|
1
|
Bateman RM, Sharpe MD, Jagger JE, Ellis
CG, Solé-Violán J, López-Rodríguez M, Herrera-Ramos E,
Ruíz-Hernández J, Borderías L, Horcajada J, et al: 36th
International symposium on intensive care and emergency medicine:
Brussels, Belgium. 15-18 march 2016. Crit Care. 20(Suppl 2):
S942016. View Article : Google Scholar
|
|
2
|
Hussain M, Khurram Syed S, Fatima M,
Shaukat S, Saadullah M, Alqahtani AM, Alqahtani T, Bin Emran T,
Alamri AH, Barkat MQ and Wu X: Acute respiratory distress syndrome
and COVID-19: A literature review. J Inflamm Res. 14:7225–7242.
2021. View Article : Google Scholar
|
|
3
|
Schuster DP: What is acute lung injury?
What is ARDS? Chest. 107:1721–1726. 1995. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Thompson BT, Chambers RC and Liu KD: Acute
respiratory distress syndrome. N Engl J Med. 377:562–572. 2017.
View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Villar J, Szakmany T, Grasselli G and
Camporota L: Redefining ARDS: A paradigm shift. Crit Care.
27:4162023. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
ARDS Definition Task Force; Ranieri VM,
Rubenfeld GD, Thompson BT, Ferguson ND, Caldwell E, Fan E,
Camporota L and Slutsky AS: Acute respiratory distress syndrome:
The berlin definition. JAMA. 307:2526–2533. 2012.PubMed/NCBI
|
|
7
|
Matthay MA, Arabi Y, Arroliga AC, Bernard
G, Bersten AD, Brochard LJ, Calfee CS, Combes A, Daniel BM,
Ferguson ND, et al: A new global definition of acute respiratory
distress syndrome. Am J Respir Crit Care Med. 209:37–47. 2024.
View Article : Google Scholar :
|
|
8
|
Gorman EA, O'Kane CM and McAuley DF: Acute
respiratory distress syndrome in adults: Diagnosis, outcomes,
long-term sequelae, and management. Lancet. 400:1157–1170. 2022.
View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Meyer NJ, Gattinoni L and Calfee CS: Acute
respiratory distress syndrome. Lancet. 398:622–637. 2021.
View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Stanski NL and Wong HR: Prognostic and
predictive enrichment in sepsis. Nat Rev Nephrol. 16:20–31. 2020.
View Article : Google Scholar :
|
|
11
|
Janga H, Cassidy L, Wang F, Spengler D,
Oestern-Fitschen S, Krause MF, Seekamp A, Tholey A and Fuchs S:
Site-specific and endothelial-mediated dysfunction of the
alveolar-capillary barrier in response to lipopolysaccharides. J
Cell Mol Med. 22:982–998. 2018. View Article : Google Scholar
|
|
12
|
Kumar V: Pulmonary innate immune response
determines the outcome of inflammation during pneumonia and
sepsis-associated acute lung injury. Front Immunol. 11:17222020.
View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Pokharel MD, Garcia-Flores A, Marciano D,
Franco MC, Fineman JR, Aggarwal S, Wang T and Black SM:
Mitochondrial network dynamics in pulmonary disease: Bridging the
gap between inflammation, oxidative stress, and bioenergetics.
Redox Biol. 70:1030492024. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Aisiku IP, Yamal JM, Doshi P, Benoit JS,
Gopinath S, Goodman JC and Robertson CS: Plasma cytokines IL-6,
IL-8, and IL-10 are associated with the development of acute
respiratory distress syndrome in patients with severe traumatic
brain injury. Crit Care. 20:2882016. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Tang N, Yang Y, Xie Y, Yang G, Wang Q, Li
C, Liu Z and Huang JA: CD274 (PD-L1) negatively regulates M1
macrophage polarization in ALI/ARDS. Front Immunol. 15:13448052024.
View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Zhao J, Zhen N, Zhou Q, Lou J, Cui W,
Zhang G and Tian B: NETs promote inflammatory injury by activating
cGAS-STING pathway in acute lung injury. Int J Mol Sci.
24:51252023. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Cui Y, Wang X, Lin F, Li W, Zhao Y, Zhu F,
Yang H, Rao M, Li Y, Liang H, et al: MiR-29a-3p improves acute lung
injury by reducing alveolar epithelial cell PANoptosis. Aging Dis.
13:899–909. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Wang SW, Zhang Q, Lu D, Fang YC, Yan XC,
Chen J, Xia ZK, Yuan QT, Chen LH, Zhang YM, et al: GPR84 regulates
pulmonary inflammation by modulating neutrophil functions. Acta
Pharmacol Sin. 44:1665–1675. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
19
|
Gong R, Luo H, Long G, Xu J, Huang C, Zhou
X, Shang Y and Zhang D: Integrative proteomic profiling of lung
tissues and blood in acute respiratory distress syndrome. Front
Immunol. 14:11589512023. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Korde A, Haslip M, Pednekar P, Khan A,
Chioccioli M, Mehta S, Lopez-Giraldez F, Bermejo S, Rojas M, Dela
Cruz C, et al: MicroRNA-1 protects the endothelium in acute lung
injury. JCI Insight. 8:e1648162023. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Wang L, Tang Y, Tang J, Liu X, Zi S, Li S,
Chen H, Liu A, Huang W, Xie J, et al: Endothelial cell-derived
extracellular vesicles expressing surface VCAM1 promote
sepsis-related acute lung injury by targeting and reprogramming
monocytes. J Extracell Vesicles. 13:e124232024. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Helou DG, Quach C, Hurrell BP, Li X, Li M,
Akbari A, Shen S, Shafiei-Jahani P and Akbari O: LAIR-1 limits
macrophage activation in acute inflammatory lung injury. Mucosal
Immunol. 16:788–800. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Park S, Kim M, Park M, Jin Y, Lee SJ and
Lee H: Specific upregulation of extracellular miR-6238 in
particulate matter-induced acute lung injury and its
immunomodulation. J Hazard Mater. 445:1304662023. View Article : Google Scholar
|
|
24
|
Blank R and Napolitano LM: Epidemiology of
ARDS and ALI. Crit Care Clin. 27:439–458. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Katzenstein AL, Bloor CM and Leibow AA:
Diffuse alveolar damage-the role of oxygen, shock, and related
factors. A review. Am J Pathol. 85:209–228. 1976.PubMed/NCBI
|
|
26
|
Razzaque MS, Nazneen A and Taguchi T:
Immunolocalization of collagen and collagen-binding heat shock
protein 47 in fibrotic lung diseases. Mod Pathol. 11:1183–1188.
1998.
|
|
27
|
Raghavendran K and Napolitano LM:
Definition of ALI/ARDS. Crit Care Clin. 27:429–437. 2011.
View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Laffey JG and Kavanagh BP: Ventilation
with lower tidal volumes as compared with traditional tidal volumes
for acute lung injury. N Engl J Med. 343:812author reply 813-4.
2000. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Gattinoni L, Marini JJ, Collino F, Maiolo
G, Rapetti F, Tonetti T, Vasques F and Quintel M: The future of
mechanical ventilation: Lessons from the present and the past. Crit
Care. 21:1832017. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Matthay MA, Ware LB and Zimmerman GA: The
acute respiratory distress syndrome. J Clin Invest. 122:2731–2740.
2012. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Rubenfeld GD and Herridge MS: Epidemiology
and outcomes of acute lung injury. Chest. 131:554–562. 2007.
View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Xia K, Sun HX, Li J, Li J, Zhao Y, Chen L,
Qin C, Chen R, Chen Z, Liu G, et al: The single-cell stereo-seq
reveals region-specific cell subtypes and transcriptome profiling
in Arabidopsis leaves. Dev Cell. 57:1299–1310 e4. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Liu SQ, Gao ZJ, Wu J, Zheng HM, Li B, Sun
S, Meng XY and Wu Q: Single-cell and spatially resolved analysis
uncovers cell heterogeneity of breast cancer. J Hematol Oncol.
15:192022. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Chen P, Tang S, Li M, Wang D, Chen C, Qiu
Y, Fang Z, Zhang H, Gao H, Weng H, et al: Single-cell and spatial
transcriptomics decodes wharton's jelly-derived mesenchymal stem
cells heterogeneity and a subpopulation with wound repair
signatures. Adv Sci (Weinh). 10:e22047862023. View Article : Google Scholar
|
|
35
|
Ji AL, Rubin AJ, Thrane K, Jiang S,
Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A,
Bergenstråhle J, et al: Multimodal analysis of composition and
spatial architecture in human squamous cell carcinoma. Cell.
