1
|
Lv T, Wang C, Zhou J, Feng X, Zhang L, Fan Z. Mechanism and role of nuclear laminin B1 in cell senescence and malignant tumors. Cell Death Discov 2024; 10:269. [PMID: 38824174 PMCID: PMC11144256 DOI: 10.1038/s41420-024-02045-9] [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: 02/20/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/03/2024] Open
Abstract
Nuclear lamin B1 (LMNB1) is a member of the nuclear lamin protein family. LMNB1 can maintain and ensure the stability of nuclear structure and influence the process of cell senescence by regulating chromatin distribution, DNA replication and transcription, gene expression, cell cycle, etc. In recent years, several studies have shown that the abnormal expression of LMNB1, a classical biomarker of cell senescence, is highly correlated with the progression of various malignant tumors; LMNB1 is therefore considered a new potential tumor marker and therapeutic target. However, the mechanism of action of LMNB1 is influenced by many factors, which are difficult to clarify at present. This article focuses on the recent progress in understanding the role of LMNB1 in cell senescence and malignant tumors and offers insights that could contribute to elucidating the mechanism of action of LMNB1 to provide a new direction for further research.
Collapse
Affiliation(s)
- Tingcong Lv
- Department of General Surgery, the Third People's Hospital of Dalian, Dalian Medical University, Dalian, China
| | - Cong Wang
- Department of General Surgery, the Third People's Hospital of Dalian, Dalian Medical University, Dalian, China
| | - Jialin Zhou
- Department of General Surgery, the Third People's Hospital of Dalian, Dalian Medical University, Dalian, China
- Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xiao Feng
- School of Chemistry, Dalian University of Technology, Dalian, China.
| | - Lijun Zhang
- Liaoning Province Key Laboratory of Corneal and Ocular Surface Diseases Research, the Third People's Hospital of Dalian, Faculty of Medicine, Dalian University of Technology, Dalian, China.
| | - Zhe Fan
- Department of General Surgery, the Third People's Hospital of Dalian, Dalian Medical University, Dalian, China.
- Liaoning Province Key Laboratory of Corneal and Ocular Surface Diseases Research, the Third People's Hospital of Dalian, Faculty of Medicine, Dalian University of Technology, Dalian, China.
| |
Collapse
|
2
|
Gambarino S, Galliano I, Clemente A, Calvi C, Montanari P, Pau A, Dini M, Bergallo M. Characteristics of RNA Stabilizer RNApro for Peripheral Blood Collection. Diagnostics (Basel) 2024; 14:971. [PMID: 38786269 PMCID: PMC11120318 DOI: 10.3390/diagnostics14100971] [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: 03/15/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Peripheral blood is the most practical tissue for human immune system gene expression profiling because it is easily accessible, whereas the site of primary infection in certain diseases may not be easily accessible. Due to the ex vivo instability of RNA transcripts, a key challenge in the gene expression analysis of blood samples is the rapid sample handling and stabilization of the mRNA by adding an RNA preservative (PAXgeneTM Blood RNA Tubes, TempusTM Blood RNA tubes, RNAlater Stabilization Reagent, RNAgard® Blood Tubes). BioMole (Turin, Italy) has developed a novel blood stabilizer, called RNApro, in which RNA is stabilized during phlebotomy and sample storage. In this study, RNApro performance intended as RNA yield, integrity, and stability was evaluated. Our results show that blood samples stored at -80 °C and re-extracted after 7 years show no differences in terms of quantity, quality, and amplificability. The samples in the RNAlater stabilization solution can be stored at room temperature for up to one week or at 4 °C for up to one month. Similar results can also be observed for PAXgene tubes, Tempus tubes, and RNAgard tubes. In agreement with these data, the RNApro stabilization solution preserves the RNA from degradation for up to 1 month at 4 °C and 1 week at room temperature. RNApro can be stored indifferently at -80, -20, 4 °C, or room temperature for up to 2 months after, and then could be stored at -80 °C for up to seven years. In summary, our study is the first to analyze the performance of an RNA stabilizer called RNApro. We can conclude that several studies have shown significant differences in gene expression analysis when the sample was preserved in different RNA stabilizers. Therefore, it is desirable to standardize the method of nucleic acid conservation when comparing data from transcriptomic analyses.
Collapse
Affiliation(s)
- Stefano Gambarino
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Clemente
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Pau
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Maddalena Dini
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| |
Collapse
|
3
|
Nevado JB, Cutiongco-de la Paz EMC, Paz-Pacheco ET, Jasul GV, Aman AYCL, Deguit CDT, San Pedro JVB, Francisco MDG. Transcriptional profiles associated with coronary artery disease in type 2 diabetes mellitus. Front Endocrinol (Lausanne) 2024; 15:1323168. [PMID: 38706700 PMCID: PMC11066158 DOI: 10.3389/fendo.2024.1323168] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/25/2024] [Indexed: 05/07/2024] Open
Abstract
Background Coronary artery disease (CAD) is a common complication of Type 2 diabetes mellitus (T2DM). Understanding the pathogenesis of this complication is essential in both diagnosis and management. Thus, this study aimed to characterize the presence of CAD in T2DM using molecular markers and pathway analyses. Methods The study is a sex- and age-frequency matched case-control design comparing 23 unrelated adult Filipinos with T2DM-CAD to 23 controls (DM with CAD). Healthy controls served as a reference. Total RNA from peripheral blood mononuclear cells (PBMCs) underwent whole transcriptomic profiling using the Illumina HumanHT-12 v4.0 expression beadchip. Differential gene expression with gene ontogeny analyses was performed, with supporting correlational analyses using weighted correlation network analysis (WGCNA). Results The study observed that 458 genes were differentially expressed between T2DM with and without CAD (FDR<0.05). The 5 top genes the transcription factor 3 (TCF3), allograft inflammatory factor 1 (AIF1), nuclear factor, interleukin 3 regulated (NFIL3), paired immunoglobulin-like type 2 receptor alpha (PILRA), and cytoskeleton-associated protein 4 (CKAP4) with AUCs >89%. Pathway analyses show differences in innate immunity activity, which centers on the myelocytic (neutrophilic/monocytic) theme. SNP-module analyses point to a possible causal dysfunction in innate immunity that triggers the CAD injury in T2DM. Conclusion The study findings indicate the involvement of innate immunity in the development of T2DM-CAD, and potential immunity markers can reflect the occurrence of this injury. Further studies can verify the mechanistic hypothesis and use of the markers.
Collapse
Affiliation(s)
- Jose B. Nevado
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Eva Maria C. Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | - Elizabeth T. Paz-Pacheco
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
| | - Gabriel V. Jasul
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
| | - Aimee Yvonne Criselle L. Aman
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Christian Deo T. Deguit
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Jana Victoria B. San Pedro
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Mark David G. Francisco
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
| |
Collapse
|
4
|
Chen Q, Guo X, Wang H, Sun S, Jiang H, Zhang P, Shang E, Zhang R, Cao Z, Niu Q, Zhang C, Liu Y, Shi L, Yu Y, Hou W, Zheng Y. Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:109-124. [PMID: 38884056 PMCID: PMC11169349 DOI: 10.1007/s43657-023-00121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 06/18/2024]
Abstract
RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00121-1.
Collapse
Affiliation(s)
- Qingwang Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Xiaorou Guo
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Shanyue Sun
- Shandong Provincial Hospital, Shandong First Medical University, Jinan, 250021 China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Peipei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Erfei Shang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Ruolan Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Zehui Cao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Quanne Niu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Chao Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yaqing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
- The International Human Phenome Institutes, Shanghai, 200438 China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Shanghai Cancer Center, Fudan University, Shanghai, 200438 China
| |
Collapse
|
5
|
Miyashita H, Takehara I, Nishimura M, Takayama G, Sumi H, Kadokura M, Nakai D. Evaluation of Collection and Processing Conditions for Gene Expression Analysis Using Human Myeloid Cells. Biopreserv Biobank 2024. [PMID: 38526566 DOI: 10.1089/bio.2023.0072] [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: 03/26/2024] Open
Abstract
Background: The population of blast cells among peripheral blood mononuclear cells (PBMCs) obtained from patients is a desirable specimen for analyzing gene expression in diseases including acute myeloid leukemia. Although the enrichment of blast cells often needs to be performed at a central laboratory, acceptable conditions for sample transport from clinical sites remain to be established. Methods: We evaluated storage temperature, duration, and tube type before initiating sample processing for the analysis of cluster of differentiation (CD)33+ myeloid cells among PBMCs as an alternative to CD34+/CD33+ blast cells. Results: CD33+ myeloid cells were successfully purified by MACS. The cell viability and the RNA integrity were sustained during storage up to 48 hours before sample processing. Storage at 4°C had minimal effects on gene expression, whereas storage at room temperature induced the senescence pathway, characterized by the expression of stress-inducible genes. A CPT tube was also better than an ethylenediaminetetraacetic acid tube for minimizing gene expression change. Conclusions: Our study provided important clues for establishing a sample handling approach for gene expression analysis with purified cell fractions from human PBMCs. To keep the variation of gene expression to a minimum, samples should be delivered at 4°C within 48 hours before processing.
Collapse
|
6
|
Orcel E, Hage H, Taha M, Boucher N, Chautard E, Courtois V, Saliou A. A single workflow for multi-species blood transcriptomics. BMC Genomics 2024; 25:282. [PMID: 38493105 PMCID: PMC10944614 DOI: 10.1186/s12864-024-10208-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Blood transcriptomic analysis is widely used to provide a detailed picture of a physiological state with potential outcomes for applications in diagnostics and monitoring of the immune response to vaccines. However, multi-species transcriptomic analysis is still a challenge from a technological point of view and a standardized workflow is urgently needed to allow interspecies comparisons. RESULTS Here, we propose a single and complete total RNA-Seq workflow to generate reliable transcriptomic data from blood samples from humans and from animals typically used in preclinical models. Blood samples from a maximum of six individuals and four different species (rabbit, non-human primate, mouse and human) were extracted and sequenced in triplicates. The workflow was evaluated using different wet-lab and dry-lab criteria, including RNA quality and quantity, the library molarity, the number of raw sequencing reads, the Phred-score quality, the GC content, the performance of ribosomal-RNA and globin depletion, the presence of residual DNA, the strandness, the percentage of coding genes, the number of genes expressed, and the presence of saturation plateau in rarefaction curves. We identified key criteria and their associated thresholds to be achieved for validating the transcriptomic workflow. In this study, we also generated an automated analysis of the transcriptomic data that streamlines the validation of the dataset generated. CONCLUSIONS Our study has developed an end-to-end workflow that should improve the standardization and the inter-species comparison in blood transcriptomics studies. In the context of vaccines and drug development, RNA sequencing data from preclinical models can be directly compared with clinical data and used to identify potential biomarkers of value to monitor safety and efficacy.
