Comprehensive Transcriptome Profiling of Peripheral Blood
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Int. J. Med. Sci. 2020, Vol. 17 2077 Ivyspring International Publisher International Journal of Medical Sciences 2020; 17(14): 2077-2086. doi: 10.7150/ijms.46910 Research Paper Comprehensive Transcriptome Profiling of Peripheral Blood Mononuclear Cells from Patients with Sepsis Tianzhou Wu1*, Xi Liang1*, Yongpo Jiang2*, Qi Chen1, Huaping Zhang6, Sheng Zhang2, Chao Zhang3, Yuhang Lv6, Jiaojiao Xin1,4, Jing Jiang1,4, Dongyan Shi1,4, Xin Chen1,5, Jun Li1,4 and Yinghe Xu6 1. Precision Medicine Center, Taizhou Central Hospital, Taizhou University Medical School, Taizhou, China. 2. Department of intensive care unit, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, China. 3. Department of intensive care unit, Taizhou Enze Medical Center (Group) Enze Hospital, Taizhou, China. 4. State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine. 5. Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China. 6. Department of intensive care unit, Taizhou Central Hospital, Taizhou University Medical School, Taizhou, China. *These authors contributed equally to this work. Corresponding authors: Yinghe Xu. M.D. Professor, Department of intensive care unit, Taizhou Central Hospital, Taizhou University Medical School, Taizhou, China, E-mail: [email protected]; Co-corresponding: Jun Li. M.D. & Ph.D. Professor, E-mail: [email protected]; Xin Chen. Ph.D. Professor. E-mail: [email protected]. © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2020.04.11; Accepted: 2020.07.14; Published: 2020.07.25 Abstract Background: Sepsis, as a clinical emergency, usually causes multiorgan dysfunction and can lead to high mortality. Establishment of specific and sensitive biomarkers for early diagnosis is critical to identify patients who would benefit from targeted therapy. In this study, we investigated this syndrome by analyzing the transcriptome of peripheral blood mononuclear cells (PBMCs) from patients with sepsis and identified sepsis-specific biomarkers. Methods: In this study, a total of 87 patients with sepsis and 40 healthy controls from a prospective multicenter cohort were enrolled. Samples from 44 subjects (24 patients with sepsis and 20 healthy controls) were sequenced and the remaining patients were included in the validation group. Using high-throughput sequencing, a gene expression profile of PBMCs from patients with sepsis was generated to elucidate the pathophysiology of sepsis and identify sepsis-specific biomarkers. Results: Principal component analysis (PCA) and unsupervised hierarchical cluster analysis showed that patients with sepsis separated from healthy controls. A total of 1639 differentially expressed genes (DEGs) were identified (|log2 fold change|>2, adjusted P value <0.05) between these two groups, with 1278 (78.0%) upregulated and 361 (22.0%) downregulated in patients with sepsis. Gene Ontology (GO) analysis of the upregulated DEGs identified 194 GO terms that were clustered into 27 groups, and analysis of the downregulated DEGs identified 20 GO terms that were clustered into 4 groups. Four unique genes were identified that could be predictive of patients with sepsis. External validation of the four genes using quantitative real-time polymerase chain reaction (qRT-PCR) was consistent with the results of mRNA sequencing, revealing their potential in sepsis diagnosis. Conclusions: The transcriptome characteristics of PBMCs, which were significantly altered in sepsis patients, provide new insights into sepsis pathogenesis. The four identified gene expression changes differentiated patients with sepsis from healthy subjects, which could serve as a convenient tool contributing to sepsis diagnosis. Key words: sepsis; transcriptomics; peripheral blood mononuclear cells; biomarker Introduction Sepsis is a potentially life-threatening condition damage, organ failure, and death. The incidence of in the intensive care unit (ICU) caused by the body's sepsis is very high (2.8 million deaths per year response to an infection, that can lead to tissue worldwide) in adults, with high mortality rates of 10– http://www.medsci.org Int. J. Med. Sci. 2020, Vol. 17 2078 50%, depending on age and disease severity [1, 2]. Study design Despite the burden on patients and the healthcare Patients were prospectively screened at 3 service system, treatment remains mainly futile. Thus, participating ICUs and enrolled between April 1, precise diagnosis and targeted therapy for sepsis is 2019, and November 20, 2019. The last follow-up was crucial to reducing mortality, with every hour