182:497–514 e22. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Bhargava M and Wendt CH: Biomarkers in
acute lung injury. Transl Res. 159:205–217. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Wang G, Ma X, Huang W, Wang S, Lou A, Wang
J, Tu Y, Cui W, Zhou W, Zhang W, et al: Macrophage biomimetic
nanoparticle-targeted functional extracellular vesicle micro-RNAs
revealed via multiomics analysis alleviate sepsis-induced acute
lung injury. J Nanobiotechnology. 22:3622024. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Du M, Garcia JGN, Christie JD, Xin J, Cai
G, Meyer NJ, Zhu Z, Yuan Q, Zhang Z, Su L, et al: Integrative omics
provide biological and clinical insights into acute respiratory
distress syndrome. Intensive Care Med. 47:761–771. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Sun D, Guan X, Moran AE, Wu LY, Qian DZ,
Schedin P, Dai MS, Danilov AV, Alumkal JJ, Adey AC, et al:
Identifying phenotype-associated subpopulations by integrating bulk
and single-cell sequencing data. Nat Biotechnol. 40:527–538. 2022.
View Article : Google Scholar :
|
|
40
|
Wu Y, Hu SS, Zhang R, Goplen NP, Gao X,
Narasimhan H, Shi A, Chen Y, Li Y, Zang C, et al: Single cell RNA
sequencing unravels mechanisms underlying senescence-like
phenotypes of alveolar macrophages. iScience. 26:1071972023.
View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Long E, Yin J, Shin JH, Li Y, Li B, Kane
A, Patel H, Sun X, Wang C, Luong T, et al: Context-aware
single-cell multiomics approach identifies cell-type-specific lung
cancer susceptibility genes. Nat Commun. 15:79952024. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Bertrams W, Jung AL and Schmeck B:
Modeling of Pneumonia and Acute Lung Injury: Bioinformatics,
Systems Medicine, and Artificial Intelligence. Systems Med.
2:573–580. 2021. View Article : Google Scholar
|
|
43
|
Lam E and dos Santos CC: Advances in
molecular acute lung injury/acute respiratory distress syndrome and
ventilator-induced lung injury: The role of genomics, proteomics,
bioinformatics and translational biology. Curr Opin Crit Care.
14:3–10. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J,
Liu Y, Feng J, Chen H, He Y and Xia R: TBtools-II: A 'one for all,
all for one' bioinformatics platform for biological big-data
mining. Mol Plant. 16:1733–1742. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
45
|
Yang J, Li Y, Liu Q, Li L, Feng A, Wang T,
Zheng S, Xu A and Lyu J: Brief introduction of medical database and
data mining technology in big data era. J Evid Based Med. 13:57–69.
2020. View Article : Google Scholar : PubMed/NCBI
|
|
46
|
Grumet FC, Coukell A, Bodmer JG, Bodmer WF
and McDevitt HO: Histocompatibility (HL-A) antigens associated with
systemic lupus erythematosus. A possible genetic predisposition to
disease. N Engl J Med. 285:193–196. 1971. View Article : Google Scholar : PubMed/NCBI
|
|
47
|
Bajwa EK: The genetics of acute lung
injury: Looking back and pointing the way forward. Crit Care.
13:1082009. View
Article : Google Scholar : PubMed/NCBI
|
|
48
|
Ergul A: Hypertension in black patients:
An emerging role of the endothelin system in salt-sensitive
hypertension. Hypertension. 36:62–67. 2000. View Article : Google Scholar : PubMed/NCBI
|
|
49
|
Shukla P and Singh KK: Uncovering
mitochondrial determinants of racial disparities in ovarian cancer.
Trends Cancer. 7:93–97. 2021. View Article : Google Scholar
|
|
50
|
Mirsaeidi M, Machado RF, Schraufnagel D,
Sweiss NJ and Baughman RP: Racial difference in sarcoidosis
mortality in the United States. Chest. 147:438–449. 2015.
View Article : Google Scholar :
|
|
51
|
Moss M and Mannino DM: Race and gender
differences in acute respiratory distress syndrome deaths in the
United States: An analysis of multiple-cause mortality data
(1979-1996). Crit Care Med. 30:1679–1685. 2002. View Article : Google Scholar : PubMed/NCBI
|
|
52
|
Flores C, Pino-Yanes Mdel M and Villar J:
A quality assessment of genetic association studies supporting
susceptibility and outcome in acute lung injury. Crit Care.
12:R1302008. View
Article : Google Scholar : PubMed/NCBI
|
|
53
|
Zhou H, Fan EK and Fan J: Cell-cell
interaction mechanisms in acute lung injury. Shock. 55:167–176.
2021. View Article : Google Scholar :
|
|
54
|
Jiang L, Kon N, Li T, Wang SJ, Su T,
Hibshoosh H, Baer R and Gu W: Ferroptosis as a p53-mediated
activity during tumour suppression. Nature. 520:57–62. 2015.
View Article : Google Scholar : PubMed/NCBI
|
|
55
|
Klein AM, Mazutis L, Akartuna I,
Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA and Kirschner
MW: Droplet barcoding for single-cell transcriptomics applied to
embryonic stem cells. Cell. 161:1187–1201. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
56
|
Xu X, Jia C, Luo S, Li Y, Xiao F, Dai H
and Wang C: Effect of HA330 resin-directed hemoadsorption on a
porcine acute respiratory distress syndrome model. Ann Intensive
Care. 7:842017. View Article : Google Scholar : PubMed/NCBI
|
|
57
|
Huang RT, Wu D, Meliton A, Oh MJ, Krause
M, Lloyd JA, Nigdelioglu R, Hamanaka RB, Jain MK, Birukova A, et
al: Experimental lung injury reduces kruppel-like factor 2 to
increase endothelial permeability via regulation of RAPGEF3-Rac1
signaling. Am J Respir Crit Care Med. 195:639–651. 2017. View Article : Google Scholar :
|
|
58
|
Montoro DT, Haber AL, Biton M, Vinarsky V,
Lin B, Birket SE, Yuan F, Chen S, Leung HM, Villoria J, et al: A
revised airway epithelial hierarchy includes CFTR-expressing
ionocytes. Nature. 560:319–324. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
59
|
Lynn H, Sun X, Casanova N, Gonzales-Garay
M, Bime C and Garcia JGN: Genomic and genetic approaches to
deciphering acute respiratory distress syndrome risk and mortality.
Antioxid Redox Signal. 31:1027–1052. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
60
|
Zhang S, Wu Z, Xie J, Yang Y, Wang L and
Qiu H: DNA methylation exploration for ARDS: A multi-omics and
multi-microarray interrelated analysis. J Transl Med. 17:3452019.
View Article : Google Scholar : PubMed/NCBI
|
|
61
|
Adrover JM, Aroca-Crevillén A, Crainiciuc
G, Ostos F, Rojas-Vega Y, Rubio-Ponce A, Cilloniz C,
Bonzón-Kulichenko E, Calvo E, Rico D, et al: Programmed 'disarming'
of the neutrophil proteome reduces the magnitude of inflammation.
Nat Immunol. 21:135–144. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
62
|
Li L, Fu WW, Wu RT, Song YH, Wu WY, Yin
SH, Li WJ and Xie MY: Protective effect of Ganoderma atrum
polysaccharides in acute lung injury rats and its metabolomics. Int
J Biol Macromol. 142:693–704. 2020. View Article : Google Scholar
|
|
63
|
Hu L, Wang Y, Sun H, Xiong Y, Zhong L, Wu
Z and Yang M: An untargeted metabolomics approach to investigate
the wine-processed mechanism of Scutellariae radix in acute lung
injury. J Ethnopharmacol. 253:1126652020. View Article : Google Scholar : PubMed/NCBI
|
|
64
|
Boyd DF, Allen EK, Randolph AG, Guo XJ,
Weng Y, Sanders CJ, Bajracharya R, Lee NK, Guy CS, Vogel P, et al:
Exuberant fibroblast activity compromises lung function via
ADAMTS4. Nature. 587:466–471. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
65
|
Jiang Y, Rosborough BR, Chen J, Das S,
Kitsios GD, McVerry BJ, Mallampalli RK, Lee JS, Ray A, Chen W and
Ray P: Single cell RNA sequencing identifies an early monocyte gene
signature in acute respiratory distress syndrome. JCI Insight.
5:e1356782020. View Article : Google Scholar : PubMed/NCBI
|
|
66
|
Wang S, Yao X, Ma S, Ping Y, Fan Y, Sun S,
He Z, Shi Y, Sun L, Xiao S, et al: A single-cell transcriptomic
landscape of the lungs of patients with COVID-19. Nat Cell Biol.
