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Byun E, McCurry SM, Kwon S, Tsai CS, Jun J, Bammler TK, Becker KJ, Thompson HJ. Fatigue, Toll-Like Receptor 4, and Pro-Inflammatory Cytokines in Adults With Subarachnoid Hemorrhage: A 6-Month Longitudinal Study. Biol Res Nurs 2024; 26:192-201. [PMID: 37788710 DOI: 10.1177/10998004231203257] [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: 10/05/2023]
Abstract
BACKGROUND Fatigue is prevalent in subarachnoid hemorrhage (SAH) survivors. Biological mechanisms underlying fatigue post-SAH are not clear. Inflammation may contribute to the development of fatigue. This study aimed to examine the associations between inflammatory markers and fatigue during the first 6 months post-SAH. Specific biomarkers examined included both early and concurrent expression of Toll-Like Receptor 4 (TLR4) messenger RNA (mRNA) and plasma concentrations of pro-inflammatory cytokines, Tumor Necrosis Factor-alpha (TNF-α), Interleukin (IL)1β, and IL6. METHODS We conducted a 6-month longitudinal study with a convenience sample of 43 SAH survivors. We collected blood samples on days 2, 3, and 7 and 2, 3, and 6 months post-SAH to assess biomarkers. Fatigue was assessed by the PROMIS Fatigue Scale at 2, 3, and 6 months. Linear mixed models were used to test the associations between early (days 2, 3, and 7) and concurrent (2, 3, and 6 months) TLR4 mRNA expression (TagMan gene expression assays) and TNF-α, IL1β, and IL6 plasma concentrations (multiplex assays) and concurrent fatigue. RESULTS 28% of SAH survivors experienced fatigue during the first 6 months post-SAH. Fatigue levels in SAH survivors were higher than those of the U.S. population and consistent during the 6 months. Experience of fatigue during the 6 months post-SAH was associated with higher IL1β plasma concentrations on day 7 and IL1β, IL6, and TNF-α plasma concentrations during the 6 months post-SAH. CONCLUSION Inflammation appears to underlie the development of fatigue in SAH survivors.
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Affiliation(s)
- Eeeseung Byun
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
| | - Susan M McCurry
- Department of Child, Family and Population Health Nursing, University of Washington, Seattle, WA, USA
| | - Suyoung Kwon
- Department of Child, Family and Population Health Nursing, University of Washington, Seattle, WA, USA
| | - Chi-Shan Tsai
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
| | - Jeehye Jun
- Red Cross College of Nursing, Chung-Ang University, Seoul, Republic of Korea
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Kyra J Becker
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Hilaire J Thompson
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, WA, USA
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Schoberleitner I, Faserl K, Tripp CH, Pechriggl EJ, Sigl S, Brunner A, Zelger B, Hermann-Kleiter N, Baier L, Steinkellner T, Sarg B, Egle D, Brunner C, Wolfram D. Silicone implant surface microtopography modulates inflammation and tissue repair in capsular fibrosis. Front Immunol 2024; 15:1342895. [PMID: 38566997 PMCID: PMC10985323 DOI: 10.3389/fimmu.2024.1342895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Excessive fibrous capsule formation around silicone mammary implants (SMI) involves immune reactions to silicone. Capsular fibrosis, a common SMI complication linked to host responses, worsens with specific implant topographies. Our study with 10 patients investigated intra- and inter-individually, reduced surface roughness effects on disease progression, wound responses, chronic inflammation, and capsular composition. The results illuminate the significant impact of surface roughness on acute inflammatory responses, fibrinogen accumulation, and the subsequent fibrotic cascade. The reduction of surface roughness to an average roughness of 4 μm emerges as a promising approach for mitigating detrimental immune reactions, promoting healthy wound healing, and curbing excessive fibrosis. The identified proteins adhering to rougher surfaces shed light on potential mediators of pro-inflammatory and pro-fibrotic processes, further emphasizing the need for meticulous consideration of surface design. The composition of the implant capsule and the discovery of intracapsular HSP60 expression highlight the intricate web of stress responses and immune activation that can impact long-term tissue outcomes.