Collapse
Affiliation(s)
- Elody Orcel
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France
| | - Hayat Hage
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France
| | - May Taha
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France
| | | | - Emilie Chautard
- SANOFI, 1541 Av. Marcel Mérieux, Marcy-L'Étoile, 69280, France
| | | | - Adrien Saliou
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France.
| |
Collapse
|
7
|
Pawlak J, Szczepankiewicz A, Skibińska M, Narożna B, Kapelski P, Zakowicz P, Gattner K, Spałek D, Mech Ł, Dmitrzak-Węglarz M. Transcriptome profiling as a biological marker for bipolar disorder sub-phenotypes. Adv Med Sci 2024; 69:61-69. [PMID: 38368745 DOI: 10.1016/j.advms.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/14/2023] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
PURPOSE Bipolar affective disorder (BP) causes major functional impairment and reduced quality of life not only for patients, but also for many close relatives. We aimed to investigate mRNA levels in BP patients to find differentially expressed genes linked to specific clinical course variants; assuming that several gene expression alterations might indicate vulnerability pathways for specific course and severity of the disease. MATERIALS We searched for up- and down-regulated genes comparing patients with diagnosis of BP type I (BPI) vs type II (BPII), history of suicide attempts, psychotic symptoms, predominance of manic/hypomanic episodes, and history of numerous episodes and comorbidity of substance use disorders or anxiety disorders. RNA was extracted from peripheral blood mononuclear cells and analyzed with use of microarray slides. RESULTS Differentially expressed genes (DEGs) were found in all disease characteristics compared. The lowest number of DEGs were revealed when comparing BPI and BPII patients (18 genes), and the highest number when comparing patients with and without psychotic symptoms (3223 genes). Down-regulated genes identified here with the use of the DAVID database were among others linked to cell migration, defense response, and inflammatory response. CONCLUSIONS The most specific transcriptome profile was revealed in BP with psychotic symptoms. Differentially expressed genes in this variant include, among others, genes involved in inflammatory and immune processes. It might suggest the overlap of biological background between BP with a history of psychotic features and schizophrenia.
Collapse
Affiliation(s)
- Joanna Pawlak
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Aleksandra Szczepankiewicz
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland; Molecular and Cell Biology Unit, Poznan University of Medical Sciences, Poznań, Poland
| | - Maria Skibińska
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Beata Narożna
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland; Molecular and Cell Biology Unit, Poznan University of Medical Sciences, Poznań, Poland
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Przemysław Zakowicz
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland; Center for Child and Adolescent Treatment in Zabór, Zielona Góra, Poland
| | - Karolina Gattner
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland; HCP Medical Center, Poznań, Poland
| | - Dominik Spałek
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland; Regional Hospital for Psychiatric and Neurological Patients, Gniezno, Poland
| | - Łukasz Mech
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznań, Poland; Regional Hospital for Psychiatric and Neurological Patients, Gniezno, Poland
| | | |
Collapse
|
8
|
Mengelkoch S, Gassen J, Lev-Ari S, Alley JC, Schüssler-Fiorenza Rose SM, Snyder MP, Slavich GM. Multi-omics in stress and health research: study designs that will drive the field forward. Stress 2024; 27:2321610. [PMID: 38425100 PMCID: PMC11216062 DOI: 10.1080/10253890.2024.2321610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Despite decades of stress research, there still exist substantial gaps in our understanding of how social, environmental, and biological factors interact and combine with developmental stressor exposures, cognitive appraisals of stressors, and psychosocial coping processes to shape individuals' stress reactivity, health, and disease risk. Relatively new biological profiling approaches, called multi-omics, are helping address these issues by enabling researchers to quantify thousands of molecules from a single blood or tissue sample, thus providing a panoramic snapshot of the molecular processes occurring in an organism from a systems perspective. In this review, we summarize two types of research designs for which multi-omics approaches are best suited, and describe how these approaches can help advance our understanding of stress processes and the development, prevention, and treatment of stress-related pathologies. We first discuss incorporating multi-omics approaches into theory-rich, intensive longitudinal study designs to characterize, in high-resolution, the transition to stress-related multisystem dysfunction and disease throughout development. Next, we discuss how multi-omics approaches should be incorporated into intervention research to better understand the transition from stress-related dysfunction back to health, which can help inform novel precision medicine approaches to managing stress and fostering biopsychosocial resilience. Throughout, we provide concrete recommendations for types of studies that will help advance stress research, and translate multi-omics data into better health and health care.
Collapse
Affiliation(s)
- Summer Mengelkoch
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Jeffrey Gassen
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Shahar Lev-Ari
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Health Promotion, Tel Aviv University, Tel Aviv, Israel
| | - Jenna C. Alley
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | | | | | - George M. Slavich
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| |
Collapse
|
9
|
Yu R, Yu Q, Li Z, Li J, Yang J, Hu Y, Zheng N, Li X, Song Y, Li J, Chen X, Du W, Su J. Transcriptome-wide map of N6-methyladenosine (m6A) profiling in coronary artery disease (CAD) with clopidogrel resistance. Clin Epigenetics 2023; 15:194. [PMID: 38098098 PMCID: PMC10722764 DOI: 10.1186/s13148-023-01602-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Clopidogrel resistance profoundly increases the risk of major cardiovascular events in coronary artery disease (CAD) patients. Here, we comprehensively analyse global m6A modification alterations in clopidogrel-resistant (CR) and non-CR patients. METHODS After RNA isolation, the RNA transcriptome expression (lncRNA, circRNA, and mRNA) was analysed via RNA-seq, and m6A peaks were identified by MeRIP-seq. The altered m6A methylation sites on mRNAs, lncRNAs, and circRNAs were identified, and then, GO and KEGG pathway analyses were performed. Through joint analysis with RNA-seq and MeRIP-seq data, differentially expressed mRNAs harbouring differentially methylated sites were identified. The changes in m6A regulator levels and the abundance of differentially methylated sites were measured by RT-PCR. The identification of m6A-modified RNAs was verified by m6A-IP-qPCR. RESULTS The expression of 2919 hypermethylated and 2519 hypomethylated mRNAs, 192 hypermethylated and 391 hypomethylated lncRNAs, and 375 hypermethylated and 546 hypomethylated circRNAs was shown to be altered in CR patients. The m6A peaks related to CR indicated lower mark density at the CDS region. Functional enrichment analysis revealed that inflammatory pathways and insulin signalling pathways might be involved in the pathological processes underlying CR. The expression of mRNAs (ST5, KDM6B, GLB1L2, and LSM14B), lncRNAs (MSTRG.13776.1 and ENST00000627981.1), and circRNAs (hsa_circ_0070675_CBC1, hsa-circRNA13011-5_CBC1, and hsa-circRNA6406-3_CBC1) was upregulated in CR patients, while the expression of mRNAs (RPS16 and CREG1), lncRNAs (MSTRG.9215.1), and circRNAs (hsa_circ_0082972_CBC1) was downregulated in CR patients. Moreover, m6A regulators (FTO, YTHDF3, and WTAP) were also differentially expressed. An additional combined analysis of gene expression and m6A peaks revealed that the expression of mRNAs (such as ST5, LYPD2, and RPS16 mRNAs) was significantly altered in the CR patients. CONCLUSION The expression of m6A regulators, the RNA transcriptome, and the m6A landscape was altered in CR patients. These findings reveal epitranscriptomic regulation in CR patients, which might be novel therapeutic targets in future.
Collapse
Affiliation(s)
- Ruoyan Yu
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, People's Republic of China
| | - Qinglin Yu
- Department of Traditional Chinese Internal Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Zhenwei Li
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, People's Republic of China
| | - Jiyi Li
- Department of Cardiology, Yuyao People's Hospital of Zhejiang Province, Yuyao, Zhejiang, People's Republic of China
| | - Jin Yang
- Department of Geriatrics, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Yingchu Hu
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, People's Republic of China
| | - Nan Zheng
- Department of Cardiology, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, People's Republic of China
| | - Xiaojin Li
- Department of Geriatrics, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Yudie Song
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Jiahui Li
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | - Xiaomin Chen
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, People's Republic of China.
| | - Weiping Du
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, People's Republic of China.
| | - Jia Su
- Department of Cardiology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, People's Republic of China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, People's Republic of China.
| |
Collapse
|
10
|
Fiorito AM, Fakra E, Sescousse G, Ibrahim EC, Rey R. Molecular mapping of a core transcriptional signature of microglia-specific genes in schizophrenia. Transl Psychiatry 2023; 13:386. [PMID: 38092734 PMCID: PMC10719376 DOI: 10.1038/s41398-023-02677-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Besides playing a central role in neuroinflammation, microglia regulate synaptic development and is involved in plasticity. Converging lines of evidence suggest that these different processes play a critical role in schizophrenia. Furthermore, previous studies reported altered transcription of microglia genes in schizophrenia, while microglia itself seems to be involved in the etiopathology of the disease. However, the regional specificity of these brain transcriptional abnormalities remains unclear. Moreover, it is unknown whether brain and peripheral expression of microglia genes are related. Thus, we investigated the expression of a pre-registered list of 10 genes from a core signature of human microglia both at brain and peripheral levels. We included 9 independent Gene Expression Omnibus datasets (764 samples obtained from 266 individuals with schizophrenia and 237 healthy controls) from 8 different brain regions and 3 peripheral tissues. We report evidence of a widespread transcriptional alteration of microglia genes both in brain tissues (we observed a decreased expression in the cerebellum, associative striatum, hippocampus, and parietal cortex of individuals with schizophrenia compared with healthy controls) and whole blood (characterized by a mixed altered expression pattern). Our results suggest that brain underexpression of microglia genes may represent a candidate transcriptional signature for schizophrenia. Moreover, the dual brain-whole blood transcriptional alterations of microglia/macrophage genes identified support the model of schizophrenia as a whole-body disorder and lend weight to the use of blood samples as a potential source of biological peripheral biomarkers.
Collapse
Affiliation(s)
- Anna M Fiorito
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Centre Hospitalier Le Vinatier, Bron, France
| | - Eric Fakra
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Department of Psychiatry, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Guillaume Sescousse
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France
- Centre Hospitalier Le Vinatier, Bron, France
| | - El Chérif Ibrahim
- Aix-Marseille Univ, CNRS, INT, Institut de Neurosciences de la Timone, Marseille, France
| | - Romain Rey
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR 5292, PSYR2 Team, University of Lyon, Lyon, France.
- Centre Hospitalier Le Vinatier, Bron, France.
- Fondation FondaMental, Créteil, France.
| |
Collapse
|
11
|
Dmitrzak-Węglarz M, Rybakowski J, Szczepankiewicz A, Kapelski P, Lesicka M, Jabłońska E, Reszka E, Pawlak J. Identification of shared disease marker genes and underlying mechanisms between major depression and rheumatoid arthritis. J Psychiatr Res 2023; 168:22-29. [PMID: 37871462 DOI: 10.1016/j.jpsychires.2023.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/28/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Both depression and rheumatoid arthritis (RA) have a very high comorbidity rate. A bilateral association is estimated to increase the mutual risk and the common denominator is inflammation being observed in both diseases. Previous studies have mainly focused on assessing peripheral blood's inflammatory and pro-inflammatory cytokines levels. We aimed to extend insights into the molecular mechanisms of depression based on hub RA genes. To do so, we prioritized RA-related genes using in-silico tools. We then investigated whether RA-related genes undergo altered expression in patients with unipolar and bipolar depression without a concurrent RA diagnosis and any exponents of active inflammation. In addition, we selected a homogeneous group of patients treated with lithium (Li), which has immunomodulatory properties. The study was performed on patients with bipolar depression (BD, n = 45; Li, n = 20), unipolar depression (UD, n = 27), and healthy controls (HC, n = 22) of both sexes. To identify DEGs in peripheral blood mononuclear cells (PBMCs), we used the SurePrint G3 Microarray and GeneSpring software. We selected a list of 180 hub genes whose altered expression we analyzed using the expression microarray results. In the entire study group, we identified altered expression of 93 of the 180 genes, including 35 down-regulated (OPRM1 gene with highest FC > 3) and 58 up-regulated (TLR4 gene with highest FC > 3). In UD patients, we observed maximally up-regulated expression of the TEK gene (FC > 3), and in BD of the CXCL8 gene (FC > 5). On the other hand, in lithium-treated patients, the gene with the most reduced expression was the TRPV1 gene. The study proved that depression and RA are produced by a partially shared "inflammatory interactome" in which the opioid and angiogenesis pathways are important.
Collapse
Affiliation(s)
| | - Janusz Rybakowski
- Department of Adult Psychiatry, Poznan University of Medical Sciences, Poland.
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poland.
