Aziz, M. et al. B-1a cells protect mice from sepsis-induced acute lung injury. Mol. Med. 24(1), 26 (2018).
Bowdish, M. E. et al. A randomized trial of mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome from COVID-19. Am. J. Respir. Crit. Care Med. 207(3), 261–270 (2023).
Neto, A. S., Dessap, A. M. & Papazian, L. Focus on ARDS. Intensive Care Med. 43(10), 1495–1497 (2017).
Tamayo, E. et al. Pro- and anti-inflammatory responses are regulated simultaneously from the first moments of septic shock. Eur. Cytokine Netw. 22(2), 82–87 (2011).
Gaieski, D. F. et al. Benchmarking the incidence and mortality of severe sepsis in the United States. Crit. Care Med. 41(5), 1167–1174 (2013).
Donnelly, J. P., Hohmann, S. F. & Wang, H. E. Unplanned readmissions after hospitalization for severe sepsis at academic medical center-affiliated hospitals. Crit. Care Med. 43(9), 1916–1927 (2015).
Nedeva, C. Inflammation and cell death of the innate and adaptive immune system during sepsis. Biomolecules 11(7), (2021).
Venet, F. et al. Early assessment of leukocyte alterations at diagnosis of septic shock. Shock 34(4), 358–363 (2010).
Khwannimit, B. & Bhurayanontachai, R. The epidemiology of, and risk factors for, mortality from severe sepsis and septic shock in a tertiary-care university hospital setting. Epidemiol. Infect. 137(9), 1333–1341 (2009).
Fleischmann, C. et al. Assessment of global incidence and mortality of hospital-treated sepsis. Current estimates and limitations. Am. J. Respir. Crit. Care Med. 193(3), 259–272 (2016).
Jiang, Y. et al. Pyroptosis in septic lung injury: Interactions with other types of cell death. Biomed. Pharmacother. 169, 115914 (2023).
Adkins, B., Levy, O. & Betz, A. G. A new unexpected twist in newborn immunity. Nat. Med. 20(1), 22–23 (2014).
Xie, J. & Dow, W. H. Longitudinal study of child immunization determinants in China. Soc. Sci. Med. 61(3), 601–611 (2005).
Hopkins, R. H. & Vyas, K. S. Adult immunization guidelines: Challenges and opportunities. Ann. Intern. Med. 152(1), 59–60 (2010).
Wu, Y. et al. Attention mechanism-based graph neural network model for effective activity prediction of SARS-CoV-2 main protease inhibitors: Application to drug repurposing as potential COVID-19 therapy. J. Chem. Inf. Model. 63(22), 7011–7031 (2023).
Song, X., Mao, M. & Qian, X. Auto-metric graph neural network based on a meta-learning strategy for the diagnosis of Alzheimer’s disease. IEEE J. Biomed. Health Inform. 25(8), 3141–3152 (2021).
Shakyawar, S. K., Sajja, B. R., Patel, J. C. & Guda, C. iCluF: An unsupervised iterative cluster-fusion method for patient stratification using multiomics data. Bioinform. Adv. 4(1), (2024).
Tan, K., Huang, W., Hu, J. & Dong, S. A multi-omics supervised autoencoder for pan-cancer clinical outcome endpoints prediction. BMC Med. Inform. Decis. Mak. 20(Suppl 3), 129 (2020).
Tian, Y., Chen, L. & Jiang, Y. LASSO-based screening for potential prognostic biomarkers associated with glioblastoma. Front. Oncol. 12, 1057383 (2022).
Hou, N. et al. Predicting 30-days mortality for MIMIC-III patients with sepsis-3: A machine learning approach using XGboost. J. Transl. Med. 18(1), 462 (2020).
He, H. et al. Identification of a novel sepsis prognosis model and analysis of possible drug application prospects: Based on scRNA-seq and RNA-seq data. Front. Immunol. 13, 888891 (2022).
Qin, H. et al. Integrated machine learning survival framework develops a prognostic model based on inter-crosstalk definition of mitochondrial function and cell death patterns in a large multicenter cohort for lower-grade glioma. J Transl Med 21(1), 588 (2023).
Kanehisa, M. et al. New approach for understanding genome variations in KEGG. Nucleic Acids Res. 47(D1), D590–D595 (2019).
Fleuren, L. M. et al. Machine learning for the prediction of sepsis: A systematic review and meta-analysis of diagnostic test accuracy. Intensive Care Med. 46(3), 383–400 (2020).