23:1314–1328. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
67
|
Guo Y, Liu Y, Zhao S, Xu W, Li Y, Zhao P,
Wang D, Cheng H, Ke Y and Zhang X: Oxidative stress-induced FABP5
S-glutathionylation protects against acute lung injury by
suppressing inflammation in macrophages. Nat Commun. 12:70942021.
View Article : Google Scholar : PubMed/NCBI
|
|
68
|
Dong X, Zhu Z, Wei Y, Ngo D, Zhang R, Du
M, Huang H, Lin L, Tejera P, Su L, et al: Plasma insulin-like
growth factor binding protein 7 contributes causally to ARDS 28-day
mortality: Evidence from multistage mendelian randomization. Chest.
159:1007–1018. 2021. View Article : Google Scholar :
|
|
69
|
Wendisch D, Dietrich O, Mari T, von
Stillfried S, Ibarra IL, Mittermaier M, Mache C, Chua RL, Knoll R,
Timm S, et al: SARS-CoV-2 infection triggers profibrotic macrophage
responses and lung fibrosis. Cell. 184:6243–6261 e27. 2021.
View Article : Google Scholar : PubMed/NCBI
|
|
70
|
Bradic M, Taleb S, Thomas B, Chidiac O,
Robay A, Hassan N, Malek J, Ait Hssain A and Abi Khalil C: DNA
methylation predicts the outcome of COVID-19 patients with acute
respiratory distress syndrome. J Transl Med. 20:5262022. View Article : Google Scholar : PubMed/NCBI
|
|
71
|
Nan W, Xiong F, Zheng H, Li C, Lou C, Lei
X, Wu H, Gao H and Li Y: Myristoyl lysophosphatidylcholine is a
biomarker and potential therapeutic target for community-acquired
pneumonia. Redox Biol. 58:1025562022. View Article : Google Scholar : PubMed/NCBI
|
|
72
|
Whitney JE, Lee IH, Lee JW and Kong SW:
Evolution of multiple omics approaches to define pathophysiology of
pediatric acute respiratory distress syndrome. Elife.
11:e774052022. View Article : Google Scholar : PubMed/NCBI
|
|
73
|
Wang K, Wang M, Liao X, Gao S, Hua J, Wu
X, Guo Q, Xu W, Sun J, He Y, et al: Locally organised and activated
Fth1(hi) neutrophils aggravate inflammation of acute lung injury in
an IL-10-dependent manner. Nat Commun. 13:77032022. View Article : Google Scholar : PubMed/NCBI
|
|
74
|
Tang X, Zhong L, Tian X, Zou Y, Hu S, Liu
J, Li P, Zhu M, Luo F and Wan H: RUNX1 promotes mitophagy and
alleviates pulmonary inflammation during acute lung injury. Signal
Transduct Target Ther. 8:2882023. View Article : Google Scholar : PubMed/NCBI
|
|
75
|
Lai Y, Li X, Li T, Li X, Nyunoya T, Chen
K, Kitsios G, Nouraie M, Zhang Y, McVerry BJ, et al: Protein
arginine N-methyltransferase 4 (PRMT4) contributes to lymphopenia
in experimental sepsis. Thorax. 78:383–393. 2023. View Article : Google Scholar
|
|
76
|
Li G, Yan K, Zhang W, Pan H and Guo P:
ARDS and aging: TYMS emerges as a promising biomarker and
therapeutic target. Front Immunol. 15:13652062024. View Article : Google Scholar : PubMed/NCBI
|
|
77
|
Gong T, Zhang X, Liu X, Ye Y, Tian Z, Yin
S, Zhang M, Tang J and Liu Y: Exosomal Tenascin-C primes macrophage
pyroptosis amplifying aberrant inflammation during sepsis-induced
acute lung injury. Transl Res. 270:66–80. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
78
|
Xia LX, Xiao YY, Jiang WJ, Yang XY, Tao H,
Mandukhail SR, Qin JF, Pan QR, Zhu YG, Zhao LX, et al: Exosomes
derived from induced cardiopulmonary progenitor cells alleviate
acute lung injury in mice. Acta Pharmacol Sin. 45:1644–1659. 2024.
View Article : Google Scholar : PubMed/NCBI
|
|
79
|
Liu P, Yang S, Shao X, Li C, Wang Z, Dai H
and Wang C: Mesenchymal stem cells-derived exosomes alleviate acute
lung injury by inhibiting alveolar macrophage pyroptosis. Stem
Cells Transl Med. 13:371–386. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
80
|
Pollenus E, Possemiers H, Knoops S, Prenen
F, Vandermosten L, Thienpont C, Abdurahiman S, Demeyer S, Cools J,
Matteoli G, et al: Single cell RNA sequencing reveals endothelial
cell killing and resolution pathways in experimental
malaria-associated acute respiratory distress syndrome. PLoS
Pathog. 20:e10119292024. View Article : Google Scholar : PubMed/NCBI
|
|
81
|
Mitsuyama Y, Matsumoto H, Togami Y, Oda S,
Onishi S, Yoshimura J, Murtatsu A, Ito H, Ogura H, Okuzaki D and
Oda J: T cell dysfunction in elderly ARDS patients based on miRNA
and mRNA integration analysis. Front Immunol. 15:13684462024.
View Article : Google Scholar : PubMed/NCBI
|
|
82
|
Zheng L, Liu C, Wang H, Zhang J, Mao L,
Dong X, Hu S, Li N, Pi D, Qiu J, et al: Intact lung tissue and
bronchoalveolar lavage fluid are both suitable for the evaluation
of murine lung microbiome in acute lung injury. Microbiome.
12:562024. View Article : Google Scholar : PubMed/NCBI
|
|
83
|
Wu G, Sun Y, Wang K, Chen Z, Wang X, Chang
F, Li T, Feng P and Xia Z: Relationship between elevated soluble
CD74 and severity of experimental and clinical ALI/ARDS. Sci Rep.
6:300672016. View Article : Google Scholar : PubMed/NCBI
|
|
84
|
Meyer NJ: Beyond single-nucleotide
polymorphisms: Genetics, genomics, and other 'omic approaches to
acute respiratory distress syndrome. Clin Chest Med. 35:673–684.
2014. View Article : Google Scholar : PubMed/NCBI
|
|
85
|
Reilly JP, Wang F, Jones TK, Palakshappa
JA, Anderson BJ, Shashaty MGS, Dunn TG, Johansson ED, Riley TR, Lim
B, et al: Plasma angiopoietin-2 as a potential causal marker in
sepsis-associated ARDS development: Evidence from Mendelian
randomization and mediation analysis. Intensive Care Med.
44:1849–1858. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
86
|
Wang Z, Beach D, Su L, Zhai R and
Christiani DC: A genome-wide expression analysis in blood
identifies pre-elafin as a biomarker in ARDS. Am J Respir Cell Mol
Biol. 38:724–732. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
87
|
Devaney J, Contreras M and Laffey JG:
Clinical review: Gene-based therapies for ALI/ARDS: Where are we
now? Crit Care. 15:2242011. View Article : Google Scholar : PubMed/NCBI
|
|
88
|
Tromp TR, Stroes ESG and Hovingh GK:
Gene-based therapy in lipid management: The winding road from
promise to practice. Expert Opin Investig Drugs. 29:483–493. 2020.