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poland.
| | - Monika Lesicka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland.
| | - Ewa Jabłońska
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland.
| | - Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, Lodz, Poland.
| | - Joanna Pawlak
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poland.
| |
Collapse
|
12
|
Wilfinger WW, Eghbalnia HR, Mackey K, Miller R, Chomczynski P. Whole blood RNA extraction efficiency contributes to variability in RNA sequencing data sets. PLoS One 2023; 18:e0291209. [PMID: 37972054 PMCID: PMC10653446 DOI: 10.1371/journal.pone.0291209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023] Open
Abstract
Numerous methodologies are used for blood RNA extraction, and large quantitative differences in recovered RNA content are reported. We evaluated three archived data sets to determine how extraction methodologies might influence mRNA and lncRNA sequencing results. The total quantity of RNA recovered /ml of blood affects RNA sequencing by impacting the recovery of weakly expressed mRNA, and lncRNA transcripts. Transcript expression (TPM counts) plotted in relation to transcript size (base pairs, bp) revealed a 30% loss of short to midsized transcripts in some data sets. Quantitative recovery of RNA is of considerable importance, and it should be viewed more judiciously. Transcripts common to the three data sets were subsequently normalized and transcript mean TPM counts and TPM count coefficient of variation (CV) were plotted in relation to increasing transcript size. Regression analysis of mean TPM counts versus transcript size revealed negative slopes in two of the three data sets suggesting a reduction of TPM transcript counts with increasing transcript size. In the third data set, the regression slope line of mRNA transcript TPM counts approximates zero and TPM counts increased in proportion to transcript size over a range of 200 to 30,000 bp. Similarly, transcript TPM count CV values also were uniformly distributed over the range of transcript sizes. In the other data sets, the regression CV slopes increased in relation to transcript size. The recovery of weakly expressed and /or short to midsized mRNA and lncRNA transcripts varies with different RNA extraction methodologies thereby altering the fundamental sequencing relationship between transcript size and TPM counts. Our analysis identifies differences in RNA sequencing results that are dependent upon the quantity of total RNA recovery from whole blood. We propose that incomplete RNA extraction directly impacts the recovery of mRNA and lncRNA transcripts from human blood and speculate these differences contribute to the "batch" effects commonly identified between sequencing results from different archived data sets.
Collapse
Affiliation(s)
| | - Hamid R. Eghbalnia
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States of America
| | - Karol Mackey
- Molecular Research Center, Inc. Cincinnati, OH, United States of America
| | - Robert Miller
- Robert Miller Enterprises, LLC, Cincinnati, OH, United States of America
| | - Piotr Chomczynski
- Molecular Research Center, Inc. Cincinnati, OH, United States of America
| |
Collapse
|
13
|
Mengelkoch S, Miryam Schüssler-Fiorenza Rose S, Lautman Z, Alley JC, Roos LG, Ehlert B, Moriarity DP, Lancaster S, Snyder MP, Slavich GM. Multi-omics approaches in psychoneuroimmunology and health research: Conceptual considerations and methodological recommendations. Brain Behav Immun 2023; 114:475-487. [PMID: 37543247 PMCID: PMC11195542 DOI: 10.1016/j.bbi.2023.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/04/2023] [Accepted: 07/30/2023] [Indexed: 08/07/2023] Open
Abstract
The field of psychoneuroimmunology (PNI) has grown substantially in both relevance and prominence over the past 40 years. Notwithstanding its impressive trajectory, a majority of PNI studies are still based on a relatively small number of analytes. To advance this work, we suggest that PNI, and health research in general, can benefit greatly from adopting a multi-omics approach, which involves integrating data across multiple biological levels (e.g., the genome, proteome, transcriptome, metabolome, lipidome, and microbiome/metagenome) to more comprehensively profile biological functions and relate these profiles to clinical and behavioral outcomes. To assist investigators in this endeavor, we provide an overview of multi-omics research, highlight recent landmark multi-omics studies investigating human health and disease risk, and discuss how multi-omics can be applied to better elucidate links between psychological, nervous system, and immune system activity. In doing so, we describe how to design high-quality multi-omics studies, decide which biological samples (e.g., blood, stool, urine, saliva, solid tissue) are most relevant, incorporate behavioral and wearable sensing data into multi-omics research, and understand key data quality, integration, analysis, and interpretation issues. PNI researchers are addressing some of the most interesting and important questions at the intersection of psychology, neuroscience, and immunology. Applying a multi-omics approach to this work will greatly expand the horizon of what is possible in PNI and has the potential to revolutionize our understanding of mind-body medicine.
Collapse
Affiliation(s)
- Summer Mengelkoch
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA.
| | | | - Ziv Lautman
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jenna C Alley
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Lydia G Roos
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Benjamin Ehlert
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Daniel P Moriarity
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | | | | | - George M Slavich
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA.
| |
Collapse
|
14
|
Anirudhan A, Ahmad SF, Emran TB, Angulo-Bejarano PI, Sharma A, Ahmed SSSJ. Comparative Efficacy of Metformin and Glimepiride in Modulating Pharmacological Network to Increase BDNF Levels and Benefit Type 2 Diabetes-Related Cognitive Impairment. Biomedicines 2023; 11:2939. [PMID: 38001940 PMCID: PMC10669717 DOI: 10.3390/biomedicines11112939] [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: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Cognitive impairment is anotable complication of type 2 diabetes (T2DM), accompanied by reduced brain-derived neurotrophic factor (BDNF) in the brain and blood. Anti-diabetic drugs reduce hyperglycemia, yet their effect on cognitive improvement is unknown. We aimed to investigate the effect of anti-diabetic drugs regulating BDNF in T2DM through computational and case-control study design. We obtained T2DMproteins viatext-mining to construct a T2DMprotein network. From the T2DMnetwork, the metformin and glimepiride interactomes and their crucial shortest-path-stimulating BDNF were identified. Using qRTPCR, the genes encoding the shortest-path proteins were assessed in four groups (untreated-T2DM, metformin-treated, glimepiride-treated, and healthy controls). Finally, ELISA was used to assess serum BDNF levels to validate drug efficacy. As a result of this investigation, aT2DMnetwork was constructed with 3683 text-mined proteins. Then, the T2DMnetwork was explored to generate a metformin and glimepiride interactome that establishes the critical shortest-path for BDNF stimulation. Metformin stimulates BDNF via APP binding to the PRKAB1 receptor. Whereas, glimepiride increases BDNF by binding to KCNJ11 via AP2M1 and ESR1 proteins. Both drug shortest-path encoding genes differed significantly between the groups. Unlike metformin, BDNF gene and protein expression rise significantly with glimepiride. Overall, glimepiride can effectively increase BDNF, which could benefit T2DM patients with cognitive deterioration.
Collapse
Affiliation(s)
- Athira Anirudhan
- Central Research Laboratory, Believers Church Medical College Hospital, Kuttapuzha, Thiruvalla 689101, Kerala, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Paola Isabel Angulo-Bejarano
- Regional Department of Bioengineering, NatProLab-Plant Innovation Lab, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- Regional Department of Bioengineering, NatProLab-Plant Innovation Lab, Tecnologico de Monterrey, Queretaro 76130, Mexico
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-Omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| |
Collapse
|
15
|
Congrave-Wilson Z, Kim M, Sutherland A, Jumarang J, Lee Y, Del Valle J, Cheng WA, da Silva Antunes R, Pannaraj PS. Effect of wash media type during PBMC isolation on downstream characterization of SARS-CoV-2-specific T cells. J Immunol Methods 2023; 519:113520. [PMID: 37390890 PMCID: PMC10306416 DOI: 10.1016/j.jim.2023.113520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Protocols for the isolation of peripheral blood mononuclear cells (PBMCs) from whole blood vary greatly between laboratories, especially in published studies of SARS-CoV-2-specific T cell responses following infection and vaccination. Research on the effects of different wash media types or centrifugation speeds and brake usage during the PBMC isolation process on downstream T cell activation and functionality is limited. Blood samples from 26 COVID-19-vaccinated participants were processed with different PBMC isolation methods using either PBS or RPMI as the wash media with high centrifugation speed and brakes or RPMI as the wash media with low speed and brakes (RPMI+ method). SARS-CoV-2 spike-specific T cells were quantified and characterized via a flow cytometry-based activation induced markers (AIM) assay and an interferon-γ (IFNγ) FluoroSpot assay and responses were compared between processing methods. Samples washed with RPMI showed higher AIM+ CD4 T cell responses than those washed with PBS and showed a shift away from naïve and towards an effector memory phenotype. The activation marker OX40 showed higher SARS-CoV-2 spike-induced upregulation on RPMI-washed CD4 T cells, while differences in CD137 upregulation were minimal between processing methods. The magnitude of the AIM+ CD8 T cell response was similar between processing methods but showed higher stimulation indices. Background frequencies of CD69+ CD8 T cells were increased in PBS-washed samples and were associated with higher baseline numbers of IFNγ-producing cells in the FluoroSpot assay. Slower braking in the RPMI+ method did not improve detection of SARS-CoV-2-specific T cells and caused longer processing times. Thus, the use of RPMI media with full centrifugation brakes during the wash steps of PBMC isolation was found to be most effective and efficient. Further studies are needed to elucidate the pathways involved in RPMI-mediated preservation of downstream T cell activity.
Collapse
Affiliation(s)
- Zion Congrave-Wilson
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Minjun Kim
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Jaycee Jumarang
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Yesun Lee
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Jennifer Del Valle
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Wesley A Cheng
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Department of Pediatrics and Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States.
| |
Collapse
|
16
|
Jiang Z, Lu Y, Shi M, Li H, Duan J, Huang J. Effects of storage temperature, storage time, and hemolysis on the RNA quality of blood specimens: A systematic quantitative assessment. Heliyon 2023; 9:e16234. [PMID: 37260878 PMCID: PMC10227325 DOI: 10.1016/j.heliyon.2023.e16234] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction Blood samples are the most common biospecimen in biobanks, and RNA from such blood samples is an important material for biomedical research. High-quality RNA is essential for consistent, reliable results. Preanalytical environmental conditions can affect the quality of blood RNA. Here, we carried out a quantitative assessment of the influence of storage temperature, storage time, and hemolysis on the RNA quality of blood specimens in biobanks. Methods Before RNA purification, blood samples from volunteers were exposed to 4 °C for 2, 6, 12, 24, or 48 h, 3 days, or 1 week, or exposed to room temperature (22-30 °C) for 1, 2, 6, 12, or 24 h. Hemolyzed samples were collected from laboratory department and some of them were prepared using the freeze-thaw method. After exposure to different preanalytical environmental conditions, the RNA simple Total RNA Kit was used to purify the RNA, following which a NanoDrop™ One and Qsep 100 Bio-Fragment Analyzer were used to assess RNA concentration, purity, and integrity. In addition, a part of the RNA was immediately reverse transcribed into cDNA when it was purified, then the relative expression levels of 18S, ACTB, HIF1α, HMOX1, and MKI67 were determined by real-time quantitative PCR. Finally, 30 blood samples were collected from the surplus samples in our laboratory department to assess their RNA quality without knowledge of their storage conditions (duration/temperature). Results For blood samples stored at 4 °C, there was a significant difference between the RNA integrity after 1 week compared to after 2 h. For blood samples stored at room temperature (22-30 °C), the RNA integrity was also significantly different at 6 h and 0 h. Hemolysis caused by freeze-thawing severely affected RNA quality, whereas clinical hemolysis generally produced no significant effects. Moreover, expression of 18S, ACTB, HIF1α, HMOX1, and MKI67 in whole blood stored under different conditions showed irregular changes, suggesting that preservation conditions are also important for gene expression. Conclusion RNA integrity was qualified for blood samples stored at 4 °C for up to 72 h or at room temperature (22-30 °C) for up to 2 h. Hemolysis usually does not affect the RNA quality of blood samples unless the hemolysis method damages leukocytes.
