Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

Abstract

Sepsis is a global health emergency, which is caused by various sources of infection that lead to changes in gene expression, protein-coding, and metabolism. Advancements in “omics” technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. In this study, we performed shotgun mass spectrometry in peripheral blood mononuclear cells (PBMC) from septic patients (N=24) and healthy controls (N=9) and combined these results with two public microarray leukocytes datasets. Through combination of transcriptome and proteome profiling, we identified 170 co‐differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Ingenuity Pathway Analysis revealed pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. Protein-protein interaction network analyses revealed two densely connected regions, which mainly included down‐regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up‐regulated genes/proteins, which were mainly related to low-density neutrophils (LDNs). LDNs were reported in sepsis and in COVID-19. Changes in gene expression level were validated using quantitative real-time PCR in PBMCs from patients with sepsis. To further support that the source of the upregulated module of genes/proteins found in our results were derived from LDNs, we identified an increase of this population by flow cytometry in PBMC samples obtained from the same cohort of septic patients included in the proteomic analysis. This study provides new insights into a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes/proteins related to LDNs and host‐defense system.

Key Signature Genes of Early Terminal Granulocytic Differentiation Distinguish Sepsis From Systemic Inflammatory Response Syndrome on Intensive Care Unit Admission

“…Our CD15 + transcriptional profiles very strongly match well-understood profiles of bone marrow promyelocytes and myelocytes ( 28 ) that both showed higher blood counts in sepsis than SIRS. From this, we conclude that genes with increased expression in sepsis compared to SIRS on ICU admission represent key signature genes of early terminal granulocytic differentiation rather than neutrophil activation as frequently concluded previously from whole blood gene classifiers of sepsis ( 49 – 51 ). This functional difference agrees with the above-introduced 2013 studies by Nierhaus et al.…”

Single-cell transcriptome profiling reveals heterogeneous neutrophils with prognostic values in sepsis

“…Neutrophils have been found to have an immunomodulatory capacity in many disease conditions ( Hassani et al., 2020 ; Tay et al., 2020 ). Neutrophils are greatly expanded and enriched during sepsis response, playing important roles in the pathogenesis and development of sepsis ( Darcy et al., 2014 ; Leite et al., 2021 ; Takizawa et al., 2021 ; Uhel et al., 2017 ). Neutrophils are heterogeneous, with each subtype having distinct transcriptome profiles and biological functions at different severity stages ( Kangelaris et al., 2021 ; Seman and Robinson, 2021 ).…”

Human peripheral blood mononuclear cells: A review of recent proteomic applications

“…In a similar study, Leite et al. combined transcriptomic and proteomic profiling to unveil molecular pathways implicated in sepsis [35]. PBMCs proteome was isolated from blood samples, proteins were digested into peptides and both qualitatively and quantitatively determined via data‐independent analysis (DIA).…”