View Article : Google Scholar : PubMed/NCBI
|
|
89
|
Ramsey LB, Brown JT, Vear SI, Bishop JR
and Van Driest SL: Gene-based dose optimization in children. Annu
Rev Pharmacol Toxicol. 60:311–331. 2020. View Article : Google Scholar
|
|
90
|
Ma A, Feng Z, Li Y, Wu Q, Xiong H, Dong M,
Cheng J, Wang Z, Yang J and Kang Y: Ferroptosis-related signature
and immune infiltration characterization in acute lung injury/acute
respiratory distress syndrome. Respir Res. 24:1542023. View Article : Google Scholar : PubMed/NCBI
|
|
91
|
Cheng H, Wang X, Yao J, Yang C and Liu J:
Mitophagy and ferroptosis in sepsis-induced ALI/ARDS: Molecular
mechanisms, interactions and therapeutic prospects of medicinal
plants. J Inflamm Res. 17:7819–7835. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
92
|
Li Y, Cao Y, Xiao J, Shang J, Tan Q, Ping
F, Huang W, Wu F, Zhang H and Zhang X: Inhibitor of
apoptosis-stimulating protein of p53 inhibits ferroptosis and
alleviates intestinal ischemia/reperfusion-induced acute lung
injury. Cell Death Differ. 27:2635–2650. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
93
|
Shen K, Wang X, Wang Y, Jia Y, Zhang Y,
Wang K, Luo L, Cai W, Li J, Li S, et al: miR-125b-5p in adipose
derived stem cells exosome alleviates pulmonary microvascular
endothelial cells ferroptosis via Keap1/Nrf2/GPX4 in sepsis lung
injury. Redox Biol. 62:1026552023. View Article : Google Scholar : PubMed/NCBI
|
|
94
|
Dodson M, Castro-Portuguez R and Zhang DD:
NRF2 plays a critical role in mitigating lipid peroxidation and
ferroptosis. Redox Biol. 23:1011072019. View Article : Google Scholar : PubMed/NCBI
|
|
95
|
Stockwell BR: Ferroptosis turns 10:
Emerging mechanisms, physiological functions, and therapeutic
applications. Cell. 185:2401–2421. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
96
|
Ma C, Liu K, Wang F, Fei X, Niu C, Li T
and Liu L: Neutrophil membrane-engineered Panax ginseng
root-derived exosomes loaded miRNA 182-5p targets NOX4/Drp-1/NLRP3
signal pathway to alleviate acute lung injury in sepsis:
Experimental studies. Int J Surg. 110:72–86. 2024.
|
|
97
|
Fan L, Bin Wang, Ma J, Ye Z, Nie X, Cheng
M, Xie Y, Gu P, Zhang Y, You X, et al: Role and mechanism of WNT5A
in benzo(a)pyrene-induced acute lung injury and lung function
decline. J Hazard Mater. 460:1323912023. View Article : Google Scholar : PubMed/NCBI
|
|
98
|
Wang Z, Chang P, Ye J, Ma W, Zhou J, Zhang
P, Chen X, Jia B, Zheng M, Huang W and Wang T: Genome-wide
landscape of mRNAs, microRNAs, lncRNAs, and circRNAs in hemorrhagic
shock-induced ALI/ARDS in rats. J Trauma Acute Care Surg.
90:827–837. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
99
|
Bai G, Li Y, Ji Y, Peng Y, Yang Z and Zhao
L: Treatments and whole exon sequencing of a case with multiple
primary lung cancer. J Cardiothorac Surg. 18:582023. View Article : Google Scholar : PubMed/NCBI
|
|
100
|
Guo W, Zhou B, Bie F, Huai Q, Xue X, Guo
L, Tan F, Xue Q, Zhao L and Gao S: Single-cell RNA sequencing
analysis reveals transcriptional heterogeneity of multiple primary
lung cancer. Clin Transl Med. 13:e14532023. View Article : Google Scholar : PubMed/NCBI
|
|
101
|
Zhang Y, Fu F, Zhang Q, Li L, Liu H, Deng
C, Xue Q, Zhao Y, Sun W, Han H, et al: Evolutionary proteogenomic
landscape from pre-invasive to invasive lung adenocarcinoma. Cell
Rep Med. 5:1013582024. View Article : Google Scholar : PubMed/NCBI
|
|
102
|
Egger G, Liang G, Aparicio A and Jones PA:
Epigenetics in human disease and prospects for epigenetic therapy.
Nature. 429:457–463. 2004. View Article : Google Scholar : PubMed/NCBI
|
|
103
|
Liao SY, Casanova NG, Bime C, Camp SM,
Lynn H and Garcia JGN: Identification of early and intermediate
biomarkers for ARDS mortality by multi-omic approaches. Sci Rep.
11:188742021. View Article : Google Scholar : PubMed/NCBI
|
|
104
|
Binnie A, Tsang JLY, Hu P, Carrasqueiro G,
Castelo-Branco P and Dos Santos CC: Epigenetics of sepsis. Crit
Care Med. 48:745–756. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
105
|
Ahmad S, Manzoor S, Siddiqui S, Mariappan
N, Zafar I and Ahmad A and Ahmad A: Epigenetic underpinnings of
inflammation: Connecting the dots between pulmonary diseases, lung
cancer and COVID-19. Semin Cancer Biol. 83:384–398. 2022.
View Article : Google Scholar
|
|
106
|
Yang IV, Lozupone CA and Schwartz DA: The
environment, epigenome, and asthma. J Allergy Clin Immunol.
140:14–23. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
107
|
Scheinecker C, Goschl L and Bonelli M:
Treg cells in health and autoimmune diseases: New insights from
single cell analysis. J Autoimmun. 110:1023762020. View Article : Google Scholar
|
|
108
|
Balnis J, Madrid A, Hogan KJ, Drake LA,
Chieng HC, Tiwari A, Vincent CE, Chopra A, Vincent PA, Robek MD, et
al: Blood DNA methylation and COVID-19 outcomes. Clin Epigenetics.
13:1182021. View Article : Google Scholar : PubMed/NCBI
|
|
109
|
Zhang Y, Jurkowska R, Soeroes S, Rajavelu
A, Dhayalan A, Bock I, Rathert P, Brandt O, Reinhardt R, Fischle W
and Jeltsch A: Chromatin methylation activity of Dnmt3a and
Dnmt3a/3L is guided by interaction of the ADD domain with the
histone H3 tail. Nucleic Acids Res. 38:4246–4253. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
110
|
Goldberg AD, Allis CD and Bernstein E:
Epigenetics: A landscape takes shape. Cell. 128:635–638. 2007.
View Article : Google Scholar : PubMed/NCBI
|
|
111
|
Wu D, Spencer CB, Ortoga L, Zhang H and
Miao C: Histone lactylation-regulated METTL3 promotes ferroptosis
via m6A-modification on ACSL4 in sepsis-associated lung injury.
Redox Biol. 74:1031942024. View Article : Google Scholar : PubMed/NCBI
|
|
112
|
Rombauts A, Bódalo Torruella M,
Abelenda-Alonso G, Perera-Bel J, Ferrer-Salvador A, Acedo-Terrades
A, Gabarrós-Subirà M, Oriol I, Gudiol C, Nonell L and Carratalà J:
Dynamics of gene expression profiling and identification of
high-risk patients for severe COVID-19. Biomedicines. 11:13482023.
View Article : Google Scholar : PubMed/NCBI
|
|
113
|
Bejaoui Y, Humaira Amanullah F, Saad M,
Taleb S, Bradic M, Megarbane A, Ait Hssain A, Abi Khalil C and El
Hajj N: Epigenetic age acceleration in surviving versus deceased
COVID-19 patients with acute respiratory distress syndrome
following hospitalization. Clin Epigenetics. 15:1862023. View Article : Google Scholar : PubMed/NCBI
|
|
114
|
Singer BD, Mock JR, Aggarwal NR, Garibaldi
BT, Sidhaye VK, Florez MA, Chau E, Gibbs KW, Mandke P, Tripathi A,
et al: Regulatory T cell DNA methyltransferase inhibition
accelerates resolution of lung inflammation. Am J Respir Cell Mol
Biol. 52:641–652. 2015. View Article : Google Scholar :
|
|
115
|
Ponting CP, Oliver PL and Reik W:
Evolution and functions of long noncoding RNAs. Cell. 136:629–641.
2009. View Article : Google Scholar : PubMed/NCBI
|
|
116
|
He X, Liu X, Zuo F, Shi H and Jing J:
Artificial intelligence-based multi-omics analysis fuels cancer
precision medicine. Semin Cancer Biol. 88:187–200. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
117
|
Xiong S, Hong Z, Huang LS, Tsukasaki Y,
Nepal S, Di A, Zhong M, Wu W, Ye Z, Gao X, et al: IL-1β suppression
of VE-cadherin transcription underlies sepsis-induced inflammatory
lung injury. J Clin Invest. 130:3684–3698. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
118
|
Qian G and Fang H, Chen A, Sun Z, Huang M,
Luo M, Cheng E, Zhang S, Wang X and Fang H: A hub gene signature as
a therapeutic target and biomarker for sepsis and geriatric
sepsis-induced ARDS concomitant with COVID-19 infection. Front
Immunol. 14:12578342023. View Article : Google Scholar : PubMed/NCBI
|
|
119
|
Zhang ZT, Xie K, Luo RJ, Zhang DY, He ZW,
Li KF, Lin SH and Xu F: Dexmedetomidine alleviates acute lung
injury by promoting Tregs differentiation via activation of
AMPK/SIRT1 pathway. Inflammopharmacology. 31:423–438. 2023.