Collapse
Affiliation(s)
- Zhijun Jiang
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Yi Lu
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Manying Shi
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Hong Li
- Central Laboratory, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Junkai Duan
- Pediatric Heart Disease Treatment Center, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Jiyi Huang
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| |
Collapse
|
17
|
Gómez-Aguililla S, Núñez C, Rubio M, Corzo M. Isolation and cryopreservation of peripheral blood mononuclear cells. Methods Cell Biol 2023; 179:127-141. [PMID: 37625870 DOI: 10.1016/bs.mcb.2023.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The study of peripheral blood mononuclear cells (PBMCs) in immune-mediated diseases, such as celiac disease (CD), is important to uncover pathogenesis, find new biomarkers and discover and evaluate new treatments. Many studies have been published about the use and value of PBMCs in CD such as those including enzyme-linked immunospot (ELISPOT) assays, flow cytometry, peptide-MHC tetramers, genetic and proteomic analyses, and in vitro and proliferation assays. We present here and easy and efficient method for isolation of PBMCs using density gradient centrifugation. We also describe a simple way to freeze PBMCs in order to preserve their number and viability and a thawing procedure leading to high rates of viability of the cryopreserved cells to be used in subsequent applications.
Collapse
Affiliation(s)
- Sara Gómez-Aguililla
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Concepción Núñez
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Mercedes Rubio
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain.
| | - María Corzo
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| |
Collapse
|
18
|
Peng Y, Wu Q, Liu H, Zhang J, Han Q, Yin F, Wang L, Chen Q, Zhang F, Feng C, Zhu H. An immune-related gene signature predicts the 28-day mortality in patients with sepsis. Front Immunol 2023; 14:1152117. [PMID: 37033939 PMCID: PMC10076848 DOI: 10.3389/fimmu.2023.1152117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Sepsis is the leading cause of death in intensive care units and is characterized by multiple organ failure, including dysfunction of the immune system. In the present study, we performed an integrative analysis on publicly available datasets to identify immune-related genes (IRGs) that may play vital role in the pathological process of sepsis, based on which a prognostic IRG signature for 28-day mortality prediction in patients with sepsis was developed and validated. Methods Weighted gene co-expression network analysis (WGCNA), Cox regression analysis and least absolute shrinkage and selection operator (LASSO) estimation were used to identify functional IRGs and construct a model for predicting the 28-day mortality. The prognostic value of the model was validated in internal and external sepsis datasets. The correlations of the IRG signature with immunological characteristics, including immune cell infiltration and cytokine expression, were explored. We finally validated the expression of the three IRG signature genes in blood samples from 12 sepsis patients and 12 healthy controls using qPCR. Results We established a prognostic IRG signature comprising three gene members (LTB4R, HLA-DMB and IL4R). The IRG signature demonstrated good predictive performance for 28-day mortality on the internal and external validation datasets. The immune infiltration and cytokine analyses revealed that the IRG signature was significantly associated with multiple immune cells and cytokines. The molecular pathway analysis uncovered ontology enrichment in myeloid cell differentiation and iron ion homeostasis, providing clues regarding the underlying biological mechanisms of the IRG signature. Finally, qPCR detection verified the differential expression of the three IRG signature genes in blood samples from 12 sepsis patients and 12 healthy controls. Discussion This study presents an innovative IRG signature for 28-day mortality prediction in sepsis patients, which may be used to facilitate stratification of risky sepsis patients and evaluate patients' immune state.
Collapse
Affiliation(s)
- Yaojun Peng
- Department of Graduate Administration, Medical School of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- Department of Emergency, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Qiyan Wu
- Institute of Oncology, The Fifth Medical Centre, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Hongyu Liu
- Department of Graduate Administration, Medical School of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- Department of Neurosurgery, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- Department of Neurosurgery, Hainan Hospital of Chinese People's Liberation Army (PLA) General Hospital, Sanya, Hainan, China
| | - Jinying Zhang
- Department of Basic Medicine, Medical School of Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Qingru Han
- Department of Emergency, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Fan Yin
- Department of Oncology, The Second Medical Center & National Clinical Research Center of Geriatric Disease, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Lingxiong Wang
- Institute of Oncology, The Fifth Medical Centre, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Qi Chen
- Department of Traditional Chinese Medicine, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Fei Zhang
- Department of Emergency, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Fei Zhang, ; Cong Feng, ; Haiyan Zhu,
| | - Cong Feng
- Department of Emergency, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Fei Zhang, ; Cong Feng, ; Haiyan Zhu,
| | - Haiyan Zhu
- Department of Emergency, The First Medical Center, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
- *Correspondence: Fei Zhang, ; Cong Feng, ; Haiyan Zhu,
| |
Collapse
|
19
|
Sarathkumara YD, Browne DJ, Kelly AM, Pattinson DJ, Rush CM, Warner J, Proietti C, Doolan DL. The Effect of Tropical Temperatures on the Quality of RNA Extracted from Stabilized Whole-Blood Samples. Int J Mol Sci 2022; 23:ijms231810609. [PMID: 36142559 PMCID: PMC9503649 DOI: 10.3390/ijms231810609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022] Open
Abstract
Whole-blood-derived transcriptional profiling is widely used in biomarker discovery, immunological research, and therapeutic development. Traditional molecular and high-throughput transcriptomic platforms, including molecular assays with quantitative PCR (qPCR) and RNA-sequencing (RNA-seq), are dependent upon high-quality and intact RNA. However, collecting high-quality RNA from field studies in remote tropical locations can be challenging due to resource restrictions and logistics of post-collection processing. The current study tested the relative performance of the two most widely used whole-blood RNA collection systems, PAXgene® and Tempus™, in optimal laboratory conditions as well as suboptimal conditions in tropical field sites, including the effects of extended storage times and high storage temperatures. We found that Tempus™ tubes maintained a slightly higher RNA quantity and integrity relative to PAXgene® tubes at suboptimal tropical conditions. Both PAXgene® and Tempus™ tubes gave similar RNA purity (A260/A280). Additionally, Tempus™ tubes preferentially maintained the stability of mRNA transcripts for two reference genes tested, Succinate dehydrogenase complex, subunit A (SDHA) and TATA-box-binding protein (TBP), even when RNA quality decreased with storage length and temperature. Both tube types preserved the rRNA transcript 18S ribosomal RNA (18S) equally. Our results suggest that Tempus™ blood RNA collection tubes are preferable to PAXgene® for whole-blood collection in suboptimal tropical conditions for RNA-based studies in resource-limited settings.
Collapse
Affiliation(s)
- Yomani D. Sarathkumara
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Daniel J. Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Ashton M. Kelly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - David J. Pattinson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Catherine M. Rush
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Jeffrey Warner
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia
| | - Carla Proietti
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Denise L. Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health of Medicine, James Cook University, Cairns, QLD 4878, Australia
- Correspondence:
| |
Collapse
|
20
|
Zou C, Ji C, Zhu Y, Liu N, Zhang S, Peng H, Zhang X, Wang H, Deng Y, Qian K. Effects of Freezing and Rewarming Methods on RNA Quality of Blood Samples. Biopreserv Biobank 2022; 21:176-183. [PMID: 35759420 DOI: 10.1089/bio.2022.0007] [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: 11/12/2022] Open
Abstract
Background: RNA extracted from human blood has been widely applied to biological, medical, and clinical research of numerous diseases. Previous studies have demonstrated that high-quality RNA is indispensable to guarantee the reliability of downstream assays. In this study, we investigated the effects of freezing procedures, rewarming methods, and blood components on RNA quality of blood samples. Methods: Rabbit blood samples were divided into two groups: (1) whole blood (WB) and (2) blood cell components (BCC) with plasma removed. Samples were frozen using four representative freezing procedures (snap freezing in liquid nitrogen, snap freezing at -80°C, traditional slow freezing, and programmable controlled rate freezing) and rewarmed by placing at 4°C or by vortexing. RNA was extracted using the phenol-chloroform RNA extraction method and measured by an Agilent bioanalyzer. Then, human blood was used to verify the best protocol obtained from the rabbit blood experiment. Results: For the four freezing procedures, there were no differences in RNA integrity. For different rewarming methods, RNA integrity number (RIN) values of RNA extracted from frozen WB and BCC samples in the vortex group were above 9, while RNA obtained from WB showed worse quality compared with BCC in the 4°C group. For verification using human blood, RIN values of frozen human WB rewarmed by vortexing ranged from 8.0 to 9.1. Conclusions: Blood components and rewarming methods could affect the RNA quality of blood samples. For scenarios where WB samples have already been cryopreserved, the vortex rewarming method is optimal for high-quality RNA. Otherwise, we would recommend centrifuging fresh WB and cryopreserving it in the form of BCC, which showed a tendency to obtain high-quality RNA by either of the two rewarming methods.
Collapse
Affiliation(s)
- Cong Zou
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chundong Ji
- Department of Urology, Affiliated Hospital of Panzhihua University, Panzhihua, China
| | - Yuan Zhu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Nan Liu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shanshan Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Peng
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xin Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanhua Deng
- Department of Urology, Affiliated Hospital of Panzhihua University, Panzhihua, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
| |
Collapse
|
21
|
Li J, Sun Z, Cui Y, Qin L, Wu F, Li Y, Du N, Li X. Knockdown of LMNB1 Inhibits the Proliferation of Lung Adenocarcinoma Cells by Inducing DNA Damage and Cell Senescence. Front Oncol 2022; 12:913740. [PMID: 35712471 PMCID: PMC9194513 DOI: 10.3389/fonc.2022.913740] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/15/2022] Open
Abstract
Background Lung cancer has considerably high mortality and morbidity rate. Lung adenocarcinoma (LUAD) tissues highly express lamin B1 (LMNB1), compared with normal tissues. In this study, we knocked down LMNB1 in LUAD cells A549 and NCI-1299 to explore the effect of its inhibition on the proliferation of cells and the potential mechanism. Methods Using bioinformatics methods, we analyzed the specificity of LMNB1 mRNA expression level in LUAD and its effect on prognosis from TCGA data. SiRNAs were used to knock down LMNB1 in the A549 cell line, and the knockdown effect was identified by western blotting and qRT-PCR. Through CCK8 cell proliferation assay, wound healing assay, TRAP, cloning formation Assay, DNase I-TUNEL assay, ATAC-seq, immunofluorescence, FISH, in vivo mouse xenograft studies, etc, we evaluated the influence and mechanism of LMNB1 on LUAD cell line proliferation in vitro and in vivo. Results According to bioinformatics analysis, LMNB1 is substantially abundant in LUAD tissues and is associated with tumor stage and patient survival (P < 0.05). After silencing LMNB1, the rate of cell growth, wound healing, the number of transwells, and the number of cell colonies all decreased significantly (P < 0.01). With the decreased LMNB1 expression, H3K9me3 protein expression decreases, chromosome accessibility increases, P53, P21, P16 and γ-H2AX protein expression increases, and the number of senescence staining positive cells increases. At the same time, in vivo mouse xenograft experiments showed that the tumor volume of the LMNB1-silenced group was significantly reduced, compared to that of the control group (P < 0.01), and the proliferation biomarker Ki-67 level (P < 0.01) was considerably reduced. Conclusions Overexpression of LMNB1 in LUAD cells is significant, which has excellent potential to be an indicator for evaluating the clinical prognosis of LUAD patients and a target for precise treatment.