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Affiliation(s)
- Ines Schoberleitner
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Faserl
- Protein Core Facility, Institute of Medical Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph H. Tripp
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Elisabeth Judith Pechriggl
- Department of Anatomy, Histology and Embryology, Institute of Clinical and Functional Anatomy, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Sigl
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Brunner
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
- INNPATH GmbH, Tirol Kliniken, Innsbruck, Austria
| | - Bettina Zelger
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Natascha Hermann-Kleiter
- Institute of Cell Genetics, Department for Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Leoni Baier
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Theresia Steinkellner
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Sarg
- Protein Core Facility, Institute of Medical Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel Egle
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christine Brunner
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dolores Wolfram
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Innsbruck, Innsbruck, Austria
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Grzybkowska A, Anczykowska K, Antosiewicz J, Olszewski S, Dzitkowska-Zabielska M, Tomczyk M. Identification of Optimal Reference Genes for qRT-PCR Normalization for Physical Activity Intervention and Omega-3 Fatty Acids Supplementation in Humans. Int J Mol Sci 2023; 24:ijms24076734. [PMID: 37047706 PMCID: PMC10094777 DOI: 10.3390/ijms24076734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
The quantitative polymerase chain reaction (qRT-PCR) technique gives promising opportunities to detect and quantify RNA targets and is commonly used in many research fields. This study aimed to identify suitable reference genes for physical exercise and omega-3 fatty acids supplementation intervention. Forty healthy, physically active men were exposed to a 12-week eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) supplementation and standardized endurance training protocol. Blood samples were collected before and after the intervention and mRNA levels of six potential reference genes were tested in the leukocytes of 18 eligible participants using the qRT-PCR method: GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), ACTB (Beta actin), TUBB (Tubulin Beta Class I), RPS18 (Ribosomal Protein S18), UBE2D2 (Ubiquitin-conjugating enzyme E2 D2), and HPRT1 (Hypoxanthine Phosphoribosyltransferase 1). The raw quantification cycle (Cq) values were then analyzed using RefFinder, an online tool that incorporates four different algorithms: NormFinder, geNorm, BestKeeper, and the comparative delta-Ct method. Delta-Ct, NormFinder, BestKeeper, and RefFinder comprehensive ranking have found GAPDH to be the most stably expressed gene. geNorm has identified TUBB and HPRT as the most stable genes. All algorithms have found ACTB to be the least stably expressed gene. A combination of the three most stably expressed genes, namely GAPDH, TUBB, and HPRT, is suggested for obtaining the most reliable results.
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Affiliation(s)
- Agata Grzybkowska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Katarzyna Anczykowska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Jędrzej Antosiewicz
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Szczepan Olszewski
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Magdalena Dzitkowska-Zabielska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
- Center of Translational Medicine, Medical University of Gdansk, 80-952 Gdansk, Poland
| | - Maja Tomczyk
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
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4
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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:biomedicines11041079. [PMID: 37189697 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Cincotta AH, Cersosimo E, Alatrach M, Ezrokhi M, Agyin C, Adams J, Chilton R, Triplitt C, Chamarthi B, Cominos N, DeFronzo RA. Bromocriptine-QR Therapy Reduces Sympathetic Tone and Ameliorates a Pro-Oxidative/Pro-Inflammatory Phenotype in Peripheral Blood Mononuclear Cells and Plasma of Type 2 Diabetes Subjects. Int J Mol Sci 2022; 23:ijms23168851. [PMID: 36012132 PMCID: PMC9407769 DOI: 10.3390/ijms23168851] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Bromocriptine-QR is a sympatholytic dopamine D2 agonist for the treatment of type 2 diabetes that has demonstrated rapid (within 1 year) substantial reductions in adverse cardiovascular events in this population by as yet incompletely delineated mechanisms. However, a chronic state of elevated sympathetic nervous system activity and central hypodopaminergic function has been demonstrated to potentiate an immune system pro-oxidative/pro-inflammatory condition and this immune phenotype is known to contribute significantly to the advancement of cardiovascular disease (CVD). Therefore, the possibility exists that bromocriptine-QR therapy may reduce adverse cardiovascular events in type 2 diabetes subjects via attenuation of this underlying chronic pro-oxidative/pro-inflammatory state. The present study was undertaken to assess the impact of bromocriptine-QR on a wide range of immune pro-oxidative/pro-inflammatory biochemical pathways and genes known to be operative