View Article : Google Scholar
|
|
120
|
Xu Z, Jiang X, Dai X and Li B: The dynamic
role of FOXP3(+) tregs and their potential therapeutic applications
during SARS-CoV-2 infection. Front Immunol. 13:9164112022.
View Article : Google Scholar : PubMed/NCBI
|
|
121
|
He G, Chen K, Wang H, Li X, Li W, Liu L,
Chen J, Yang D, Hu J, Xu D, et al: Fudosteine attenuates acute lung
injury in septic mice by inhibiting pyroptosis via the
TXNIP/NLRP3/GSDMD pathway. Eur J Pharmacol. 926:1750472022.
View Article : Google Scholar : PubMed/NCBI
|
|
122
|
Tsubaki H, Tooyama I and Walker DG:
Thioredoxin-interacting protein (TXNIP) with focus on brain and
neurodegenerative diseases. Int J Mol Sci. 21:93572020. View Article : Google Scholar : PubMed/NCBI
|
|
123
|
Lee S, Nakahira K, Dalli J, Siempos II,
Norris PC, Colas RA, Moon JS, Shinohara M, Hisata S, Howrylak JA,
et al: NLRP3 inflammasome deficiency protects against microbial
sepsis via increased lipoxin B4 synthesis. Am J Respir Crit Care
Med. 196:713–726. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
124
|
Conesa A, Madrigal P, Tarazona S,
Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ,
Elo LL, Zhang X and Mortazavi A: A survey of best practices for
RNA-seq data analysis. Genome Biol. 17:132016. View Article : Google Scholar : PubMed/NCBI
|
|
125
|
Reilly JP, Christie JD and Meyer NJ: Fifty
years of research in ARDS. genomic contributions and opportunities.
Am J Respir Crit Care Med. 196:1113–1121. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
126
|
Restrepo-Pérez L, Joo C and Dekker C:
Paving the way to single-molecule protein sequencing. Nat
Nanotechnol. 13:786–796. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
127
|
Jin Y, Lee SJ, Minshall RD and Choi AM:
Caveolin-1: A critical regulator of lung injury. Am J Physiol Lung
Cell Mol Physiol. 300:L151–L160. 2011. View Article : Google Scholar
|
|
128
|
Davey A, McAuley DF and O'Kane CM: Matrix
metalloproteinases in acute lung injury: Mediators of injury and
drivers of repair. Eur Respir J. 38:959–970. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
129
|
Mura M, Han B, Andrade CF, Seth R, Hwang
D, Waddell TK, Keshavjee S and Liu M: The early responses of VEGF
and its receptors during acute lung injury: Implication of VEGF in
alveolar epithelial cell survival. Crit Care. 10:R1302006.
View Article : Google Scholar : PubMed/NCBI
|
|
130
|
Uchida T, Shirasawa M, Ware LB, Kojima K,
Hata Y, Makita K, Mednick G, Matthay ZA and Matthay MA: Receptor
for advanced glycation end-products is a marker of type I cell
injury in acute lung injury. Am J Respir Crit Care Med.
173:1008–1015. 2006. View Article : Google Scholar : PubMed/NCBI
|
|
131
|
Fremont RD, Koyama T, Calfee CS, Wu W,
Dossett LA, Bossert FR, Mitchell D, Wickersham N, Bernard GR,
Matthay MA, et al: Acute lung injury in patients with traumatic
injuries: Utility of a panel of biomarkers for diagnosis and
pathogenesis. J Trauma. 68:1121–1127. 2010.
|
|
132
|
Ding Z, Wang N, Ji N and Chen ZS:
Proteomics technologies for cancer liquid biopsies. Mol Cancer.
21:532022. View Article : Google Scholar : PubMed/NCBI
|
|
133
|
Hanash S: Disease proteomics. Nature.
422:226–232. 2003. View Article : Google Scholar : PubMed/NCBI
|
|
134
|
Rao Z, Liu S, Li Z, Wang Q, Gao F, Peng H,
Ren D, Zang Y, Li H, Li Y, et al: Alarmin-loaded extracellular
lipid droplets induce airway neutrophil infiltration during type 2
inflammation. Immunity. 57:2514–2529.e7. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
135
|
Zhou Y, Huang X, Yu H, Shi H, Chen M, Song
J, Tang W, Teng F, Li C, Yi L, et al: TMT-based quantitative
proteomics revealed protective efficacy of Icariside II against
airway inflammation and remodeling via inhibiting LAMP2, CTSD and
CTSS expression in OVA-induced chronic asthma mice. Phytomedicine.
118:1549412023. View Article : Google Scholar : PubMed/NCBI
|
|
136
|
Bowler RP, Ellison MC and Reisdorph N:
Proteomics in pulmonary medicine. Chest. 130:567–574. 2006.
View Article : Google Scholar : PubMed/NCBI
|
|
137
|
Zi SF, Wu XJ, Tang Y, Liang YP, Liu X,
Wang L, Li SL, Wu CD, Xu JY, Liu T, et al: Endothelial cell-derived
extracellular vesicles promote aberrant neutrophil trafficking and
subsequent remote lung injury. Adv Sci (Weinh). 11:e24006472024.
View Article : Google Scholar : PubMed/NCBI
|
|
138
|
Bowler RP, Duda B, Chan ED, Enghild JJ,
Ware LB, Matthay MA and Duncan MW: Proteomic analysis of pulmonary
edema fluid and plasma in patients with acute lung injury. Am J
Physiol Lung Cell Mol Physiol. 286:L1095–L1104. 2004. View Article : Google Scholar : PubMed/NCBI
|
|
139
|
Rozanova S, Barkovits K, Nikolov M,
Schmidt C, Urlaub H and Marcus K: Quantitative mass
spectrometry-based proteomics: An overview. Methods Mol Biol.
2228:85–116. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
140
|
Shuken SR: An introduction to mass
spectrometry-based proteomics. J Proteome Res. 22:2151–2171. 2023.
View Article : Google Scholar : PubMed/NCBI
|
|
141
|
Gao CL, Song JQ, Yang ZN, Wang H, Wu XY,
Shao C, Dai HX, Chen K, Guo YW, Pang T and Li XW: Chemoproteomics
of marine natural product naamidine J unveils CSE1L as a
therapeutic target in acute lung injury. J Am Chem Soc. Sep
26–2024.Epub ahead of print. View Article : Google Scholar
|
|
142
|
Hsu CY, Fu SH, Chien MW, Liu YW, Chen SJ
and Sytwu HK: Post-translational modifications of transcription
factors harnessing the etiology and pathophysiology in colonic
diseases. Int J Mol Sci. 21:32072020. View Article : Google Scholar : PubMed/NCBI
|
|
143
|
Zhu G, Jin L, Sun W, Wang S and Liu N:
Proteomics of post-translational modifications in colorectal
cancer: Discovery of new biomarkers. Biochim Biophys Acta Rev
Cancer. 1877:1887352022. View Article : Google Scholar : PubMed/NCBI
|
|
144
|
Li Y, Huang Y and Li T: PTM-X: Prediction
of post-translational modification crosstalk within and across
proteins. Methods Mol Biol. 2499:275–283. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
145
|
Ran H, Li C, Zhang M, Zhong J and Wang H:
Neglected PTM in animal adipogenesis: E3-mediated ubiquitination.
Gene. 878:1475742023. View Article : Google Scholar : PubMed/NCBI
|
|
146
|
Ebert T, Tran N, Schurgers L, Stenvinkel P
and Shiels PG: Ageing-oxidative stress, PTMs and disease. Mol
Aspects Med. 86:1010992022. View Article : Google Scholar
|
|
147
|
Zhang WJ, Zhou Y, Zhang Y, Su YH and Xu T:
Protein phosphorylation: A molecular switch in plant signaling.
Cell Rep. 42:1127292023. View Article : Google Scholar : PubMed/NCBI
|
|
148
|
Shindo S, Kakizaki S, Sakaki T, Kawasaki
Y, Sakuma T, Negishi M and Shizu R: Phosphorylation of nuclear
receptors: Novelty and therapeutic implications. Pharmacol Ther.
248:1084772023. View Article : Google Scholar : PubMed/NCBI
|
|
149
|
Paulo JA and Schweppe DK: Advances in
quantitative high-throughput phosphoproteomics with sample
multiplexing. Proteomics. 21:e20001402021. View Article : Google Scholar : PubMed/NCBI
|
|
150
|
Zhao A, Guo C, Wang L, Chen S, Xu Q, Cheng
J, Zhang J, Jiang J, Di J, Zhang H, et al: Xiebai San alleviates
acute lung injury by inhibiting the phosphorylation of the
ERK/Stat3 pathway and regulating multiple metabolisms.