Yan, F. et al. Association between the stress hyperglycemia ratio and 28-day all-cause mortality in critically ill patients with sepsis: A retrospective cohort study and predictive model establishment based on machine learning. Cardiovasc. Diabetol. 23(1), 163 (2024).
Kalimouttou, A. et al. Machine-learning-derived sepsis bundle of care. Intensive Care Med. 49(1), 26–36 (2023).
Yu, P. et al. Pyroptosis: Mechanisms and diseases. Signal Transduct. Target Ther. 6(1), 128 (2021).
Ho, J. et al. Pathological role and diagnostic value of endogenous host defense peptides in adult and neonatal sepsis: A systematic review. Shock 47(6), 673–679 (2017).
Barbeiro, D. F. et al. Cathelicidin LL-37 bloodstream surveillance is down regulated during septic shock. Microbes Infect 15(5), 342–346 (2013).
Hu, Z. et al. Antimicrobial cathelicidin peptide LL-37 inhibits the LPS/ATP-induced pyroptosis of macrophages by dual mechanism. PLoS ONE 9(1), e85765 (2014).
Wang, Q. et al. LL-37 improves sepsis-induced acute lung injury by suppressing pyroptosis in alveolar epithelial cells. Int. Immunopharmacol. 129, 111580 (2024).
Rubin, J. B. et al. Sex differences in cancer mechanisms. Biol. Sex Differ. 11(1), 17 (2020).
Wang, X. et al. Diagnostic and predictive values of pyroptosis-related genes in sepsis. Front. Immunol. 14, 1105399 (2023).
Chen, Y. et al. Revealing novel pyroptosis-related therapeutic targets for sepsis based on machine learning. BMC Med. Genom. 16(1), 23 (2023).
Wang, L. et al. Significant difference of differential expression pyroptosis-related genes and their correlations with infiltrated immune cells in sepsis. Front. Cell Infect. Microbiol. 12, 1005392 (2022).
Li, L. L. et al. The activation of IL-17 signaling pathway promotes pyroptosis in pneumonia-induced sepsis. Ann. Transl. Med. 8(11), 674 (2020).
Li, Z. H., Wang, Y. & Yu, X. Y. Exploring the role of pyroptosis and immune infiltration in sepsis based on bioinformatic analysis. Immunobiology 229(5), 152826 (2024).
Chen, J. et al. Meta-analysis of the role of neutrophil to lymphocyte ratio in neonatal sepsis. BMC Infect. Dis. 23(1), 837 (2023).
Akhmaltdinova, L. L., Zhumadilova, Z. A., Kolesnichenko, S. I. et al. The presence of PDL-1 on CD8+ lymphocytes is linked to survival in neonatal sepsis. Children (Basel) 9(8), (2022).
Minns, M. S. et al. NLRP3 selectively drives IL-1beta secretion by Pseudomonas aeruginosa infected neutrophils and regulates corneal disease severity. Nat. Commun. 14(1), 5832 (2023).
Mankan, A. K. et al. The NLRP3/ASC/Caspase-1 axis regulates IL-1beta processing in neutrophils. Eur. J. Immunol. 42(3), 710–715 (2012).
Chen, H. et al. NLRP12 collaborates with NLRP3 and NLRC4 to promote pyroptosis inducing ganglion cell death of acute glaucoma. Mol. Neurodegener. 15(1), 26 (2020).
Rao, Z. et al. Pyroptosis in inflammatory diseases and cancer. Theranostics 12(9), 4310–4329 (2022).
Guo, Q. et al. Pyroptosis orchestrates immune responses in endometriosis. Int. Immunopharmacol. 118, 110141 (2023).
Karki, P. et al. Amphipathic helical peptide L37pA protects against lung vascular endothelial dysfunction caused by truncated oxidized phospholipids via antagonism with CD36 receptor. Am. J. Respir. Cell Mol. Biol. 70(1), 11–25 (2024).
Wiernicki, B. et al. Cancer cells dying from ferroptosis impede dendritic cell-mediated anti-tumor immunity. Nat. Commun. 13(1), 3676 (2022).
McCullough, K. & Bolisetty, S. Iron homeostasis and ferritin in sepsis-associated kidney injury. Nephron 144(12), 616–620 (2020).
Gordeuk, V. R. et al. Decreased concentrations of tumor necrosis factor-alpha in supernatants of monocytes from homozygotes for hereditary hemochromatosis. Blood 79(7), 1855–1860 (1992).