in the genesis and progression of CVD. Inflammatory peripheral blood mononuclear cell biology is both a significant contributor to cardiovascular disease and also a marker of the body’s systemic pro-inflammatory status. Therefore, this study investigated the effects of 4-month circadian-timed (within 2 h of waking in the morning) bromocriptine-QR therapy (3.2 mg/day) in type 2 diabetes subjects whose glycemia was not optimally controlled on the glucagon-like peptide 1 receptor agonist on (i) gene expression status (via qPCR) of a wide array of mononuclear cell pro-oxidative/pro-inflammatory genes known to participate in the genesis and progression of CVD (OXR1, NRF2, NQO1, SOD1, SOD2, CAT, GSR, GPX1, GPX4, GCH1, HMOX1, BiP, EIF2α, ATF4, PERK, XBP1, ATF6, CHOP, GSK3β, NFkB, TXNIP, PIN1, BECN1, TLR2, TLR4, TLR10, MAPK8, NLRP3, CCR2, GCR, L-selectin, VCAM1, ICAM1) and (ii) humoral measures of sympathetic tone (norepinephrine and normetanephrine), whole-body oxidative stress (nitrotyrosine, TBARS), and pro-inflammatory factors (IL-1β, IL-6, IL-18, MCP-1, prolactin, C-reactive protein [CRP]). Relative to pre-treatment status, 4 months of bromocriptine-QR therapy resulted in significant reductions of mRNA levels in PBMC endoplasmic reticulum stress-unfolded protein response effectors [GRP78/BiP (34%), EIF2α (32%), ATF4 (29%), XBP1 (25%), PIN1 (14%), BECN1 (23%)], oxidative stress response proteins [OXR1 (31%), NRF2 (32%), NQO1 (39%), SOD1 (52%), CAT (26%), GPX1 (33%), GPX4 (31%), GCH1 (30%), HMOX1 (40%)], mRNA levels of TLR pro-inflammatory pathway proteins [TLR2 (46%), TLR4 (20%), GSK3β (19%), NFkB (33%), TXNIP (18%), NLRP3 (32%), CCR2 (24%), GCR (28%)], mRNA levels of pro-inflammatory cellular receptor proteins CCR2 and GCR by 24% and 28%, and adhesion molecule proteins L-selectin (35%) and VCAM1 (24%). Relative to baseline, bromocriptine-QR therapy also significantly reduced plasma levels of norepinephrine and normetanephrine by 33% and 22%, respectively, plasma pro-oxidative markers nitrotyrosine and TBARS by 13% and 10%, respectively, and pro-inflammatory factors IL-18, MCP1, IL-1β, prolactin, and CRP by 21%,13%, 12%, 42%, and 45%, respectively. These findings suggest a unique role for circadian-timed bromocriptine-QR sympatholytic dopamine agonist therapy in reducing systemic low-grade sterile inflammation to thereby reduce cardiovascular disease risk.
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Affiliation(s)
- Anthony H. Cincotta
- VeroScience LLC, Tiverton, RI 02878, USA
- Correspondence: ; Tel.: +1-401-816-0525
| | - Eugenio Cersosimo
- Texas Diabetes Institute, University Health System, San Antonio, TX 78207, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Mariam Alatrach
- Texas Diabetes Institute, University Health System, San Antonio, TX 78207, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | - Christina Agyin
- Texas Diabetes Institute, University Health System, San Antonio, TX 78207, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - John Adams
- Texas Diabetes Institute, University Health System, San Antonio, TX 78207, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Robert Chilton
- Texas Diabetes Institute, University Health System, San Antonio, TX 78207, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Curtis Triplitt
- Texas Diabetes Institute, University Health System, San Antonio, TX 78207, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | | | - Ralph A. DeFronzo
- Texas Diabetes Institute, University Health System, San Antonio, TX 78207, USA
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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Bantulà M, Arismendi E, Picado C, Mullol J, Roca-Ferrer J, Tubita V. Reference Gene Validation for RT-qPCR in PBMCs from Asthmatic Patients with or without Obesity. Methods Protoc 2022; 5:35. [PMID: 35645343 PMCID: PMC9149987 DOI: 10.3390/mps5030035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/10/2022] [Accepted: 04/19/2022] [Indexed: 01/26/2023] Open
Abstract
Obesity is known to impair the efficacy of glucocorticoid medications for asthma control. Glucocorticoid-induced gene expression studies may be useful to discriminate those obese asthmatic patients who present a poor response to glucocorticoids. The expression of genes of interest is normalized with respect to reference genes (RGs). Ideally, RGs have a stable expression in different samples and are not affected by experimental conditions. The objective of this work was to analyze suitable RGs to study the role of glucocorticoid-induced genes in obese asthmatic patients in further research. The gene expression of eight potential RGs (GUSB, B2M, POLR2A, PPIA, ACTB, GAPDH, HPRT1, and TBP) was assessed with reverse transcription-quantitative polymerase chain reaction in peripheral blood mononuclear cells (PBMCs) from asthmatic, obese asthmatic, and healthy individuals. Their stability was analyzed using four different algorithms-BestKeeper, ΔCt, geNorm, and NormFinder. geNorm analysis recommended the use of a minimum of three genes for normalization. Moreover, intergroup variation due to the treatment was calculated by NormFinder, which found that B2M was the gene that was least affected by different treatments. Comprehensive rankings indicated GUSB and HPRT1 as the best RGs for qPCR in PBMCs from healthy and asthmatic subjects, while B2M and PPIA were the best for obese asthmatic subjects. Finally, our results demonstrated that B2M and HPRT1 were the most stable RGs among all groups, whereas ACTB, TBP, and GAPDH were the worst shared ones.