Phytomedicine. 128:1553972024. View Article : Google Scholar : PubMed/NCBI
|
|
151
|
Li N, Liu B, Xiong R, Li G, Wang B and
Geng Q: HDAC3 deficiency protects against acute lung injury by
maintaining epithelial barrier integrity through preserving
mitochondrial quality control. Redox Biol. 63:1027462023.
View Article : Google Scholar : PubMed/NCBI
|
|
152
|
Zeng X, Lan Y, Xiao J, Hu L, Tan L, Liang
M, Wang X, Lu S, Peng T and Long F: Advances in phosphoproteomics
and its application to COPD. Expert Rev Proteomics. 19:311–324.
2022. View Article : Google Scholar
|
|
153
|
Chen L, Huang L, Gu Y, Cang W, Sun P and
Xiang Y: Lactate-lactylation hands between metabolic reprogramming
and immunosuppression. Int J Mol Sci. 23:119432022. View Article : Google Scholar : PubMed/NCBI
|
|
154
|
Jing F, Zhang J, Zhang H and Li T:
Unlocking the multifaceted molecular functions and diverse disease
implications of lactylation. Biol Rev Camb Philos Soc. Sep
16–2024.Epub ahead of print. View Article : Google Scholar : PubMed/NCBI
|
|
155
|
Garcia-Alvarez M, Marik P and Bellomo R:
Sepsis-associated hyperlactatemia. Crit Care. 18:5032014.
View Article : Google Scholar : PubMed/NCBI
|
|
156
|
Fan M, Yang K, Wang X, Zhang X, Xu J, Tu
F, Gill PS, Ha T, Williams DL and Li C: Lactate impairs vascular
permeability by inhibiting HSPA12B expression via GPR81-dependent
signaling in sepsis. Shock. 58:304–312. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
157
|
Yao G and Yang Z: Glypican-3 knockdown
inhibits the cell growth, stemness, and glycolysis development of
hepatocellular carcinoma cells under hypoxic microenvironment
through lactylation. Arch Physiol Biochem. 130:546–554. 2024.
|
|
158
|
Wang J, Yang P, Yu T, Gao M, Liu D, Zhang
J, Lu C, Chen X, Zhang X and Liu Y: Lactylation of PKM2 suppresses
inflammatory metabolic adaptation in pro-inflammatory macrophages.
Int J Biol Sci. 18:6210–6225. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
159
|
Dichtl S, Lindenthal L, Zeitler L, Behnke
K, Schlösser D, Strobl B, Scheller J, El Kasmi KC and Murray PJ:
Lactate and IL6 define separable paths of inflammatory metabolic
adaptation. Sci Adv. 7:eabg35052021. View Article : Google Scholar : PubMed/NCBI
|
|
160
|
Wang L, Li S, Luo H, Lu Q and Yu S: PCSK9
promotes the progression and metastasis of colon cancer cells
through regulation of EMT and PI3K/AKT signaling in tumor cells and
phenotypic polarization of macrophages. J Exp Clin Cancer Res.
41:3032022. View Article : Google Scholar : PubMed/NCBI
|
|
161
|
Cockram PE, Kist M, Prakash S, Chen SH,
Wertz IE and Vucic D: Ubiquitination in the regulation of
inflammatory cell death and cancer. Cell Death Differ. 28:591–605.
2021. View Article : Google Scholar : PubMed/NCBI
|
|
162
|
Li L, Wei J, Li S, Jacko AM, Weathington
NM, Mallampalli RK, Zhao J and Zhao Y: The deubiquitinase USP13
stabilizes the anti-inflammatory receptor IL-1R8/Sigirr to suppress
lung inflammation. EBioMedicine. 45:553–562. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
163
|
Qian Y, Wang Z, Lin H, Lei T, Zhou Z,
Huang W, Wu X, Zuo L, Wu J, Liu Y, et al: TRIM47 is a novel
endothelial activation factor that aggravates
lipopolysaccharide-induced acute lung injury in mice via K63-linked
ubiquitination of TRAF2. Signal Transduct Target Ther. 7:1482022.
View Article : Google Scholar : PubMed/NCBI
|
|
164
|
Li J, Deng SH, Li J, Li L, Zhang F, Zou Y,
Wu DM and Xu Y: Obacunone alleviates ferroptosis during
lipopolysaccharide-induced acute lung injury by upregulating
Nrf2-dependent antioxidant responses. Cell Mol Biol Lett.
27:292022. View Article : Google Scholar : PubMed/NCBI
|
|
165
|
Gao L, Zhang W, Shi XH, Chang X, Han Y,
Liu C, Jiang Z and Yang X: The mechanism of linear ubiquitination
in regulating cell death and correlative diseases. Cell Death Dis.
14:6592023. View Article : Google Scholar : PubMed/NCBI
|
|
166
|
De Silva ARI and Page RC: Ubiquitination
detection techniques. Exp Biol Med (Maywood). 248:1333–1346. 2023.
View Article : Google Scholar : PubMed/NCBI
|
|
167
|
Wishart DS: Metabolomics for investigating
physiological and pathophysiological processes. Physiol Rev.
99:1819–1875. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
168
|
McGarrah RW, Crown SB, Zhang GF, Shah SH
and Newgard CB: Cardiovascular metabolomics. Circ Res.
122:1238–1258. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
169
|
Zampieri M, Sekar K, Zamboni N and Sauer
U: Frontiers of high-throughput metabolomics. Curr Opin Chem Biol.
36:15–23. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
170
|
Paglia G and Astarita G: Metabolomics and
lipidomics using traveling-wave ion mobility mass spectrometry. Nat
Protoc. 12:797–813. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
171
|
Evans CR, Karnovsky A, Kovach MA,
Standiford TJ, Burant CF and Stringer KA: Untargeted LC-MS
metabolomics of bronchoalveolar lavage fluid differentiates acute
respiratory distress syndrome from health. J Proteome Res.
13:640–649. 2014. View Article : Google Scholar :
|
|
172
|
Fan L, Meng K, Meng F, Wu Y and Lin L:
Metabolomic characterization benefits the identification of acute
lung injury in patients with type A acute aortic dissection. Front
Mol Biosci. 10:12221332023. View Article : Google Scholar : PubMed/NCBI
|
|
173
|
Tzanakis K, Nattkemper TW, Niehaus K and
Albaum SP: MetHoS: A platform for large-scale processing, storage
and analysis of metabolomics data. BMC Bioinformatics. 23:2672022.
View Article : Google Scholar : PubMed/NCBI
|
|
174
|
Lind L, Fall T, Ärnlöv J, Elmståhl S and
Sundström J: Large-Scale Metabolomics and the Incidence of
Cardiovascular Disease. J Am Heart Assoc. 12:e0268852023.
View Article : Google Scholar : PubMed/NCBI
|
|
175
|
Serkova NJ, Standiford TJ and Stringer KA:
The emerging field of quantitative blood metabolomics for biomarker
discovery in critical illnesses. Am J Respir Crit Care Med.
184:647–655. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
176
|
Muthubharathi BC, Gowripriya T and
Balamurugan K: Metabolomics: Small molecules that matter more. Mol
Omics. 17:210–229. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
177
|
Ingelfinger F, Beltrán E, Gerdes LA and
Becher B: Single-cell multiomics in neuroinflammation. Curr Opin
Immunol. 76:1021802022. View Article : Google Scholar : PubMed/NCBI
|
|
178
|
Zormpas E, Queen R, Comber A and Cockell
SJ: Mapping the transcriptome: Realizing the full potential of
spatial data analysis. Cell. 186:5677–5689. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
179
|
Fatumo S, Chikowore T, Choudhury A, Ayub
M, Martin AR and Kuchenbaecker K: A roadmap to increase diversity
in genomic studies. Nat Med. 28:243–250. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
180
|
Kan M, Shumyatcher M and Himes BE: Using
omics approaches to understand pulmonary diseases. Respir Res.
18:1492017. View Article : Google Scholar : PubMed/NCBI
|
|
181
|
Fagerberg L, Hallström BM, Oksvold P,
Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S,
Danielsson A, Edlund K, et al: Analysis of the human
tissue-specific expression by genome-wide integration of
transcriptomics and antibody-based proteomics. Mol Cell Proteomics.
13:397–406. 2014. View Article : Google Scholar :
|
|
182
|
Robles-Remacho A, Sanchez-Martin RM and
Diaz-Mochon JJ: Spatial transcriptomics: Emerging technologies in
tissue gene expression profiling. Anal Chem. 95:15450–15460. 2023.
