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Identification of Novel Short C-Terminal Transcripts of Human SERPINA1 Gene. PLoS One 2017; 12:e0170533. [PMID: 28107454 PMCID: PMC5249162 DOI: 10.1371/journal.pone.0170533] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 12/22/2022] Open
Abstract
Human SERPINA1 gene is located on chromosome 14q31-32.3 and is organized into three (IA, IB, and IC) non-coding and four (II, III, IV, V) coding exons. This gene produces α1-antitrypsin (A1AT), a prototypical member of the serpin superfamily of proteins. We demonstrate that human peripheral blood leukocytes express not only a product corresponding to the transcript coding for the full-length A1AT protein but also two short transcripts (ST1C4 and ST1C5) of A1AT. In silico sequence analysis revealed that the last exon of the short transcripts contains an Open Reading Frame (ORF) and thus putatively can produce peptides. We found ST1C4 expression across different human tissues whereas ST1C5 was mainly restricted to leukocytes, specifically neutrophils. A high up-regulation (10-fold) of short transcripts was observed in isolated human blood neutrophils after activation with lipopolysaccharide. Parallel analyses by liquid chromatography-mass spectrometry identified peptides corresponding to C-terminal region of A1AT in supernatants of activated but not naïve neutrophils. Herein we report for the first time a tissue specific expression and regulation of short transcripts of SERPINA1 gene, and the presence of C-terminal peptides in supernatants from activated neutrophils, in vitro. This gives a novel insight into the studies on the transcription of SERPINA1 gene.
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Abstract
α1-Antitrypsin deficiency (A1ATD) is an inherited disorder caused by mutations in SERPINA1, leading to liver and lung disease. It is not a rare disorder but frequently goes underdiagnosed or misdiagnosed as asthma, chronic obstructive pulmonary disease (COPD) or cryptogenic liver disease. The most frequent disease-associated mutations include the S allele and the Z allele of SERPINA1, which lead to the accumulation of misfolded α1-antitrypsin in hepatocytes, endoplasmic reticulum stress, low circulating levels of α1-antitrypsin and liver disease. Currently, there is no cure for severe liver disease and the only management option is liver transplantation when liver failure is life-threatening. A1ATD-associated lung disease predominately occurs in adults and is caused principally by inadequate protease inhibition. Treatment of A1ATD-associated lung disease includes standard therapies that are also used for the treatment of COPD, in addition to the use of augmentation therapy (that is, infusions of human plasma-derived, purified α1-antitrypsin). New therapies that target the misfolded α1-antitrypsin or attempt to correct the underlying genetic mutation are currently under development.
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Wu TS, Yang JJ, Wang YW, Yu FY, Liu BH. Mycotoxin ochratoxin A disrupts renal development via a miR-731/prolactin receptor axis in zebrafish. Toxicol Res (Camb) 2016; 5:519-529. [PMID: 30090366 PMCID: PMC6062247 DOI: 10.1039/c5tx00360a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/22/2015] [Indexed: 12/24/2022] Open
Abstract
Mycotoxin ochratoxin A (OTA) frequently contaminates various food and feed products, including cereals, coffee and wine. While the nephrotoxicity and teratogenicity of OTA have been extensively documented, the molecular mechanisms associated with OTA toxicity remained poorly understood in a developing organism. We showed that zebrafish embryos exposed to OTA demonstrated incorrect heart looping and small heart chambers. OTA also impaired the renal morphology and reduced the glomerular filtration rate of the embryonic zebrafish. The treatment of embryos with OTA attenuated the expression of the prolactin receptor, a gene (PRLRa) that has a key role in organogenesis and osmoregulation in vertebrates. OTA not only inhibited the phosphorylation of STAT5 and AKT, but also down-regulated the level of serpina1 mRNA in a dose-dependent manner. On the other hand, the microRNA profiling based on RNA sequencing revealed the up-regulation of microRNA-731 (miR-731) in the OTA-treated embryos. Further in silico analysis predicted that PRLRa was a target gene of miR-731. AntagomiR-731 restored PRLRa levels that had been reduced by OTA and also recovered the pronephros morphology that was damaged by OTA. These observations suggest that the exposure to OTA adversely affected the organogenesis of zebrafish, and the modulation of miR-731 and the PRLR signaling cascade contributed to the abnormal renal development mediated by OTA.
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Affiliation(s)
- Ting-Shuan Wu
- Graduate Institute of Toxicology , College of Medicine , National Taiwan University , Taipei , Taiwan . ; ; Tel: +886-2-23123456, ext 88602
| | - Jiann-Jou Yang
- Department of Biomedical Sciences , Chung Shan Medical University , Taiwan .
| | - Yan-Wei Wang
- Department of Biomedical Sciences , Chung Shan Medical University , Taiwan .
| | - Feng-Yih Yu
- Department of Biomedical Sciences , Chung Shan Medical University , Taiwan .
- Department of Medical Research , Chung Shan Medical University Hospital , Taichung , Taiwan
| | - Biing-Hui Liu
- Graduate Institute of Toxicology , College of Medicine , National Taiwan University , Taipei , Taiwan . ; ; Tel: +886-2-23123456, ext 88602
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Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease. PLoS One 2015; 10:e0140885. [PMID: 26480348 PMCID: PMC4610675 DOI: 10.1371/journal.pone.0140885] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/30/2015] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies aim to correlate genotype with phenotype. Many common diseases including Type II diabetes, Alzheimer’s, Parkinson’s and Chronic Obstructive Pulmonary Disease (COPD) are complex genetic traits with hundreds of different loci that are associated with varied disease risk. Identifying common features in the genes associated with each disease remains a challenge. Furthermore, the role of post-transcriptional regulation, and in particular alternative splicing, is still poorly understood in most multigenic diseases. We therefore compiled comprehensive lists of genes associated with Type II diabetes, Alzheimer’s, Parkinson’s and COPD in an attempt to identify common features of their corresponding mRNA transcripts within each gene set. The SERPINA1 gene is a well-recognized genetic risk factor of COPD and it produces 11 transcript variants, which is exceptional for a human gene. This led us to hypothesize that other genes associated with COPD, and complex disorders in general, are highly transcriptionally diverse. We found that COPD-associated genes have a statistically significant enrichment in transcript complexity stemming from a disproportionately high level of alternative splicing, however, Type II Diabetes, Alzheimer’s and Parkinson’s disease genes were not significantly enriched. We also identified a subset of transcriptionally complex COPD-associated genes (~40%) that are differentially expressed between mild, moderate and severe COPD. Although the genes associated with other lung diseases are not extensively documented, we found preliminary data that idiopathic pulmonary disease genes, but not cystic fibrosis modulators, are also more transcriptionally complex. Interestingly, complex COPD transcripts are more often the product of alternative acceptor site usage. To verify the biological importance of these alternative transcripts, we used RNA-sequencing analyses to determine that COPD-associated genes are frequently expressed in lung and liver tissues and are regulated in a tissue-specific manner. Additionally, many complex COPD-associated genes are spliced differently between COPD and non-COPD patients. Our analysis therefore suggests that post-transcriptional regulation, particularly alternative splicing, is an important feature specific to COPD disease etiology that warrants further investigation.
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