Collapse
Affiliation(s)
- Jiangbo Li
- Department of Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Zhijia Sun
- Medical School of Chinese People's Liberation Army (PLA), Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yingshu Cui
- Medical School of Chinese People's Liberation Army (PLA), Chinese People's Liberation Army General Hospital, Beijing, China
| | - Lingmei Qin
- Department of Biology, Beijing Institute of Biotechnology, Beijing, China
| | - Fengyun Wu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Yufang Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Nan Du
- Department of Oncology, Fourth Medical Center of Chinese PLA General Hospital, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Xiaosong Li
- Department of Oncology, Fourth Medical Center of Chinese PLA General Hospital, Chinese People's Liberation Army General Hospital, Beijing, China.,Department of Oncology, Seventh Medical Center of Chinese PLA General Hospital, Chinese People's Liberation Army General Hospital, Beijing, China
| |
Collapse
|
22
|
Chiang ZC, Fang S, Shen YK, Cui D, Weng H, Wang D, Zhao Y, Lin J, Chen Q. Development of Novel CD47-Specific ADCs Possessing High Potency Against Non-Small Cell Lung Cancer in vitro and in vivo. Front Oncol 2022; 12:857927. [PMID: 35646646 PMCID: PMC9133542 DOI: 10.3389/fonc.2022.857927] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/13/2022] [Indexed: 12/18/2022] Open
Abstract
Targeted therapies hold promise for efficiently and accurately delivering cytotoxic drugs directly to tumor tissue to exert anticancer effects. CD47 is a membrane protein expressed in a variety of malignant tumors and hematopoietic cells, which plays a key role in immune escape and tumor progression. Although CD47 immunocheckpoint therapy has been developed in recent years, many patients cannot benefit from it because of its low efficiency. To strengthen and extend the therapeutic efficacy of anti-CD47 monoclonal antibody (mAb), we used the newly developed 7DC2 and 7DC4 mAbs as the targeting payload adaptor and VCMMAE as the toxin payload to construct novel CD47-specific immunotoxin (7DC-VCMMAE) by engineering cysteine residues. These CD47-specific ADCs have the better cell penetration, excellent DAR, similar payload distribution and good antigen-binding affinity. In vitro, 7DC-VCMMAE treatment induced death of non-small cell lung cancer (NSCLC) cell lines 95D and SPC-A1, but not A549 that express low levels of CD47 on the cell membrane. This finding suggests that 7DC-VCMMAE may possess greater therapeutic effect on NSCLC tumors expressing a high level of CD47 antigen; however, 7DC-VCMMAE treatment also promoted phagocytosis of A549 cells by macrophages. In vivo, 7DC-VCMMAE treatment had remarkable antitumor effects in a NSCLC cell line-derived xenograft (CDX) mouse model based on nonobese diabetic/severe combined immunodeficient (NOD/SCID). In summary, this study combined VCMMAE with anti-CD47 mAbs, emphasizing a novel and promising immunotherapy method for direct killing of NSCLC, which provides a valuable new way to meet the needs of the cancer therapy field.
Collapse
Affiliation(s)
- Zu-Chian Chiang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China.,The Cancer Center, Union Hospital, Fujian Medical University, Fuzhou, China.,College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, China
| | - Shubin Fang
- The Cancer Center, Union Hospital, Fujian Medical University, Fuzhou, China
| | - Yang-Kun Shen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Dongya Cui
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Huanjiao Weng
- The Cancer Center, Union Hospital, Fujian Medical University, Fuzhou, China
| | - Dawei Wang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yuxiang Zhao
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Jizhen Lin
- The Cancer Center, Union Hospital, Fujian Medical University, Fuzhou, China.,The Department of Otolaryngology, Head and Neck Surgery, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| |
Collapse
|
23
|
Delayed processing of blood samples impairs the accuracy of mRNA-based biomarkers. Sci Rep 2022; 12:8196. [PMID: 35581252 PMCID: PMC9113984 DOI: 10.1038/s41598-022-12178-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
The transcriptome of peripheral white blood cells (PWBCs) are indicators of an organism’s physiological state, thus making them a prime biological sample for mRNA-based biomarker discovery. Here, we designed an experiment to evaluate the impact of delayed processing of whole blood samples on gene transcript abundance in PWBCs. We hypothesized that storing blood samples for 24 h at 4 °C would cause RNA degradation resulting in altered transcriptome profiles. There were no statistical differences in RNA quality parameters among samples processed after one, three, six, or eight hours post collection. Additionally, no significant differences were noted in RNA quality parameters or gene transcript abundance between samples collected from the jugular and coccygeal veins. However, samples processed after 24 h of storage had a lower RNA integrity number value (P = 0.03) in comparison to those processed after one hour of storage. Using RNA-sequencing, we identified four and 515 genes with differential transcript abundance in samples processed after storage for eight and 24 h, respectively, relative to samples processed after one hour. Sequencing coverage of transcripts was similar between samples from the 24-h and one-hour groups, thus showing no indication of RNA degradation. This alteration in transcriptome profiles can impair the accuracy of mRNA-based biomarkers, therefore, blood samples collected for mRNA-based biomarker discovery should be refrigerated immediately and processed within six hours post-sampling.
Collapse
|
24
|
Robinson EL, Baker AH, Brittan M, McCracken I, Condorelli G, Emanueli C, Srivastava PK, Gaetano C, Thum T, Vanhaverbeke M, Angione C, Heymans S, Devaux Y, Pedrazzini T, Martelli F. Dissecting the transcriptome in cardiovascular disease. Cardiovasc Res 2022; 118:1004-1019. [PMID: 33757121 PMCID: PMC8930073 DOI: 10.1093/cvr/cvab117] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
The human transcriptome comprises a complex network of coding and non-coding RNAs implicated in a myriad of biological functions. Non-coding RNAs exhibit highly organized spatial and temporal expression patterns and are emerging as critical regulators of differentiation, homeostasis, and pathological states, including in the cardiovascular system. This review defines the current knowledge gaps, unmet methodological needs, and describes the challenges in dissecting and understanding the role and regulation of the non-coding transcriptome in cardiovascular disease. These challenges include poor annotation of the non-coding genome, determination of the cellular distribution of transcripts, assessment of the role of RNA processing and identification of cell-type specific changes in cardiovascular physiology and disease. We highlight similarities and differences in the hurdles associated with the analysis of the non-coding and protein-coding transcriptomes. In addition, we discuss how the lack of consensus and absence of standardized methods affect reproducibility of data. These shortcomings should be defeated in order to make significant scientific progress and foster the development of clinically applicable non-coding RNA-based therapeutic strategies to lessen the burden of cardiovascular disease.
Collapse
Affiliation(s)
- Emma L Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
- The Division of Cardiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Ian McCracken
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - G Condorelli
- Humanitas Research Hospital, Humanitas University, Via Manzoni 113, Rozzano, MI 20089, Italy
| | - C Emanueli
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - P K Srivastava
- Imperial College, National Heart and Lung Institute, Hammersmith campus, Du Cane Road, London W12 0NN, UK
| | - C Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, Pavia 27100, Italy
| | - T Thum
- Hannover Medical School, Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Carl-Neuberg-Straße 1 30625 Hannover, Germany
| | - M Vanhaverbeke
- UZ Gasthuisberg Campus, KU Leuven, Herestraat 49 3000 Leuven, Belgium
| | - C Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, TS4 3BX, UK
| | - S Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Universiteitssingel 50, 6229 Maastricht University, Maastricht, The Netherlands
| | - Y Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg
| | - T Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, 1011 Lausanne, Switzerland
| | - F Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, Piazza Edmondo Malan, 2, 20097 San Donato, Milan, Italy
| | | |
Collapse
|
25
|
Martire S, Valentino P, Marnetto F, Mirabile L, Capobianco M, Bertolotto A. The impact of pre-freezing storage time and temperature on gene expression of blood collected in EDTA tubes. Mol Biol Rep 2022; 49:4709-4718. [PMID: 35279776 PMCID: PMC9262796 DOI: 10.1007/s11033-022-07320-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/02/2022] [Indexed: 12/03/2022]
Abstract
Background Blood is a common source of RNA for gene expression studies. However, it is known to be vulnerable to pre-analytical variables. Although RNA stabilization systems have been shown to reduce such influence, traditional EDTA tubes are still widely used since they are less expensive and enable to study specific leukocyte populations. This study aimed to assess the influence of storage time and temperature between blood sampling and handling on RNA from peripheral blood mononuclear cells (PBMCs). Methods and results Nine blood samples were collected in EDTA tubes from 10 healthy donors. One tube from each donor was immediately processed for PBMC isolation, while the others were first incubated at either 4 degrees Celsius (°C) or room temperature for 2, 4, 6 and 24 h. RNA yield and quality and the expression level of fourt housekeeping (B2M, CASC3, GAPDH, HPRT1) and 8 target genes (CD14, CD19, CD20, IL10, MxA, TNF, TNFAIP3, NR4A2) were compared between samples. RNA yield, quality and integrity did not vary significantly with time and temperature. B2M was the most stable housekeeping gene, while the others were increasingly influenced by storing time, especially at 4 °C. Even when normalized to B2M, the expression level of some target genes, particularly TNFAIP3 and NR4A2, was highly affected by delays in blood processing at either temperature, already from 2 h. Conclusion Pre-analytical processing has a great impact on transcript expression from blood collected in EDTA tubes, especially on genes related to inflammation. Standardized procedure of blood handling are needed to obtain reliable results. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07320-5.
Collapse
Affiliation(s)
- Serena Martire
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy.
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy.
| | - Paola Valentino
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy
| | - Fabiana Marnetto
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy
| | - Luca Mirabile
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
| | - Marco Capobianco
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- SCDO Neurologia and CRESM, University Hospital AOU San Luigi Gonzaga, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Antonio Bertolotto
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Koelliker Hospital, 10100, Turin, Italy
| |
Collapse
|
26
|
Dmitrzak-Weglarz M, Szczepankiewicz A, Rybakowski J, Kapelski P, Bilska K, Skibinska M, Reszka E, Lesicka M, Jablonska E, Wieczorek E, Bukowska-Olech E, Pawlak J. Transcriptomic profiling as biological markers of depression - A pilot study in unipolar and bipolar women. World J Biol Psychiatry 2021; 22:744-756. [PMID: 33821765 DOI: 10.1080/15622975.2021.1907715] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVES A significant challenge in psychiatry is the differential diagnosis of depressive episodes in the course of mood disorders. Gene expression profiling may provide an opportunity for such distinguishment. METHODS We studied differentially expressed genes in women with a depressive episode in the course of unipolar depression (UD) (n = 24) and bipolar disorder types I (BDI) (n = 13) and II (BDII) (n = 19), and healthy controls (n = 15). RESULTS Different types of depression varied in the number and type of up or down-regulated genes. The pathway analysis showed: in UD, up-regulated rheumatoid arthritis pathway (including ITGB2, CXCL8, TEK, TLR4 genes), and down-regulated taste transduction pathway (TAS2R10, TAS2R46, TAS2R14, TAS2R43, TAS2R45, TAS2R19, TAS2R13, TAS2R20, GNG13); in BDI, eight down-regulated pathways: glutamatergic synapse, retrograde endocannabinoid signalling, axon guidance, calcium signalling, nicotine addiction, PI3K-Akt signalling, drug metabolism - cytochrome P450, and morphine addiction; in BDII, up-regulated osteoclast differentiation and Notch signalling pathway, and down-regulated type I diabetes mellitus pathway. Distinct expression markers analysis uncovered the unique for UD, up-regulated bladder cancer pathway (HBEGF and CXCL8 genes). CONCLUSIONS This pilot study suggests a probability of differentiating depression in the course of UD, BDI, and II, based on transcriptomic profiling.