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Affiliation(s)
- Marina Bantulà
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
| | - Ebymar Arismendi
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Department of Pneumology, Hospital Clinic, 08036 Barcelona, Spain
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - César Picado
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Department of Pneumology, Hospital Clinic, 08036 Barcelona, Spain
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Joaquim Mullol
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
- Rhinology Unit and Smell Clinic, ENT Department, Hospital Clinic, 08036 Barcelona, Spain
| | - Jordi Roca-Ferrer
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Valeria Tubita
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
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Li S, Zhu Y, Wei C, Li C, Chen W, Jiang S, Yuan D, Xu R. Identification of Molecular Correlations Between DHRS4 and Progressive Neurodegeneration in Amyotrophic Lateral Sclerosis By Gene Co-Expression Network Analysis. Front Immunol 2022; 13:874978. [PMID: 35479082 PMCID: PMC9035787 DOI: 10.3389/fimmu.2022.874978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/15/2022] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease, and its candidate biomarkers have not yet been fully elucidated in previous studies. Therefore, with the present study, we aim to define and verify effective biomarkers of ALS by bioinformatics. Here, we employed differentially expressed gene (DEG) analysis, weighted gene co-expression network analysis (WGCNA), enrichment analysis, immune infiltration analysis, and protein-protein interaction (PPI) to identify biomarkers of ALS. To validate the biomarkers, we isolated the lumbar spinal cord from mice and characterized them using Western blotting and immunofluorescence. The results showed that Dhrs4 expression in the spinal cord was upregulated with the progression of SOD1G93A mice, and the upregulation of DHRS4 and its synergistic DHRS3 might be primarily associated with the activation of the complement cascade in the immune system (C1QA, C1QB, C1QC, C3, and ITGB2), which might be a novel mechanism that induces spinal neurodegeneration in ALS. We propose that DHRS4 and its synergistic DHRS3 are promising molecular markers for detecting ALS progression.
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Affiliation(s)
| | | | | | | | | | | | | | - Renshi Xu
- Department of Neurology, Jiangxi Provincial People’s Hospital, Affiliated People’s Hospital of Nanchang University, Nanchang, China
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Liu YJ, Kuo HC, Chern Y. A system-wide mislocalization of RNA-binding proteins in motor neurons is a new feature of ALS. Neurobiol Dis 2021; 160:105531. [PMID: 34634461 DOI: 10.1016/j.nbd.2021.105531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 01/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a motor neuron disease characterized by progressive degeneration of motor neurons. Mislocalization of TAR DNA-binding protein 43 (TDP-43) is an early event in the formation of cytoplasmic TDP-43-positive inclusions in motor neurons and a hallmark of ALS. However, the underlying mechanism and the pathogenic impact of this mislocalization are relatively unexplored. We previously reported that abnormal AMPK activation mediates TDP-43 mislocalization in motor neurons of humans and mice with ALS. In the present study, we hypothesized that other nuclear proteins are mislocalized in the cytoplasm of motor neurons due to the AMPK-mediated phosphorylation of importin-α1 and subsequently contribute to neuronal degeneration in ALS. To test this hypothesis, we analyzed motor neurons of sporadic ALS patients and found that when AMPK is activated, importin-α1 is abnormally located in the nucleus. Multiple integrative molecular and cellular approaches (including proteomics, immunoprecipitation/western blot analysis, immunohistological evaluations and gradient analysis of preribosomal complexes) were employed to demonstrate that numerous RNA binding proteins are mislocalized in a rodent motor neuron cell line (NSC34) and human motor neurons derived from iPSCs during AMPK activation. We used comparative proteomic analysis of importin-α1 complexes that were immunoprecipitated with a phosphorylation-deficient mutant of importin-α1 (importin-α1-S105A) and a phosphomimetic mutant of importin-α1 (importin-α1-S105D) to identify 194 proteins that have stronger affinity for the unphosphorylated form than the phosphorylated form of importin-α1. Furthermore, GO and STRING analyses suggested that RNA processing and protein translation is the major machinery affected by abnormalities in the AMPK-importin-α1 axis. Consistently, the expression of importin-α1-S105D alters the assembly of preribosomal complexes and increases cell apoptosis. Collectively, we propose that by impairing importin-α1-mediated nuclear import, abnormal AMPK activation in motor neurons alters the cellular distribution of many RNA-binding proteins, which pathogenically affect multiple cellular machineries in motor neurons and contribute to ALS pathogenesis.
