Evans L, Rhodes A, Alhazzani W, Antonelli M, Coopersmith CM, French C, et al. Executive summary: surviving sepsis campaign: international guidelines for the management of sepsis and septic shock 2021. Crit Care Med. 2021;49:1974–82.
Hou J, Chen Q, Wu X, Zhao D, Reuveni H, Licht T, et al. S1PR3 signaling drives bacterial killing and is required for survival in bacterial sepsis. Am J Respir Crit Care Med. 2017;196:1559–70.
Fleischmann C, Scherag A, Adhikari NK, Hartog CS, Tsaganos T, Schlattmann P, et al. Assessment of global incidence and mortality of hospital-treated sepsis. Current estimates and limitations. Am J Respir Crit Care Med. 2016;193:259–72.
van Vught LA, Klein Klouwenberg PM, Spitoni C, Scicluna BP, Wiewel MA, Horn J, et al. Incidence, risk factors, and attributable mortality of secondary infections in the intensive care unit after admission for sepsis. JAMA. 2016;315:1469–79.
Prescott HC, Angus DC. Enhancing recovery from sepsis: a review. JAMA. 2018;319:62–75.
Wang J, Sun Y, Teng S, Li K. Prediction of sepsis mortality using metabolite biomarkers in the blood: a meta-analysis of death-related pathways and prospective validation. BMC Med. 2020;18:83.
Rubio I, Osuchowski MF, Shankar-Hari M, Skirecki T, Winkler MS, Lachmann G, et al. Current gaps in sepsis immunology: new opportunities for translational research. Lancet Infect Dis. 2019;19:e422–36.
Nakamori Y, Park EJ, Shimaoka M. Immune deregulation in sepsis and septic shock: reversing immune paralysis by targeting PD-1/PD-L1 pathway. Front Immunol. 2021;11: 624279.
van der Poll T, van de Veerdonk FL, Scicluna BP, Netea MG. The immunopathology of sepsis and potential therapeutic targets. Nat Rev Immunol. 2017;17:407–20.
Venet F, Monneret G. Advances in the understanding and treatment of sepsis-induced immunosuppression. Nat Rev Nephrol. 2018;14:121–37.
Hutchins NA, Unsinger J, Hotchkiss RS, Ayala A. The new normal: immunomodulatory agents against sepsis immune suppression. Trends Mol Med. 2014;20:224–33.
Hotchkiss RS, Monneret G, Payen D. Immunosuppression in sepsis: a novel understanding of the disorder and a new therapeutic approach. Lancet Infect Dis. 2013;13:260–8.
Reinhart K, Bauer M, Riedemann NC, Hartog CS. New approaches to sepsis: molecular diagnostics and biomarkers. Clin Microbiol Rev. 2012;25:609–34.
Steinhagen F, Schmidt SV, Schewe JC, Peukert K, Klinman DM, Bode C. Immunotherapy in sepsis-brake or accelerate? Pharmacol Ther. 2020;208: 107476.
van’t Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002;415:530–6.
Cuocolo R, Caruso M, Perillo T, Ugga L, Petretta M. Machine learning in oncology: a clinical appraisal. Cancer Lett. 2020;481:55–62.
Adams CR, Htwe HH, Marsh T, Wang AL, Montoya ML, Subbaraj L, et al. Transcriptional control of subtype switching ensures adaptation and growth of pancreatic cancer. Elife. 2019;8: e45313.
Xie P, Ma Y, Yu S, An R, He J, Zhang H. Development of an immune-related prognostic signature in breast cancer. Front Genet. 2020;10:1390.
Li X, Wen D, Li X, Yao C, Chong W, Chen H. Identification of an immune signature predicting prognosis risk and lymphocyte infiltration in colon cancer. Front Immunol. 2020;11:1678.
Wang J, Yu S, Chen G, Kang M, Jin X, Huang Y, et al. A novel prognostic signature of immune-related genes for patients with colorectal cancer. J Cell Mol Med. 2020;24:8491–504.
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. 2013;41:D991–5.
Scicluna BP, Klein Klouwenberg PM, van Vught LA, Wiewel MA, Ong DS, Zwinderman AH, et al. A molecular biomarker to diagnose community-acquired pneumonia on intensive care unit admission. Am J Respir Crit Care Med. 2015;192:826–35.
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, et al. ArrayExpress update—from bulk to single-cell expression data. Nucleic Acids Res. 2019;47(D1):D711–5.
Davenport EE, Burnham KL, Radhakrishnan J, Humburg P, Hutton P, Mills TC, et al. Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study. Lancet Respir Med. 2016;4(4):259–71.
Simon N, Friedman J, Hastie T, Tibshirani R. Regularization paths for Cox’s proportional hazards model via coordinate descent. J Stat Softw. 2011;39:1–13.
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011;39(Database issue):D561–8.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43: e47.
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30.
Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12:453–7.
Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160:48–61.
Singer M, Deutschman CS, Seymour CW, Shankar-Hari M, Annane D, Bauer M, et al. The third international consensus definitions for sepsis and septic shock (Sepsis-3). JAMA. 2016;315:801–10.
Bolanaki M, Möckel M, Winning J, Bauer M, Reinhart K, Stacke A, et al. Diagnostic performance of procalcitonin for the early identification of sepsis in patients with elevated qSOFA score at emergency admission. J Clin Med. 2021;10:3869.