of completed on February 18, 2020. Adult patients (aged delay increasing mortality risk [3]. >18 years) who were admitted to the ICU with sepsis Recent findings in transcriptome analysis have were enrolled in the study. Healthy subjects (with 0 in given us a greater understanding of the mechanisms SOFA and without infection) were also recruited as behind diseases. Genome-wide gene expression the control group from Physical Examination Center profiling is extensively used to discover new potential during the same time. Sepsis was defined as the biomarkers for the diagnosis or prediction of disease presence of an infection combined with an acute severity and identification of novel drug targets. change in SOFA score of 2 or more points [10]. However, tissue sampling has limited the accurate Detailed clinical data and outcomes for all enrolled investigation of sepsis pathogenesis. Therefore, blood patients were collected and recorded in case report can be used as a surrogate and can be obtained with a forms at admission and during the 28/90-day minimally invasive procedure. Many studies have follow-up. indicated that the messenger ribonucleic acid (mRNA) expression levels of specific genes in peripheral blood Methods of mRNA sequencing/mRNA mononuclear cells (PBMCs) can serve as a signature of sequencing sample preparation specific diseases, such as active pulmonary Samples were obtained from 105 patients with tuberculosis [4] and enterocolitis syndrome [5]. an acute change in SOFA score of 2 or more points Recently, many genes have also been identified for following admission to ICU, and 10 mL whole blood sepsis diagnosis and prognosis; for example, sample were taken. PBMCs were immediately SeptiCyte Lab combined with CEACAM4, LAMP1, isolated by Ficoll-PaqueTM PLUS medium (GE PLA2G7, and PLAC8 genes was identified to Healthcare, Uppsala, Sweden). Eighty-seven patients determine which patients had sepsis [6]. Meanwhile, diagnosed with infection were finally defined as seven genes (DYRK2, CCNB1IP1, TDRD9, ZAP70, sepsis, and their samples were used for mRNA ARL14EP, MDC1, and ADGRE3) had been identified sequencing or validation, as well as, samples of 40 as predictors of septic patients and their relationships healthy controls. Total RNA, which was freshly with clinical outcomes were observed [7]. However, extracted, was stored at -80°C for subsequent testing. these biomarkers lack sensitivity and specificity and A sequencing library was then prepared following the have been analyzed by microarray data [8, 9]. manufacturer’s instructions (TruSeqTM Small RNA We hypothesized that the pathological process of Sample Preparation Kit, Illumina, San Diego, CA, sepsis changes the transcriptome profile of PBMCs. In USA), consisting of purification of poly-A-containing this study, we characterized the transcriptome profile mRNA molecules, fragmentation of mRNA, end of PBMCs in patients with sepsis using high- repair, addition of a single ‘A’ base, ligation of throughput sequencing to establish alterations adapters, reverse transcription, PCR amplification present in gene expression patterns and identify and pooled gel purification steps. The pooled library potential biomarkers that could serve as a convenient consisted of sequences with lengths of approximately tool to improve sepsis diagnosis. 250 nucleotides. The library was sequenced using the HiSeq 2500 sequencing system (Illumina, San Diego, Methods CA, USA). The study was approved by the Clinical Research Ethics Committee of Taizhou Central Quantitative real-time polymerase chain Hospital (Taizhou University Medical School) reaction (Registration number: 2019-016, Principal Quantitative real-time polymerase chain reaction investigator: Yinghe Xu, Date of registration: (qRT-PCR) was used to validate the results of the February 26, 2019). This study was registered in the transcriptome analysis. Total RNA was isolated from Chinese Clinical Trial Registry (ChiCTR1900022081, PBMCs and reverse transcribed. qRT-PCR was Principal investigator: Yinghe Xu, Date of registration: performed using a two-step protocol. Complementary March 21, 2019). The trial was registered prior to DNA (cDNA) was synthesized using a RevertAid patient enrollment. Written informed consent was First Strand cDNA Synthesis Kit (Thermo, IL, USA). obtained from all participators or their legal The amount of cDNA was optimized so that representative. amplification of both control gene cDNA and the cDNAs of interest were in the exponential phase. http://www.medsci.org Int. J. Med. Sci. 2020, Vol. 17 2079 qRT-PCRs were performed with PowerUp SYBR enrichment analysis.