Collapse
Affiliation(s)
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Janusz Rybakowski
- Department of Adult Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Karolina Bilska
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Skibinska
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Edyta Reszka
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Monika Lesicka
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Ewa Jablonska
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Edyta Wieczorek
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | | | - Joanna Pawlak
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| |
Collapse
|
27
|
Keyloun JW, Campbell R, Carney BC, Yang R, Miller SA, Detwiler L, Gautam A, Moffatt LT, Hammamieh R, Jett M, Shupp JW. Early Transcriptomic Response to Burn Injury: Severe Burns Are Associated With Immune Pathway Shutdown. J Burn Care Res 2021; 43:306-314. [PMID: 34791339 PMCID: PMC9890902 DOI: 10.1093/jbcr/irab217] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Burn injury induces a systemic hyperinflammatory response with detrimental side effects. Studies have described the biochemical changes induced by severe burns, but the transcriptome response is not well characterized. The goal of this work is to characterize the blood transcriptome after burn injury. Burn patients presenting to a regional center between 2012 and 2017 were prospectively enrolled. Blood was collected on admission and at predetermined time points (hours 2, 4, 8, 12, and 24). RNA was isolated and transcript levels were measured with a gene expression microarray. To identify differentially regulated genes (false-discovery rate ≤0.1) by burn injury severity, patients were grouped by TBSA above or below 20% and statistically enriched pathways were identified. Sixty-eight patients were analyzed, most patients were male with a median age of 41 (interquartile range, 30.5-58.5) years, and TBSA of 20% (11%-34%). Thirty-five patients had % TBSA injury ≥20%, and this group experienced greater mortality (26% vs 3%, P = .008). Comparative analysis of genes from patients with </≥20% TBSA revealed 1505, 613, 380, 63, 1357, and 954 differentially expressed genes at hours 0, 2, 4, 8, 12, and 24, respectively. Pathway analysis revealed an initial up-regulation in several immune/inflammatory pathways within the ≥20% TBSA groups followed by shutdown. Severe burn injury is associated with an early proinflammatory immune response followed by shutdown of these pathways. Examination of the immunoinflammatory response to burn injury through differential gene regulation and associated immune pathways by injury severity may identify mechanistic targets for future intervention.
Collapse
Affiliation(s)
| | | | - Bonnie C Carney
- Firefighters’ Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia, USA,Department of Surgery, Georgetown University School of Medicine, Washington, District of Columbia, USA,Department of Biochemistry, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Ruoting Yang
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Stacy-Ann Miller
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA,Oak Ridge Institute for Science and Education, Silver Spring, Maryland, USA
| | - Leanne Detwiler
- The Geneva Foundation, Silver Spring, Maryland, USA,Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lauren T Moffatt
- Firefighters’ Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, District of Columbia, USA,Department of Surgery, Georgetown University School of Medicine, Washington, District of Columbia, USA,Department of Biochemistry, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Marti Jett
- Headquarters Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jeffrey W Shupp
- Address correspondence to Jeffrey W. Shupp, MD, The Burn Center, 110 Irving Street, NW, Suite 3B-55, Washington, DC 20010, USA.
| | | |
Collapse
|
28
|
How long does the mRNA remains stable in untreated whole bovine blood? Mol Biol Rep 2021; 49:789-795. [PMID: 34655019 DOI: 10.1007/s11033-021-06808-w] [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: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND High quality and quantity of messenger RNA (mRNA) are required for accuracy of gene expression studies and other RNA-based downstream applications. Since RNA is considered a labile macromolecular prone to degradation, which may result in falsely altered gene expression patterns, several commercial stabilizing reagents have been developed aiming to keep RNA stable for long period. However, for studies involving large number of experimental samples, the high costs related to these specific reagents may constitute a barrier. METHODS AND RESULTS In this context the present study was designed aiming to evaluate the stability of mRNA in whole bovine blood collected in EDTA tubes during storage at common fridge (4 °C). Whole blood samples were collected from six Holstein calves and submitted to RNA extraction in each different interval: immediately after blood sampling (< 2 h), at 1-day post-sampling (dps), 2 dps, 3 dps, 7 dps and 14dps intervals. RNA integrity and purity were evaluated, and RT-qPCR assays were run using seven different genes (B2M, ACTB, PPIA, GAPDH, YWHAZ, CD4 and IFN-γ) aiming to evaluate the presence of altered gene transcription during storage. All extracted RNA samples presented high purity, while optimal integrity and unaltered gene expression were observed in whole experimental group up to 3 days of storage. CONCLUSION Bovine blood RNA remained stable in K3EDTA tubes for 3 days stored at common fridge and can be successfully and accurately used for gene expression studies.
Collapse
|
29
|
Hayman T, Hickey P, Amann-Zalcenstein D, Bennett C, Ataide R, Sthity RA, Khandaker AM, Islam KM, Stracke K, Yassi N, Watson R, Long J, Westcott J, Krebs NF, King JC, Black RE, Islam MM, McDonald CM, Pasricha SR. Zinc Supplementation with or without Additional Micronutrients Does Not Affect Peripheral Blood Gene Expression or Serum Cytokine Level in Bangladeshi Children. Nutrients 2021; 13:nu13103516. [PMID: 34684517 PMCID: PMC8541127 DOI: 10.3390/nu13103516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/27/2021] [Accepted: 10/04/2021] [Indexed: 11/30/2022] Open
Abstract
Preventive zinc supplementation provided as a stand-alone dispersible tablet, or via home fortification as multiple micronutrient powders (MNPs), has been considered a potential strategy to prevent zinc deficiency and improve health (including immune) outcomes among children in low- and middle-income countries. However, the impact of zinc supplementation on immune profiles has not been well characterized. We sought to define the effect of zinc supplementation on peripheral blood gene expression and cytokine levels among young children in Dhaka, Bangladesh. In a sub-study of a large randomized, controlled, community-based efficacy trial where children 9–11 months of age received one of the following interventions on a daily basis for 24 weeks: (1) MNPs containing 10 mg of zinc; (2) dispersible tablet containing 10 mg zinc; or (3) placebo powder, we used RNA sequencing to profile the peripheral blood gene expression, as well as highly sensitive multiplex assays to detect cytokine profiles. We profiled samples from 100 children enrolled in the parent trial (zinc MNPs 28, zinc tablets 39, placebo 33). We did not detect an effect from either zinc intervention on differential peripheral blood gene expression at the end of the intervention, or an effect from the intervention on changes in gene expression from baseline. We also did not detect an effect from either intervention on cytokine concentrations. Exploratory analysis did not identify an association between undernutrition (defined as stunting, underweight or wasting) and peripheral blood gene expression. Zinc interventions in children did not produce a gene expression or cytokine signature in the peripheral blood. However, this study demonstrates a proof of principle that sensitive multi-omic techniques can be applied to samples collected in field studies.
Collapse
Affiliation(s)
- Thomas Hayman
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (T.H.); (C.B.); (R.A.); (K.S.); (N.Y.); (R.W.)
| | - Peter Hickey
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; (P.H.); (D.A.-Z.)
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Daniela Amann-Zalcenstein
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; (P.H.); (D.A.-Z.)
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Cavan Bennett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (T.H.); (C.B.); (R.A.); (K.S.); (N.Y.); (R.W.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; (P.H.); (D.A.-Z.)
| | - Ricardo Ataide
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (T.H.); (C.B.); (R.A.); (K.S.); (N.Y.); (R.W.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; (P.H.); (D.A.-Z.)
| | - Rahvia Alam Sthity
- International Centre for Diarrheal Disease Research, Nutrition and Clinical Services Division, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.A.S.); (A.M.K.); (K.M.I.); (M.M.I.)
| | - Afsana Mim Khandaker
- International Centre for Diarrheal Disease Research, Nutrition and Clinical Services Division, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.A.S.); (A.M.K.); (K.M.I.); (M.M.I.)
| | - Kazi Munisul Islam
- International Centre for Diarrheal Disease Research, Nutrition and Clinical Services Division, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.A.S.); (A.M.K.); (K.M.I.); (M.M.I.)
| | - Katharina Stracke
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (T.H.); (C.B.); (R.A.); (K.S.); (N.Y.); (R.W.)
| | - Nawaf Yassi
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (T.H.); (C.B.); (R.A.); (K.S.); (N.Y.); (R.W.)
- Melbourne Brain Centre, Departments of Medicine and Neurology, The Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3050, Australia
| | - Rosie Watson
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (T.H.); (C.B.); (R.A.); (K.S.); (N.Y.); (R.W.)
- Department of Medicine, The Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3050, Australia
| | - Julie Long
- Department of Pediatrics, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.L.); (J.W.); (N.F.K.)
| | - Jamie Westcott
- Department of Pediatrics, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.L.); (J.W.); (N.F.K.)
| | - Nancy F. Krebs
- Department of Pediatrics, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA; (J.L.); (J.W.); (N.F.K.)
- International Zinc Nutrition Consultative Group, University of California, San Francisco, CA 94158, USA; (J.C.K.); (R.E.B.); (C.M.M.)
| | - Janet C. King
- International Zinc Nutrition Consultative Group, University of California, San Francisco, CA 94158, USA; (J.C.K.); (R.E.B.); (C.M.M.)
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Robert E. Black
- International Zinc Nutrition Consultative Group, University of California, San Francisco, CA 94158, USA; (J.C.K.); (R.E.B.); (C.M.M.)
- Institute for International Programs, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Md. Munirul Islam
- International Centre for Diarrheal Disease Research, Nutrition and Clinical Services Division, Bangladesh (icddr,b), Dhaka 1212, Bangladesh; (R.A.S.); (A.M.K.); (K.M.I.); (M.M.I.)
| | - Christine M. McDonald
- International Zinc Nutrition Consultative Group, University of California, San Francisco, CA 94158, USA; (J.C.K.); (R.E.B.); (C.M.M.)
- Departments of Pediatrics and Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, CA 94158, USA
| | - Sant-Rayn Pasricha
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (T.H.); (C.B.); (R.A.); (K.S.); (N.Y.); (R.W.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia; (P.H.); (D.A.-Z.)
- Diagnostic Haematology, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia
- Clinical Haematology at the Peter MacCallum Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia
- Correspondence:
| |
Collapse
|
30
|
Haack AJ, Lim FY, Kennedy DS, Day JH, Adams KN, Lee JJ, Berthier E, Theberge AB. homeRNA: A Self-Sampling Kit for the Collection of Peripheral Blood and Stabilization of RNA. Anal Chem 2021; 93:13196-13203. [PMID: 34546711 DOI: 10.1021/acs.analchem.1c02008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Gene expression analysis (e.g., targeted gene panels and transcriptomics) from whole blood can elucidate mechanisms of the immune function and aid in the discovery of biomarkers. Conventional venipuncture offers only a small snapshot of our broad immune landscape as immune responses may occur outside of the time and location parameters available for conventional venipuncture. A self-operated method that enables flexible sampling of liquid whole blood coupled with immediate stabilization of cellular RNA is instrumental in facilitating capture and preservation of acute or transient immune fluxes. To this end, we developed homeRNA, a kit for self-collection of peripheral blood (∼0.5 mL) and immediate stabilization of cellular RNA, using the Tasso-SST blood collection device with a specially designed stabilizer tube containing RNAlater. To assess the feasibility of homeRNA for self-collection and stabilization of whole blood RNA, we conducted a pilot study (n = 47 participants) in which we sent homeRNA to participants aged 21-69, located across 10 US states (94% successful blood collections, n = 61/65). Among participants who successfully collected blood, 93% reported no or minimal pain/discomfort using the kit (n = 39/42), and 79% reported very easy/somewhat easy stabilization protocol (n = 33/42). Total RNA yield from the stabilized samples ranged between 0.20 and 5.99 μg (mean = 1.51 μg), and all but one RNA integrity number values were above 7.0 (mean = 8.1), indicating limited RNA degradation. The results from this study demonstrate the self-collection and RNA stabilization of whole blood with homeRNA by participants themselves in their own home.