View Article : Google Scholar : PubMed/NCBI
|
|
183
|
Banavasi H, Nguyen P, Osman H and Soubani
AO: Management of ARDS - what works and what does not. Am J Med
Sci. 362:13–23. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
184
|
Li H, Li D, Ledru N, Xuanyuan Q, Wu H,
Asthana A, Byers LN, Tullius SG, Orlando G, Waikar SS and Humphreys
BD: Transcriptomic, epigenomic, and spatial metabolomic cell
profiling redefines regional human kidney anatomy. Cell Metab.
36:1105–1125.e10. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
185
|
Xiong X, James BT, Boix CA, Park YP,
Galani K, Victor MB, Sun N, Hou L, Ho LL, Mantero J, et al:
Epigenomic dissection of Alzheimer's disease pinpoints causal
variants and reveals epigenome erosion. Cell. 186:4422–4437.e21.
2023. View Article : Google Scholar : PubMed/NCBI
|
|
186
|
Ozsolak F and Milos PM: RNA sequencing:
Advances, challenges and opportunities. Nat Rev Genet. 12:87–98.
2011. View Article : Google Scholar :
|
|
187
|
Marand AP, Chen Z, Gallavotti A and
Schmitz RJ: A cis-regulatory atlas in maize at single-cell
resolution. Cell. 184:3041–3055.e21. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
188
|
Tejera P, Wang Z, Zhai R, Su L, Sheu CC,
Taylor DM, Chen F, Gong MN, Thompson BT and Christiani DC: Genetic
polymorphisms of peptidase inhibitor 3 (elafin) are associated with
acute respiratory distress syndrome. Am J Respir Cell Mol Biol.
41:696–704. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
189
|
Sun X, Sun BL, Sammani S, Bermudez T,
Dudek SM, Camp SM and Garcia JGN: Genetic and epigenetic regulation
of the non-muscle myosin light chain kinase isoform by lung
inflammatory factors and mechanical stress. Clin Sci (Lond).
35:963–977. 2021. View Article : Google Scholar
|
|
190
|
Adyshev DM, Moldobaeva N, Mapes B,
Elangovan V and Garcia JG: MicroRNA regulation of nonmuscle myosin
light chain kinase expression in human lung endothelium. Am J
Respir Cell Mol Biol. 49:58–66. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
191
|
Kovacs-Kasa A, Zaied AA, Leanhart S,
Koseoglu M, Sridhar S, Lucas R, Fulton DJ, Vazquez JA and Annex BH:
Elevated cytokine levels in plasma of patients with SARS-CoV-2 do
not contribute to pulmonary microvascular endothelial permeability.
Microbiol Spectr. 10:e01671212022. View Article : Google Scholar : PubMed/NCBI
|
|
192
|
Albini A, Calabrone L, Carlini V,
Benedetto N, Lombardo M, Bruno A and Noonan DM: Preliminary
evidence for IL-10-induced ACE2 mRNA expression in lung-derived and
endothelial cells: Implications for SARS-Cov-2 ARDS pathogenesis.
Front Immunol. 12:7181362021. View Article : Google Scholar : PubMed/NCBI
|
|
193
|
Xian H, Liu Y, Rundberg Nilsson A,
Gatchalian R, Crother TR, Tourtellotte WG, Zhang Y, Aleman-Muench
GR, Lewis G, Chen W, et al: Metformin inhibition of mitochondrial
ATP and DNA synthesis abrogates NLRP3 inflammasome activation and
pulmonary inflammation. Immunity. 54:1463–1477.e11. 2021.
View Article : Google Scholar : PubMed/NCBI
|
|
194
|
Wang Y, Liu B, Zhao G, Lee Y, Buzdin A, Mu
X, Zhao J, Chen H and Li X: Spatial transcriptomics: Technologies,
applications and experimental considerations. Genomics.
115:1106712023. View Article : Google Scholar : PubMed/NCBI
|
|
195
|
Han J, Zhang X, Cai M, Tian F, Xu Y, Chen
H, He W, Zhang J and Tian H: TSPO deficiency exacerbates acute lung
injury via NLRP3 inflammasome-mediated pyroptosis. Chin Med J
(Engl). 137:1592–1602. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
196
|
Xu H, Sheng S, Luo W, Xu X and Zhang Z:
Acute respiratory distress syndrome heterogeneity and the septic
ARDS subgroup. Front Immunol. 14:12771612023. View Article : Google Scholar : PubMed/NCBI
|
|
197
|
Tang W, Wu S, Tang Y, Ma J, Ao Y, Liu L
and Wei K: Microarray analysis identifies lncFirre as a potential
regulator of obesity-related acute lung injury. Life Sci.
340:1224592024. View Article : Google Scholar : PubMed/NCBI
|
|
198
|
Zou L, Yu Q, Zhang L, Yuan X, Fang F and
Xu F: Identification of inflammation related lncRNAs and Gm33647 as
a potential regulator in septic acute lung injury. Life Sci.
282:1198142021. View Article : Google Scholar : PubMed/NCBI
|
|
199
|
Sivakumar P, Ammar R, Thompson JR, Luo Y,
Streltsov D, Porteous M, McCoubrey C, Cantu E III, Beers MF, Jarai
G and Christie JD: Integrated plasma proteomics and lung
transcriptomics reveal novel biomarkers in idiopathic pulmonary
fibrosis. Respir Res. 22:2732021. View Article : Google Scholar : PubMed/NCBI
|
|
200
|
Sinha S, Rosin NL, Arora R, Labit E,
Jaffer A, Cao L, Farias R, Nguyen AP, de Almeida LGN, Dufour A, et
al: Dexamethasone modulates immature neutrophils and interferon
programming in severe COVID-19. Nat Med. 28:201–211. 2022.
View Article : Google Scholar :
|
|
201
|
Ramaswamy A, Brodsky NN, Sumida TS, Comi
M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, et al:
Immune dysregulation and autoreactivity correlate with disease
severity in SARS-CoV-2-associated multisystem inflammatory syndrome
in children. Immunity. 54:1083–1095.e7. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
202
|
Tong F, Shen W, Zhao J, Hu Y, Zhao Q, Lv
H, Liu F, Meng Z and Liu J: Silencing information regulator 1
ameliorates lipopolysaccharide-induced acute lung injury in rats
via the upregulation of caveolin-1. Biomed Pharmacother.
165:1150182023. View Article : Google Scholar : PubMed/NCBI
|
|
203
|
Ren Y, Li L, Wang MM, Cao LP, Sun ZR, Yang
ZZ, Zhang W, Zhang P and Nie SN: Pravastatin attenuates
sepsis-induced acute lung injury through decreasing pulmonary
microvascular permeability via inhibition of Cav-1/eNOS pathway.
Int Immunopharmacol. 100:1080772021. View Article : Google Scholar : PubMed/NCBI
|
|
204
|
Liang X, Wei SQ, Lee SJ, Fung JK, Zhang M,
Tanaka A, Choi AM and Jin Y: p62 sequestosome 1/light chain 3b
complex confers cytoprotection on lung epithelial cells after
hyperoxia. Am J Respir Cell Mol Biol. 48:489–496. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
205
|
Tanaka A, Jin Y, Lee SJ, Zhang M, Kim HP,
Stolz DB, Ryter SW and Choi AM: Hyperoxia-induced LC3B interacts
with the Fas apoptotic pathway in epithelial cell death. Am J
Respir Cell Mol Biol. 46:507–514. 2012. View Article : Google Scholar :
|
|
206
|
Chen ZH, Lam HC, Jin Y, Kim HP, Cao J, Lee
SJ, Ifedigbo E, Parameswaran H, Ryter SW and Choi AM: Autophagy
protein microtubule-associated protein 1 light chain-3B (LC3B)
activates extrinsic apoptosis during cigarette smoke-induced
emphysema. Proc Natl Acad Sci USA. 107:18880–18885. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
207
|
Baysoy A, Bai Z, Satija R and Fan R: The
technological landscape and applications of single-cell
multi-omics. Nat Rev Mol Cell Biol. 24:695–713. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
208
|
Wong HR, Cvijanovich NZ, Allen GL, Thomas
NJ, Freishtat RJ, Anas N, Meyer K, Checchia PA, Lin R, Shanley TP,
et al: Validation of a gene expression-based subclassification
strategy for pediatric septic shock. Crit Care Med. 39:2511–2517.
2011. View Article : Google Scholar : PubMed/NCBI
|
|
209
|
Rao A, Barkley D, França GS and Yanai I:
Exploring tissue architecture using spatial transcriptomics.