Giamarellos-Bourboulis EJ, Norrby-Teglund A, Mylona V, Savva A, Tsangaris I, Dimopoulou I, et al. Risk assessment in sepsis: a new prognostication rule by APACHE II score and serum soluble urokinase plasminogen activator receptor. Crit Care. 2012;16:R149.
Ait-Oufella H, Lemoinne S, Boelle PY, Galbois A, Baudel JL, Lemant J, et al. Mottling score predicts survival in septic shock. Intensive Care Med. 2011;37:801–7.
Oh TK, Ji E, Na HS, Min B, Jeon YT, Do SH, et al. C-reactive protein to albumin ratio predicts 30-day and 1-year mortality in postoperative patients after admission to the intensive care unit. J Clin Med. 2018;7:39.
Faix JD. Biomarkers of sepsis. Crit Rev Clin Lab Sci. 2013;50:23–36.
Rosadini CV, Kagan JC. Early innate immune responses to bacterial LPS. Curr Opin Immunol. 2017;44:14–9.
Seeley JJ, Baker RG, Mohamed G, Bruns T, Hayden MS, Deshmukh SD, et al. Induction of innate immune memory via microRNA targeting of chromatin remodelling factors. Nature. 2018;559:114–9.
Wong HR. Pediatric sepsis biomarkers for prognostic and predictive enrichment. Pediatr Res. 2022;91:283–8.
Iglesias J, Vassallo AV, Liesenfeld O, Levine JS, Patel VV, Sullivan JB, et al. A 33-mRNA classifier is able to produce inflammopathic, daaptive, and coagulopathic endotypes with prognostic significance: the outcomes of metabolic resuscitation using ascorbic acid, thiamine, and glucocorticoids in the early treatment of sepsis (ORANGES) trial. J Pers Med. 2020;11:9.
Shapiro NI, Trzeciak S, Hollander JE, Birkhahn R, Otero R, Osborn TM, et al. A prospective, multicenter derivation of a biomarker panel to assess risk of organ dysfunction, shock, and death in emergency department patients with suspected sepsis. Crit Care Med. 2009;37:96–104.
Jekarl DW, Kim JY, Ha JH, Lee S, Yoo J, Kim M, et al. Diagnosis and prognosis of sepsis based on use of cytokines, chemokines, and growth factors. Dis Mark. 2019;2019:1089107.
Vandenbroucke RE, Vanlaere I, Van Hauwermeiren F, Van Wonterghem E, Wilson C, Libert C. Pro-inflammatory effects of matrix metalloproteinase 7 in acute inflammation. Mucosal Immunol. 2014;7:579–88.
Zhang S, Li N, Chen W, Fu Q, Liu Y. Time series gene expression profiles analysis identified several potential biomarkers for sepsis. DNA Cell Biol. 2020;39:1862–71.
Liu S, Huang Z, Deng X, Zou X, Li H, Mu S, et al. Identification of key candidate biomarkers for severe influenza infection by integrated bioinformatical analysis and initial clinical validation. J Cell Mol Med. 2021;25:1725–38.
Liu T, Guo Y, Zhao J, He S, Bai Y, Wang N, et al. Systems pharmacology and verification of ShenFuHuang formula in zebrafish model reveal multi-scale treatment strategy for septic syndrome in COVID-19. Front Pharmacol. 2020;11: 584057.
Kim KW, Vallon-Eberhard A, Zigmond E, Farache J, Shezen E, Shakhar G, et al. In vivo structure/function and expression analysis of the CX3C chemokine fractalkine. Blood. 2011;118:e156–67.
Friggeri A, Cazalis MA, Pachot A, Cour M, Argaud L, Allaouchiche B, et al. Decreased CX3CR1 messenger RNA expression is an independent molecular biomarker of early and late mortality in critically ill patients. Crit Care. 2016;20:204.
Pachot A, Cazalis MA, Venet F, Turrel F, Faudot C, Voirin N, et al. Decreased expression of the fractalkine receptor CX3CR1 on circulating monocytes as new feature of sepsis-induced immunosuppression. J Immunol. 2008;180:6421–9.
Nylén C, Aoi W, Abdelmoez AM, Lassiter DG, Lundell LS, Wallberg-Henriksson H, et al. IL6 and LIF mRNA expression in skeletal muscle is regulated by AMPK and the transcription factors NFYC, ZBTB14, and SP1. Am J Physiol Endocrinol Metab. 2018;315:E995-1004.
Dubey S, Yoon H, Cohen MS, Nagarkatti P, Nagarkatti M, Karan D. Withaferin A associated differential regulation of inflammatory cytokines. Front Immunol. 2018;9:195.
Kumakura M, Kawaguchi A, Nagata K. Actin-myosin network is required for proper assembly of influenza virus particles. Virology. 2015;476:141–50.
Xini A, Pistiki A, Lada M, Giamarellos-Bourboulis EJ, Dimopoulos G. Association of the early absolute CD64-expressing neutrophil count and sepsis outcome. Eur J Clin Microbiol Infect Dis. 2019;38:1123–8.
Hanna MOF, Abdelhameed AM, Abou-Elalla AA, Hassan RM, Kostandi I. Neutrophil and monocyte receptor expression in patients with sepsis: implications for diagnosis and prognosis of sepsis. Pathog Dis. 2019;77:ftz055.