Collapse
Affiliation(s)
- Amanda J Haack
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,School of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Fang Yun Lim
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dakota S Kennedy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John H Day
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Karen N Adams
- Institute of Translational Health Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Jing J Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Erwin Berthier
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ashleigh B Theberge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,Department of Urology, School of Medicine, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
31
|
Fruits of Vitex doniana sweet: toxicity profile, anti-inflammatory and antioxidant activities, and quantification of one of its bioactive constituents oleanolic acid. Heliyon 2021; 7:e07910. [PMID: 34522807 PMCID: PMC8424515 DOI: 10.1016/j.heliyon.2021.e07910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/06/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022] Open
Abstract
Background Vitex doniana Sweet fruit, an under-utilised crop specie of Ghana, has not been validated for its ethnomedical use in managing inflammatory conditions. Therefore, the study sought to investigate its anti-inflammatory and antioxidant activities as well as isolate and quantify one of its active constituents. Materials and methods In-vivo anti-inflammatory activity of the methanol fruit extract was evaluated using the carrageenan-induced oedema model in chicks. The in-vitro antioxidant property was also investigated using the 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. The acute and subacute toxicity studies of the fruit extract were evaluated in rodent models. Results No signs of autonomic and central nervous system stimulation/depression were recorded. The LD50 by oral route, was estimated to be beyond 3000 mg/kg. Subacute studies revealed an increase in red blood cell and lymphocyte counts. Liver enzymes, serum proteins and bilirubin levels did not significantly increase. The crude extracts at doses of 10, 30 and 100 mg/kg inhibited paw oedema considerably. The ethyl acetate fraction showed the highest antioxidant activity (IC50 = 99.35 ± 0.77 μg/mL). Oleanolic acid, isolated from the ethyl acetate extract, showed significant anti-inflammatory and antioxidant activities. A sensitive high-performance liquid chromatography method for the detection and estimation of oleanolic acid, as a biomarker compound for V. doniana fruit, was developed and validated for quality assurance purposes. Conclusion The extract of V. doniana fruits possesses considerable anti-inflammatory and antioxidant properties and was non-toxic under laboratory conditions.
Collapse
|
32
|
Dmitrzak-Weglarz M, Szczepankiewicz A, Rybakowski J, Kapelski P, Bilska K, Skibinska M, Reszka E, Lesicka M, Jablonska E, Wieczorek E, Pawlak J. Expression Biomarkers of Pharmacological Treatment Outcomes in Women with Unipolar and Bipolar Depression. PHARMACOPSYCHIATRY 2021; 54:261-268. [PMID: 34470067 DOI: 10.1055/a-1546-9483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION This study aimed to find the expression biomarkers of pharmacological treatment response in a naturalistic hospital setting. Through gene expression profiling, we were able to find differentially-expressed genes (DEGs) in unipolar (UD) and bipolar (BD) depressed women. METHODS We performed gene expression profiling in hospitalized women with unipolar (n=24) and bipolar depression (n=32) who achieved clinical improvement after pharmacological treatment (without any restriction). To identify DEGs in peripheral blood mononuclear cells (PBMCs), we used the SurePrint G3 Microarray and GeneSpring software. RESULTS After pharmacological treatment, UD and BD varied in the number of regulated genes and ontological pathways. Also, the pathways of neurogenesis and synaptic transmission were significantly up-regulated. Our research focused on DEGs with a minimum fold change (FC) of more than 2. For both types of depression, 2 up-regulated genes, OPRM1 and CELF4 (p=0.013), were significantly associated with treatment response (defined as a 50% reduction on the Hamilton Depression Rating Scale [HDRS]). We also uncovered the SHANK3 (p=0.001) gene that is unique for UD and found that the RASGRF1 (p=0.010) gene may be a potential specific biomarker of treatment response for BD. CONCLUSION Based on transcriptomic profiling, we identified potential expression biomarkers of treatment outcomes for UD and BD. We also proved that the Ras-GEF pathway associated with long-term memory, female stress response, and treatment response modulation in animal studies impacts treatment efficacy in patients with BD. Further studies focused on the outlined genes may help provide predictive markers of treatment outcomes in UD and BD.
Collapse
Affiliation(s)
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poland
| | - Janusz Rybakowski
- Department of Adult Psychiatry, Poznan University of Medical Sciences, Poland
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poland
| | - Karolina Bilska
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poland
| | - Maria Skibinska
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poland
| | - Edyta Reszka
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Monika Lesicka
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Ewa Jablonska
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Edyta Wieczorek
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Joanna Pawlak
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poland
| |
Collapse
|
33
|
Hope CM, Huynh D, Wong YY, Oakey H, Perkins GB, Nguyen T, Binkowski S, Bui M, Choo AYL, Gibson E, Huang D, Kim KW, Ngui K, Rawlinson WD, Sadlon T, Couper JJ, Penno MAS, Barry SC. Optimization of Blood Handling and Peripheral Blood Mononuclear Cell Cryopreservation of Low Cell Number Samples. Int J Mol Sci 2021; 22:ijms22179129. [PMID: 34502038 PMCID: PMC8431655 DOI: 10.3390/ijms22179129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/14/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Rural/remote blood collection can cause delays in processing, reducing PBMC number, viability, cell composition and function. To mitigate these impacts, blood was stored at 4 °C prior to processing. Viable cell number, viability, immune phenotype, and Interferon-γ (IFN-γ) release were measured. Furthermore, the lowest protective volume of cryopreservation media and cell concentration was investigated. Methods: Blood from 10 individuals was stored for up to 10 days. Flow cytometry and IFN-γ ELISPOT were used to measure immune phenotype and function on thawed PBMC. Additionally, PBMC were cryopreserved in volumes ranging from 500 µL to 25 µL and concentration from 10 × 106 cells/mL to 1.67 × 106 cells/mL. Results: PBMC viability and viable cell number significantly reduced over time compared with samples processed immediately, except when stored for 24 h at RT. Monocytes and NK cells significantly reduced over time regardless of storage temperature. Samples with >24 h of RT storage had an increased proportion in Low-Density Neutrophils and T cells compared with samples stored at 4 °C. IFN-γ release was reduced after 24 h of storage, however not in samples stored at 4 °C for >24 h. The lowest protective volume identified was 150 µL with the lowest density of 6.67 × 106 cells/mL. Conclusion: A sample delay of 24 h at RT does not impact the viability and total viable cell numbers. When long-term delays exist (>4 d) total viable cell number and cell viability losses are reduced in samples stored at 4 °C. Immune phenotype and function are slightly altered after 24 h of storage, further impacts of storage are reduced in samples stored at 4 °C.
Collapse
Affiliation(s)
- Christopher M. Hope
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
- Women’s and Children’s Hospital, Adelaide, SA 5006, Australia
| | - Dao Huynh
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Ying Ying Wong
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Griffith Boord Perkins
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Trung Nguyen
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Sabrina Binkowski
- Children’s Diabetes Centre, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (S.B.); (A.Y.L.C.)
| | - Minh Bui
- Child Health Research Unit, Barwon Health, Geelong, VIC 3220, Australia;
| | - Ace Y. L. Choo
- Children’s Diabetes Centre, Telethon Kids Institute, The University of Western Australia, Perth, WA 6009, Australia; (S.B.); (A.Y.L.C.)
| | - Emily Gibson
- School of Women’s and Children’s Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia; (E.G.); (K.W.K.); (W.D.R.)
| | - Dexing Huang
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; (D.H.); (K.N.)
| | - Ki Wook Kim
- School of Women’s and Children’s Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia; (E.G.); (K.W.K.); (W.D.R.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Katrina Ngui
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia; (D.H.); (K.N.)
| | - William D. Rawlinson
- School of Women’s and Children’s Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia; (E.G.); (K.W.K.); (W.D.R.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Timothy Sadlon
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Jennifer J. Couper
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
- Women’s and Children’s Hospital, Adelaide, SA 5006, Australia
| | - Megan A. S. Penno
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
| | - Simon C. Barry
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (C.M.H.); (D.H.); (Y.Y.W.); (H.O.); (G.B.P.); (T.N.); (T.S.); (J.J.C.); (M.A.S.P.)
- Women’s and Children’s Hospital, Adelaide, SA 5006, Australia
- Correspondence:
| | | |
Collapse
|
34
|
Yamagata H, Kobayashi A, Tsunedomi R, Seki T, Kobayashi M, Hagiwara K, Chen C, Uchida S, Okada G, Fuchikami M, Kamishikiryo T, Iga JI, Numata S, Kinoshita M, Kato TA, Hashimoto R, Nagano H, Okamoto Y, Ueno S, Ohmori T, Nakagawa S. Optimized protocol for the extraction of RNA and DNA from frozen whole blood sample stored in a single EDTA tube. Sci Rep 2021; 11:17075. [PMID: 34426633 PMCID: PMC8382694 DOI: 10.1038/s41598-021-96567-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/11/2021] [Indexed: 01/27/2023] Open
Abstract
Cryopreservation of whole blood is useful for DNA collection, and clinical and basic research. Blood samples in ethylenediaminetetraacetic acid disodium salt (EDTA) tubes stored at − 80 °C are suitable for DNA extraction, but not for high-quality RNA extraction. Herein, a new methodology for high-quality RNA extraction from human blood samples is described. Quickly thawing frozen whole blood on aluminum blocks at room temperature could minimize RNA degradation, and improve RNA yield and quality compared with thawing the samples in a 37 °C water bath. Furthermore, the use of the NucleoSpin RNA kit increased RNA yield by fivefold compared with the PAXgene Blood RNA Kit. Thawing blood samples on aluminum blocks significantly increased the DNA yield by ~ 20% compared with thawing in a 37 °C water bath or on ice. Moreover, by thawing on aluminum blocks and using the NucleoSpin RNA and QIAamp DNA Blood kits, the extraction of RNA and DNA of sufficient quality and quantity was achieved from frozen EDTA whole blood samples that were stored for up to 8.5 years. Thus, extracting RNA from frozen whole blood in EDTA tubes after long-term storage is feasible. These findings may help advance gene expression analysis, as well as biomarker research for various diseases.
Collapse
Affiliation(s)
- Hirotaka Yamagata
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Ayumi Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Ryouichi Tsunedomi
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Tomoe Seki
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Masaaki Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Kosuke Hagiwara
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Chong Chen
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Shusaku Uchida
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.,SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin‑Kawahara‑cho, Sakyo‑ku, Kyoto, 606‑8507, Japan
| | - Go Okada
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Manabu Fuchikami
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Toshiharu Kamishikiryo
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Makoto Kinoshita
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8553, Japan
| | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Yasumasa Okamoto
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Shuichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Shin Nakagawa
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| |
Collapse
|
35
|
Akhlaghi M, Karrabi M, Atabti H, Raoofi A, Mousavi Khaneghah A. Investigation of the role of IL18, IL-1β and NLRP3 inflammasome in reducing expression of FLG-2 protein in Psoriasis vulgaris skin lesions. Biotech Histochem 2021; 97:277-283. [PMID: 34313166 DOI: 10.1080/10520295.2021.1954692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We investigated the effects of the NACHT leucine-rich repeat- and PYD-containing proteins (NLRP3) inflammasome, interleukin -18 (IL-18) and interleukin-1 beta (IL-1β) cytokines on the expression of filaggrin-2 (FLG-2) protein in psoriasis patients. Peripheral blood mononuclear cells (PBMC), including T cells, were isolated from psoriasis patients and healthy donors. Ribonucleic acid (RNA) extraction and reverse transcription-polymerase chain reaction (RT-PCR) were performed for all specimens. Immunohistochemical analysis for FLG-2 in normal and psoriatic epidermal tissue also was performed. Western blot was used to separate and identify FLG-2 protein, and immunohistochemical staining was performed to assess FLG-2 expression for psoriasis skin lesions and normal skin. RT-PCR analysis indicated that NLRP3 inflammasome, IL-18 cytokine and IL-1β cytokine expression were increased in psoriatic epidermis compared to normal skin. We found that the expression of FLG-2 was decreased in psoriatic epidermis compared to normal skin. Higher levels of NLRP3 help decrease the FLG-2 level.