Nature. 596:211–220. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
210
|
Computational Pan-Genomics Consortium:
Computational pan-genomics: Status, promises and challenges. Brief
Bioinform. 19:118–135. 2018.
|
|
211
|
Vandereyken K, Sifrim A, Thienpont B and
Voet T: Methods and applications for single-cell and spatial
multi-omics. Nat Rev Genet. 24:494–515. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
212
|
Zhang Y, Shan P, Srivastava A, Li Z and
Lee PJ: Endothelial stanniocalcin 1 maintains mitochondrial
bioenergetics and prevents oxidant-induced lung injury via
toll-like receptor 4. Antioxid Redox Signal. 30:1775–1796. 2019.
View Article : Google Scholar :
|
|
213
|
Wang Y, Chen D, Xie H, Jia M, Sun X, Peng
F, Guo F and Tang D: AUF1 protects against ferroptosis to alleviate
sepsis-induced acute lung injury by regulating NRF2 and ATF3. Cell
Mol Life Sci. 79:2282022. View Article : Google Scholar : PubMed/NCBI
|
|
214
|
Ghiasi M, Kheirandish Zarandi P, Dayani A,
Salimi A and Shokri E: Potential therapeutic effects and nano-based
delivery systems of mesenchymal stem cells and their isolated
exosomes to alleviate acute respiratory distress syndrome caused by
COVID-19. Regen Ther. 27:319–328. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
215
|
Deng H, Zhu L, Zhang Y, Zheng L, Hu S,
Zhou W, Zhang T, Xu W, Chen Y, Zhou H, et al: Differential lung
protective capacity of exosomes derived from human adipose tissue,
bone marrow, and umbilical cord mesenchymal stem cells in
sepsis-induced acute lung injury. Oxid Med Cell Longev.
2022:78378372022. View Article : Google Scholar : PubMed/NCBI
|
|
216
|
Xian H, Watari K, Sanchez-Lopez E,
Offenberger J, Onyuru J, Sampath H, Ying W, Hoffman HM, Shadel GS
and Karin M: Oxidized DNA fragments exit mitochondria via mPTP- and
VDAC-dependent channels to activate NLRP3 inflammasome and
interferon signaling. Immunity. 55:1370–1385.e8. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
217
|
Li J, Bai Y, Tang Y, Wang X, Cavagnaro MJ,
Li L, Li Z, Zhang Y and Shi J: A 4-benzene-indol derivative
alleviates LPS-induced acute lung injury through inhibiting the
NLRP3 inflammasome. Front Immunol. 13:8121642022. View Article : Google Scholar : PubMed/NCBI
|
|
218
|
Xie H, Liu X, Zhou Q, Huang T, Zhang L,
Gao J, Wang Y, Liu Y, Yan T, Zhang S and Wang CY: DNA Methylation
Modulates Aging Process in Adipocytes. Aging Dis. 13:433–446. 2022.
View Article : Google Scholar : PubMed/NCBI
|
|
219
|
Picard M, Scott-Boyer MP, Bodein A, Périn
O and Droit A: Integration strategies of multi-omics data for
machine learning analysis. Comput Struct Biotechnol J.
19:3735–3746. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
220
|
Poirion OB, Jing Z, Chaudhary K, Huang S
and Garmire LX: DeepProg: An ensemble of deep-learning and
machine-learning models for prognosis prediction using multi-omics
data. Genome Med. 13:1122021. View Article : Google Scholar : PubMed/NCBI
|
|
221
|
Ravindran U and Gunavathi C: A survey on
gene expression data analysis using deep learning methods for
cancer diagnosis. Prog Biophys Mol Biol. 177:1–13. 2023. View Article : Google Scholar
|
|
222
|
P D and G C: A systematic review on
machine learning and deep learning techniques in cancer survival
prediction. Prog Biophys Mol Biol. 174:62–71. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
223
|
Schmidt-Erfurth U, Sadeghipour A, Gerendas
BS, Waldstein SM and Bogunović H: Artificial intelligence in
retina. Prog Retin Eye Res. 67:1–29. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
224
|
Cui H, Wang C, Maan H, Pang K, Luo F, Duan
N and Wang B: mscGPT: Toward building a foundation model for
single-cell multi-omics using generative AI. Nat Methods.
21:1470–1480. 2024. View Article : Google Scholar : PubMed/NCBI
|
|
225
|
Kang M, Ko E and Mersha TB: A roadmap for
multi-omics data integration using deep learning. Brief Bioinform.
23:bbab4542022. View Article : Google Scholar :
|
|
226
|
Lin M, Xu F, Sun J, Song J, Shen Y, Lu S,
Ding H, Lan L, Chen C, Ma W, et al: Integrative multi-omics
analysis unravels the host response landscape and reveals a serum
protein panel for early prognosis prediction for ARDS. Crit Care.
28:2132024. View Article : Google Scholar : PubMed/NCBI
|
|
227
|
Zhang S, Huang W, Wu X, Chen H, Wang L,
Chao J, Xie J and Qiu H: IBR1, a novel endogenous IFIH1-binding
dsRNA, governs IFIH1 activation and M1 macrophage polarisation in
ARDS. Clin Transl Med. 14:e700272024. View Article : Google Scholar : PubMed/NCBI
|
|
228
|
Fang X, Bai C and Wang X: Bioinformatics
insights into acute lung injury/acute respiratory distress
syndrome. Clin Transl Med. 1:92012. View Article : Google Scholar
|
|
229
|
Zhang Z, Navarese EP, Zheng B, Meng Q, Liu
N, Ge H, Pan Q, Yu Y and Ma X: Analytics with artificial
intelligence to advance the treatment of acute respiratory distress
syndrome. J Evid Based Med. 13:301–312. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
230
|
Ober-Reynolds B, Wang C, Ko JM, Rios EJ,
Aasi SZ, Davis MM, Oro AE and Greenleaf WJ: Integrated single-cell
chromatin and transcriptomic analyses of human scalp identify
gene-regulatory programs and critical cell types for hair and skin
diseases. Nat Genet. 55:1288–1300. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
231
|
Hwang B, Lee JH and Bang D: Single-cell
RNA sequencing technologies and bioinformatic pipelines. Exp Mol
Med. 50:1–14. 2018. View Article : Google Scholar
|
|
232
|
Wang Y and Navin NE: Advances and
applications of single-cell sequencing technologies. Mol Cell.
58:598–609. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
233
|
Gawad C, Koh W and Quake SR: Single-cell
genome sequencing: Current state of the science. Nat Rev Genet.
17:175–188. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
234
|
Yang R, Zheng T, Xiang H, Liu M and Hu K:
Lung single-cell RNA profiling reveals response of pulmonary
capillary to sepsis-induced acute lung injury. Front Immunol.
15:13089152024. View Article : Google Scholar : PubMed/NCBI
|
|
235
|
Kang ZY, Huang QY, Zhen NX, Xuan NX, Zhou
QC, Zhao J, Cui W, Zhang ZC and Tian BP: Heterogeneity of immune
cells and their communications unveiled by transcriptome profiling
in acute inflammatory lung injury. Front Immunol. 15:13824492024.
View Article : Google Scholar : PubMed/NCBI
|
|
236
|
Suvà ML and Tirosh I: Single-Cell RNA
sequencing in cancer: Lessons learned and emerging challenges. Mol
Cell. 75:7–12. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
237
|
Halpern KB, Shenhav R, Matcovitch-Natan O,
Toth B, Lemze D, Golan M, Massasa EE, Baydatch S, Landen S, Moor
AE, et al: Single-cell spatial reconstruction reveals global
division of labour in the mammalian liver. Nature. 542:352–356.
2017. View Article : Google Scholar : PubMed/NCBI
|
|
238
|
Van de Sande B, Lee JS, Mutasa-Gottgens E,
Naughton B, Bacon W, Manning J, Wang Y, Pollard J, Mendez M, Hill
J, et al: Applications of single-cell RNA sequencing in drug
discovery and development. Nat Rev Drug Discov. 22:496–520. 2023.
View Article : Google Scholar : PubMed/NCBI
|
|
239
|
Greener JG, Kandathil SM, Moffat L and
Jones DT: A guide to machine learning for biologists. Nat Rev Mol
Cell Biol. 23:40–55. 2022. View Article : Google Scholar
|
|
240
|
Handelman GS, Kok HK, Chandra RV, Razavi
AH, Lee MJ and Asadi H: eDoctor: Machine learning and the future of
medicine. J Intern Med. 284:603–619. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
241
|
Deo RC: Machine learning in medicine.
Circulation. 132:1920–1930. 2015. View Article : Google Scholar : PubMed/NCBI
|