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Affiliation(s)
- Yu-Ju Liu
- Division of Neuroscience, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Yijuang Chern
- Division of Neuroscience, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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9
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Łuczkowska K, Rutka M, Rogińska D, Paczkowska E, Baumert B, Milczarek S, Górska M, Kulig P, Osękowska B, Janowski M, Safranow K, Sommerfeld K, Borowiecka E, Zawodny P, Koclęga A, Helbig G, Machaliński B. The Potential Role of Proinflammatory Cytokines and Complement Components in the Development of Drug-Induced Neuropathy in Patients with Multiple Myeloma. J Clin Med 2021; 10:jcm10194584. [PMID: 34640602 PMCID: PMC8509696 DOI: 10.3390/jcm10194584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/27/2021] [Accepted: 10/02/2021] [Indexed: 01/15/2023] Open
Abstract
The launch of novel chemotherapeutic agents-in particular, proteasome inhibitors and immunomodulatory drugs-dramatically changed multiple myeloma (MM) therapy, improving the response rate and prolonging progression-free survival. However, none of the anti-MM drugs are deprived of side effects. Peripheral neuropathy (PN) seems to be one of the most pressing problems. Despite extensive research in this area, the pathogenesis of drug-induced peripheral neuropathy (DiPN) has not yet been fully elucidated. In the present study, we aimed to assess the potential relationship between proinflammatory factors and the development of PN in MM patients with particular emphasis on the application of VTD (bortezomib, thalidomide, dexamethasone) regimen. Our analysis identified increased concentrations of CCL2, IL-1β, and IFN-γ in plasma of MM patients during treatment, both with and without symptoms of PN, compared with untreated neuropathy-free MM patients. At the same time, the plasma concentration of IL-1β in patients with neuropathy was significantly increased compared with patients without PN before and during treatment. Moreover, the results were enhanced at the transcript level by performing global mRNA expression analysis using microarray technology. The most significant changes were observed in the expression of genes responsible for regulating immunological and apoptotic processes. An in-depth understanding of the mechanisms responsible for the development of DiPN might in the future reduce the incidence of PN and accelerate diagnosis, allowing the choice of neuropathy-free treatment strategies for MM.
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Affiliation(s)
- Karolina Łuczkowska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
| | - Magdalena Rutka
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
| | - Dorota Rogińska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
| | - Edyta Paczkowska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
| | - Bartłomiej Baumert
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
| | - Sławomir Milczarek
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
| | - Martyna Górska
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
| | - Piotr Kulig
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
| | - Bogumiła Osękowska
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
| | - Michał Janowski
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
| | - Krzysztof Safranow
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Krzysztof Sommerfeld
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
| | - Ewa Borowiecka
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
| | - Piotr Zawodny
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
| | - Anna Koclęga
- Department of Hematology and Bone Marrow Transplantation, Medical University of Silesia, 40-027 Katowice, Poland; (A.K.); (G.H.)
| | - Grzegorz Helbig
- Department of Hematology and Bone Marrow Transplantation, Medical University of Silesia, 40-027 Katowice, Poland; (A.K.); (G.H.)
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.Ł.); (M.R.); (D.R.); (E.P.); (S.M.); (M.G.); (P.K.); (P.Z.)
- Department of Bone Marrow Transplantation, Pomeranian Medical University, 71-252 Szczecin, Poland; (B.B.); (B.O.); (M.J.); (K.S.); (E.B.)