Collapse
Affiliation(s)
- Maedeh Akhlaghi
- Student Research Committee, Cellular and Molecular Research Center, School of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Maryam Karrabi
- Cellular and Molecular Research Center, School of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Hadi Atabti
- Department of Immunology and Biology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Raoofi
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran.,Department of Anatomy, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Amin Mousavi Khaneghah
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas (UNICAMP), Campinas, Brazil
| |
Collapse
|
36
|
Ginger Extract Modulates the Production of Chemokines CCL17, CCL20, CCL22, and CXCL10 and the Gene Expression of Their Receptors in Peripheral Blood Mononuclear Cells from Peptic Ulcer Patients Infected with Helicobacter pylori. Jundishapur J Nat Pharm Prod 2021. [DOI: 10.5812/jjnpp.100824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: The imbalanced expression of chemokines plays critical role in the development of Helicobacter pylori-mediated complications. Objectives: Our aim was to determine ginger extract (GE) effects on the expression of chemokines CCL17, CCL20, CCL22, and CXCL10, as well as CCR4, CCR6, and CXCR3 receptors by peripheral blood mononuclear cells (PBMCs) from H. pylori -infected patients with peptic ulcer (PU). Methods: Peripheral blood mononuclear cells were obtained from 20 patients with H. pylori-associated PU, 20 H. pylori-infected asymptomatic subjects (HAS), and 20 non-infected healthy subjects (NHS). The PBMCs were stimulated by 10 µg/mL of H. pylori-derived crude extract (HPCE) in the presence of 0, 10, 20, and 30 µg/mL of GE. After 36 hours, the supernatant and the RNA extracted from the cells were tested for chemokine concentration and chemokine receptor expression using ELISA and real-time PCR techniques, respectively. Results: In PU patients, treating HPCE-stimulated PBMCs with 10, 20, or 30 µg/mL GE reduced the production of CXCL10 (1.47, 1.5, and 1.53 folds, respectively, P < 0.001 for all), CCL20 (1.44, 1.62, and 1.65 folds, respectively, P < 0.003), and treatment with 30 µg/mL GE increased CCL17 (1.28-fold, P < 0.001) and CCL22 (1.59-fold, P < 0.001) production compared with untreated HPCE-stimulated PBMCs. In PU patients, the HPCE-stimulated PBMCs treated with 10, 20, or 30 µg/mL GE expressed lower levels of CXCR3 (1.9, 3, and 3.5 folds, respectively, P < 0.001) and CCR6 (2.3, 2.7, and 2.8 folds, respectively, P < 0.002) while treating with 10 µg/mL GE upregulated CCR4 (1.7 fold, P = 0.003) compared with untreated HPCE-stimulated PBMCs. Conclusions: Ginger extract modulated the expression of chemokines and their receptors in the PBMCs derived from H. pylori-infected PU patients. The therapeutic potentials of ginger for treating HP-related complications need to be further explored.
Collapse
|
37
|
Dmitrzak-Weglarz M, Banach E, Bilska K, Narozna B, Szczepankiewicz A, Reszka E, Jablonska E, Kapelski P, Skibinska M, Pawlak J. Molecular Regulation of the Melatonin Biosynthesis Pathway in Unipolar and Bipolar Depression. Front Pharmacol 2021; 12:666541. [PMID: 33981243 PMCID: PMC8107693 DOI: 10.3389/fphar.2021.666541] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Melatonin is a neurohormone that maintains the circadian rhythms of the body. By regulating the secretion of other hormones and neurotransmitters, it acts as a pleiotropic modulator that affects, for example, reproductive, immune, cardiovascular, sleep, and wake systems and mood. Thus, synthetic melatonin has become an essential component in the treatment of depressive disorders. Although we know the pathway of melatonin action in the brain, we lack comprehensive cross-sectional studies on the periphery of depressed patients. This study aimed to comprehensively analyze the differences between healthy control subjects (n = 84) and unipolar and bipolar depression patients (n = 94), including an analysis of the melatonin pathway at the level of the genes and serum biomarkers. An innovative approach is a pilot study based on gene expression profiling carried out on clinical and cell culture models using agomelatine and melatonin. We confirmed the melatonin biosynthesis pathway's molecular regulation dysfunctions, with a specific pattern for unipolar and bipolar depression, at the AANAT gene, its polymorphisms (rs8150 and rs3760138), and examined the serum biomarkers (serotonin, AANAT, ASMT, and melatonin). The biological pathway analysis uncovered pathways and genes that were uniquely altered after agomelatine treatment in a clinical model and melatonin treatment in a cell culture model. In both models, we confirmed the immunomodulatory effect of melatonin agents in depression.
Collapse
Affiliation(s)
| | - Ewa Banach
- Laboratory of Neurobiology, Department of Molecular and Cellular Neurobiology, Nencki Institute, Warsaw, Poland
| | - Karolina Bilska
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Beata Narozna
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Aleksandra Szczepankiewicz
- Laboratory of Molecular and Cell Biology, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Edyta Reszka
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Ewa Jablonska
- Department of Molecular Genetics and Epigenetics, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Paweł Kapelski
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Skibinska
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Pawlak
- Department of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| |
Collapse
|
38
|
Zhang SQ, Pan SM, Liang SX, Han YS, Chen HB, Li JC. Research status and prospects of biomarkers for nasopharyngeal carcinoma in the era of high‑throughput omics (Review). Int J Oncol 2021; 58:9. [PMID: 33649830 PMCID: PMC7910009 DOI: 10.3892/ijo.2021.5188] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/21/2021] [Indexed: 02/07/2023] Open
Abstract
As a malignant tumor type, nasopharyngeal carcinoma (NPC) is characterized by distinct geographical, ethnic and genetic differences; presenting a major threat to human health in many countries, especially in Southern China. At present, no accurate and effective methods are available for the early diagnosis, efficacious evaluation or prognosis prediction for NPC. As such, a large number of patients have locoregionally advanced NPC at the time of initial diagnosis. Many patients show toxic reactions to overtreatment and have risks of cancer recurrence and distant metastasis owing to insufficient treatment. To solve these clinical problems, high‑throughput '‑omics' technologies are being used to screen and identify specific molecular biomarkers for NPC. Because of the lack of comprehensive descriptions regarding NPC biomarkers, the present study summarized the research progress that has been made in recent years to discover NPC biomarkers, highlighting the existing problems that require exploration. In view of the lack of authoritative reports at present, study design factors that affect the screening of biomarkers are also discussed here and prospects for future research are proposed to provide references for follow‑up studies of NPC biomarkers.
Collapse
Affiliation(s)
- Shan-Qiang Zhang
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Wujiang, Shaoguan, Guangdong 512025, P.R. China
| | - Su-Ming Pan
- Department of Radiotherapy, Yue Bei People's Hospital, Shantou University Medical College, Wujiang, Shaoguan, Guangdong 512025, P.R. China
| | - Si-Xian Liang
- Department of Radiotherapy, Yue Bei People's Hospital, Shantou University Medical College, Wujiang, Shaoguan, Guangdong 512025, P.R. China
| | - Yu-Shuai Han
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, P.R. China
| | - Hai-Bin Chen
- Department of Histology and Embryology, Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Ji-Cheng Li
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Wujiang, Shaoguan, Guangdong 512025, P.R. China
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, P.R. China
- Correspondence to: Professor Ji-Cheng Li, Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, 133 Huimin South Road, Wujiang, Shaoguan, Guangdong 512025, P.R. China, E-mail:
| |
Collapse
|
39
|
Crnko S, Schutte H, Doevendans PA, Sluijter JPG, van Laake LW. Minimally Invasive Ways of Determining Circadian Rhythms in Humans. Physiology (Bethesda) 2021; 36:7-20. [DOI: 10.1152/physiol.00018.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Circadian rhythm exerts a critical role in mammalian health and disease. A malfunctioning circadian clock can be a consequence, as well as the cause of several pathophysiologies. Clinical therapies and research may also be influenced by the clock. Since the most suitable manner of revealing this rhythm in humans is not yet established, we discuss existing methods and seek to determine the most feasible ones.
Collapse
Affiliation(s)
- Sandra Crnko
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Hilde Schutte
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Pieter A. Doevendans
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
- Central Military Hospital, Utrecht, The Netherlands
| | - Joost P. G. Sluijter
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
- Utrecht University, Utrecht, The Netherlands
| | - Linda W. van Laake
- Department of Cardiology, Experimental Cardiology Laboratory, Division of Heart and Lungs, University Medical Centre Utrecht and Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, Circulatory Health Laboratory, University Medical Centre Utrecht, Utrecht, The Netherlands
| |
Collapse
|
40
|
Widespread transcriptional disruption of the microRNA biogenesis machinery in brain and peripheral tissues of individuals with schizophrenia. Transl Psychiatry 2020; 10:376. [PMID: 33149139 PMCID: PMC7642431 DOI: 10.1038/s41398-020-01052-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/16/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
In schizophrenia, altered transcription in brain and peripheral tissues may be due to altered expression of the microRNA biogenesis machinery genes. In this study, we explore the expression of these genes both at the cerebral and peripheral levels. We used shinyGEO application to analyze gene expression from ten Gene Expression Omnibus datasets, in order to perform differential expression analyses for eight genes encoding the microRNA biogenesis machinery. First, we compared expression of the candidate genes between control subjects and individuals with schizophrenia in postmortem cerebral samples from seven different brain regions. Then, we compared the expression of the candidate genes between control subjects and individuals with schizophrenia in three peripheral tissues. In brain and peripheral tissues of individuals with schizophrenia, we report distinct altered expression patterns of the microRNA biogenesis machinery genes. In the dorsolateral prefrontal cortex, associative striatum and cerebellum of individuals with schizophrenia, we observed an overexpression pattern of some candidate genes suggesting a heightened miRNA production in these brain regions. Additionally, mixed transcriptional abnormalities were identified in the hippocampus. Moreover, in the blood and olfactory epithelium of individuals with schizophrenia, we observed distinct aberrant transcription patterns of the candidate genes. Remarkably, in individuals with schizophrenia, we report DICER1 overexpression in the dorsolateral prefrontal cortex, hippocampus and cerebellum as well as a congruent DICER1 upregulation in the blood compartment suggesting that it may represent a peripheral marker. Transcriptional disruption of the miRNA biogenesis machinery may contribute to schizophrenia pathogenesis both in brain and peripheral tissues.
Collapse
|
41
|
Effects of processing conditions on stability of immune analytes in human blood. Sci Rep 2020; 10:17328. [PMID: 33060628 PMCID: PMC7566484 DOI: 10.1038/s41598-020-74274-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022] Open
Abstract
Minimizing variability in collection and processing of human blood samples for research remains a challenge. Delaying plasma or serum isolation after phlebotomy (processing delay) can cause perturbations of numerous analytes. Thus, a comprehensive understanding of how processing delay affects major endpoints used in human immunology research is necessary. Therefore, we studied how processing delay affects commonly measured cytokines and immune cell populations. We hypothesized that short-term time delays inherent to human research in serum and plasma processing impact commonly studied immunological analytes. Blood from healthy donors was subjected to processing delays commonly encountered in sample collection, and then assayed by 62-plex Luminex panel, 40-parameter mass cytometry panel, and 540,000 transcript expression microarray. Variance for immunological analytes was estimated using each individual’s baseline as a control. In general, short-term processing delay led to small changes in plasma and serum cytokines (range − 10.8 to 43.5%), markers and frequencies of peripheral blood mononuclear cell phenotypes (range 0.19 to 3.54 fold), and whole blood gene expression (stable for > 20 K genes)—with several exceptions described herein. Importantly, we built an open-access web application allowing investigators to estimate the degree of variance expected from processing delay for measurements of interest based on the data reported here.
Collapse
|