Cardoso, E. M. et al. Hepatic damage in C282Y homozygotes relates to low numbers of CD8+ cells in the liver lobuli. Eur. J. Clin. Invest. 31(1), 45–53 (2001).
Kang, H. M. et al. Ubiquitination of MAP1LC3B by pVHL is associated with autophagy and cell death in renal cell carcinoma. Cell Death Dis. 10(4), 279 (2019).
Zhou, B. et al. Ferroptosis is a type of autophagy-dependent cell death. Semin. Cancer Biol. 66, 89–100 (2020).
Liu, J. et al. Autophagy-dependent ferroptosis: Machinery and regulation. Cell Chem. Biol. 27(4), 420–435 (2020).
Kang, R. & Tang, D. Autophagy and ferroptosis – What’s the connection?. Curr. Pathobiol. Rep. 5(2), 153–159 (2017).
Qu, H. et al. Identifying CTH and MAP1LC3B as ferroptosis biomarkers for prognostic indication in gastric cancer decoding. Sci. Rep. 14(1), 4352 (2024).
Chen, G., Li, L. & Tao, H. Bioinformatics identification of ferroptosis-related biomarkers and therapeutic compounds in ischemic stroke. Front. Neurol. 12, 745240 (2021).
Yu, Y., Dong, G. & Niu, Y. Construction of ferroptosis-related gene signatures for identifying potential biomarkers and immune cell infiltration in osteoarthritis. Artif. Cells Nanomed. Biotechnol. 52(1), 449–461 (2024).
Di, C. et al. Identification of autophagy-related genes and immune cell infiltration characteristics in sepsis via bioinformatic analysis. J. Thorac. Dis. 15(4), 1770–1784 (2023).
Lindell, R. B. et al. Impaired lymphocyte responses in pediatric sepsis vary by pathogen type and are associated with features of immunometabolic dysregulation. Shock 57(6), 191–199 (2022).
Reed, M. et al. Deficiency of autophagy protein Map1-LC3b mediates IL-17-dependent lung pathology during respiratory viral infection via ER stress-associated IL-1. Mucosal Immunol. 8(5), 1118–1130 (2015).
Bonam, S. R. et al. Pharmacological targets at the lysosomal autophagy-NLRP3 inflammasome crossroads. Trends Pharmacol. Sci. 45(1), 81–101 (2024).
Busch, K. et al. Inhibition of the NLRP3/IL-1beta axis protects against sepsis-induced cardiomyopathy. J. Cachexia Sarcopenia Muscle 12(6), 1653–1668 (2021).
Zhou, R. et al. A role for mitochondria in NLRP3 inflammasome activation. Nature 469(7329), 221–225 (2011).
Loi, M. et al. Macroautophagy proteins control MHC class I levels on dendritic cells and shape anti-viral CD8(+) T cell responses. Cell Rep. 15(5), 1076–1087 (2016).
Hubbard-Lucey, V. M. et al. Autophagy gene Atg16L1 prevents lethal T cell alloreactivity mediated by dendritic cells. Immunity 41(4), 579–591 (2014).
Hao, C. et al. Translocator protein (TSPO) alleviates neuropathic pain by activating spinal autophagy and nuclear SIRT1/PGC-1alpha signaling in a Rat L5 SNL model. J. Pain Res. 15, 767–778 (2022).
Mahemuti, Y. et al. TSPO exacerbates acute cerebral ischemia/reperfusion injury by inducing autophagy dysfunction. Exp. Neurol. 369, 114542 (2023).
Jin, G. L. et al. Koumine regulates macrophage M1/M2 polarization via TSPO, alleviating sepsis-associated liver injury in mice. Phytomedicine 107, 154484 (2022).
Wang, Z. & Wang, Z. The role of macrophages polarization in sepsis-induced acute lung injury. Front. Immunol. 14, 1209438 (2023).
Guo, L. et al. Platelet MHC class I mediates CD8+ T-cell suppression during sepsis. Blood 138(5), 401–416 (2021).
Jensen, I. J. et al. Sepsis-induced T cell immunoparalysis: The ins and outs of impaired T cell immunity. J. Immunol. 200(5), 1543–1553 (2018).
Heidarian, M., Griffith, T. S. & Badovinac, V. P. Sepsis-induced changes in differentiation, maintenance, and function of memory CD8 T cell subsets. Front. Immunol. 14, 1130009 (2023).
Lozano-Rodriguez, R. et al. The prognostic impact of SIGLEC5-induced impairment of CD8(+) T cell activation in sepsis. EBioMedicine 97, 104841 (2023).