- Correspondence:
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Reference Genes for Expression Studies in Human CD8 + Naïve and Effector Memory T Cells under Resting and Activating Conditions. Sci Rep 2020; 10:9411. [PMID: 32523060 PMCID: PMC7286888 DOI: 10.1038/s41598-020-66367-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/15/2020] [Indexed: 12/20/2022] Open
Abstract
Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is widely used for mRNA quantification. To accurately measure changing gene transcript levels under different experimental conditions, the use of appropriate reference gene transcripts is instrumental. In T cell immunology, suitable reference genes have been reported for bulk CD4+ and CD8+ T cells. However, many CD4+ and CD8+ T cell subsets have been described in the past. Although they respond differently to given activation stimuli, proper validation of suitable reference genes in these subsets is lacking. In this study, we evaluated twelve commonly used reference gene products in human naïve (NV) and effector memory (EM) CD8+ T cells under non-activated and activated (2 h, 10 h and 20 h) conditions. We used five different statistical approaches for data analysis. Our results show that a number of widely used reference transcripts become differentially expressed under activating conditions. Using them as references markedly alters results as exemplified with IFNG mRNA expression. The only candidate reference gene products that remained stable during the activation process were 18S rRNA and SDHA mRNA, encouraging their usage as reference gene products for RT-qPCR experiments, when quantifying mRNA levels in human NV and EM CD8+ T cells.
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11
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Influence of Magnetite Nanoparticles and Quantum Dots on the Expression of Reference Genes in Peripheral Blood Cells. Bull Exp Biol Med 2018; 166:264-267. [PMID: 30488202 DOI: 10.1007/s10517-018-4329-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Indexed: 01/09/2023]
Abstract
We studied the influence of magnetite nanoparticles (FeO•Fe2O3) and quantum dots (CdSe/ZnS coated with mercaptopropionic acid) on the expression of 5 common reference genes (BA, B2M, PPIA, UBC, and YWHAZ) in peripheral blood cells from 20 volunteers by reverse transcription PCR method. The stability of the expression of reference genes varied depending of the cells type and chemical structure of nanoparticles. The level of YWHAZ mRNA after exposure by nanoparticles demonstrated highest stability in lymphocytes, neutrophils, and monocytes. Stability of YWHAZ expression was confirmed by Western blotting. Our findings suggest that YWHAZ is the most suitable as the reference gene.
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12
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Dzaki N, Azzam G. Assessment of Aedes albopictus reference genes for quantitative PCR at different stages of development. PLoS One 2018; 13:e0194664. [PMID: 29554153 PMCID: PMC5858815 DOI: 10.1371/journal.pone.0194664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/07/2018] [Indexed: 11/23/2022] Open
Abstract
Members of the Aedes genus of mosquitoes are widely recognized as vectors of viral diseases. Ae.albopictus is its most invasive species, and are known to carry viruses such as Dengue, Chikugunya and Zika. Its emerging importance puts Ae.albopictus on the forefront of genetic interaction and evolution studies. However, a panel of suitable reference genes specific for this insect is as of now undescribed. Nine reference genes, namely ACT, eEF1-γ, eIF2α, PP2A, RPL32, RPS17, PGK1, ILK and STK were evaluated. Expression patterns of the candidate reference genes were observed in a total of seventeen sample types, separated by stage of development and age. Gene stability was inferred from obtained quantification data through three widely cited evaluation algorithms i.e. BestKeeper, geNorm, and NormFinder. No single gene showed a satisfactory degree of stability throughout all developmental stages. Therefore, we propose combinations of PGK and ILK for early embryos; RPL32 and RPS17 for late embryos, all four larval instars, and pupae samples; eEF1-γ with STK for adult males; eEF1-γ with RPS17 for non-blood fed females; and eEF1-γ with eIF2α for both blood-fed females and cell culture. The results from this study should be able to provide a more informed selection of normalizing genes during qPCR in Ae.albopictus.
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Affiliation(s)
- Najat Dzaki
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Vector Control and Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- * E-mail:
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13
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Liu S, Meng C, Xu G, Jian H, Wang F. Validation of reference genes for reverse transcription real-time quantitative PCR analysis in the deep-sea bacterium Shewanella psychrophila WP2. FEMS Microbiol Lett 2018. [DOI: 10.1093/femsle/fny048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Canxin Meng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Guanpeng Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 200240 Shanghai, PR China
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