|
1
|
Strongman H, Kausar I and Maher TM:
Incidence, prevalence, and survival of patients with idiopathic
pulmonary fibrosis in the UK. Adv Ther. 35:724–736. 2018.
View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Ma HY, Li Q, Wong WR, N'Diaye EN, Caplazi
P, Bender H, Huang Z, Arlantico A, Jeet S, Wong A, et al: LOXL4,
but not LOXL2, is the critical determinant of pathological collagen
cross-linking and fibrosis in the lung. Sci Adv. 9:eadf01332023.
View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Mei Q, Yang Z, Xiang Z, Zuo H, Zhou Z,
Dong X, Zhang L, Song W, Wang Y, Hu Q, et al: Pharmacological
inhibition of MDM4 alleviates pulmonary fibrosis. Theranostics.
13:2787–2799. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Zhang X, Hu X, Zhang Y, Liu B, Pan H, Liu
Z, Yao Z, Zhu Q, Wu C and Shen T: Impaired autophagy-accelerated
senescence of alveolar type II epithelial cells drives pulmonary
fibrosis induced by single-walled carbon nanotubes. J
Nanobiotechnology. 21:692023. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Ma J, Cai H, Long X, Cheng K, Xu X, Zhang
D and Li J: Hyaluronic acid bioinspired polymers for the regulation
of cell chondrogenic and osteogenic differentiation. Int J Biol
Macromol. 161:1011–1020. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Carton F and Malatesta M:
Nanotechnological research for regenerative medicine: The role of
hyaluronic acid. Int J Mol Sci. 25:39752024. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Collum SD, Chen NY, Hernandez AM,
Hanmandlu A, Sweeney H, Mertens TCJ, Weng T, Luo F, Molina JG,
Davies J, et al: Inhibition of hyaluronan synthesis attenuates
pulmonary hypertension associated with lung fibrosis. Br J
Pharmacol. 174:3284–3301. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
8
|
Bjermer L, Lundgren R and Hällgren R:
Hyaluronan and type III procollagen peptide concentrations in
bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis.
Thorax. 44:126–131. 1989. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Yao ZY, Gong JS, Liu YR, Jiang JY, Zhang
YS, Su C, Li H, Kang CL, Liu L, Xu ZH and Shi JS: Genetic variation
reveals the enhanced microbial hyaluronan biosynthesis via
atmospheric and room temperature plasma. Carbohydr Polym.
312:1208092023. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Bart G, Vico NO, Hassinen A, Pujol FM,
Deen AJ, Ruusala A, Tammi RH, Squire A, Heldin P, Kellokumpu S and
Tammi MI: Fluorescence resonance energy transfer (FRET) and
proximity ligation assays reveal functionally relevant homo- and
heteromeric complexes among hyaluronan synthases HAS1, HAS2, and
HAS3. J Biol Chem. 290:11479–11490. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Yang J, Wang L, Zhang Z, Sun Q and Zhang
Y: Downregulation of HAS-2 regulates the chondrocyte cytoskeleton
and induces cartilage degeneration by activating the RhoA/ROCK
signaling pathway. Int J Mol Med. 52:572023. View Article : Google Scholar
|
|
12
|
Ge Z, Chen Y, Ma L, Hu F and Xie L:
Macrophage polarization and its impact on idiopathic pulmonary
fibrosis. Front Immunol. 15:14449642024. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Barrett T, Wilhite SE, Ledoux P,
Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH,
Sherman PM, Holko M, et al: NCBI GEO: Archive for functional
genomics data sets-update. Nucleic Acids Res. 41(Database Issue):
D991–D995. 2013. View Article : Google Scholar :
|
|
14
|
Cecchini MJ, Hosein K, Howlett CJ, Joseph
M and Mura M: Comprehensive gene expression profiling identifies
distinct and overlapping transcriptional profiles in non-specific
interstitial pneumonia and idiopathic pulmonary fibrosis. Respir
Res. 19:1532018. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Li H, Zhao C, Muhetaer G, Guo L, Yao K,
Zhang G, Ji Y, Xing S, Zhou J and Huang X: Integrated
RNA-sequencing and network pharmacology approach reveals the
protection of Yiqi Huoxue formula against idiopathic pulmonary
fibrosis by interfering with core transcription factors.
Phytomedicine. 104:1543012022. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Love MI, Huber W and Anders S: Moderated
estimation of fold change and dispersion for RNA-seq data with
DESeq2. Genome Biol. 15:5502014. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Martin M: Cutadapt removes adapter
sequences from high-throughput sequencing reads. EMBnet J.
17:10–12. 2011. View Article : Google Scholar
|
|
18
|
Dobin A, Davis CA, Schlesinger F, Drenkow
J, Zaleski C, Jha S, Batut P, Chaisson M and Gingeras TR: STAR:
Ultrafast universal RNA-seq aligner. Bioinformatics. 29:15–21.
2013. View Article : Google Scholar
|
|
19
|
Liao Y, Smyth GK and Shi W: featureCounts:
An efficient general purpose program for assigning sequence reads
to genomic features. Bioinformatics. 30:923–930. 2014. View Article : Google Scholar
|
|
20
|
Wolf FA, Angerer P and Theis FJ: SCANPY:
Large-scale single-cell gene expression data analysis. Genome Biol.
19:152018. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Wolock SL, Lopez R and Klein AM: Scrublet:
Computational identification of cell doublets in single-cell
transcriptomic data. Cell Syst. 8:281–291.e9. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Satija R, Farrell JA, Gennert D, Schier AF
and Regev A: Spatial reconstruction of single-cell gene expression
data. Nat Biotechnol. 33:495–502. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Livak KJ and Schmittgen TD: Analysis of
relative gene expression data using real-time quantitative PCR and
the 2(-Delta Delta C(T)) method. Methods. 25:402–408. 2001.
View Article : Google Scholar
|
|
24
|
Fuentes-Mateos R, Santos E and
Fernández-Medarde A: Optimized protocol for isolation and culture
of murine neonatal primary lung fibroblasts. Methods Protoc.
6:142023. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Liang J, Jiang D, Jung Y, Xie T, Ingram J,
Church T, Degan S, Leonard M, Kraft M and Noble PW: Role of
hyaluronan and hyaluronan-binding proteins in human asthma. J
Allergy Clin Immunol. 128:403–411.e3. 2011. View Article : Google Scholar
|
|
26
|
Fleming J, Magana P, Nair S, Tsenkov M,
Bertoni D, Pidruchna I, Lima Afonso MQ, Midlik A, Paramval U, Žídek
A, et al: AlphaFold protein structure database and 3D-beacons: New
data and capabilities. J Mol Biol. 437:1689672025. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Hess B: P-LINCS: A parallel linear
constraint solver for molecular simulation. J Chem Theory Comput.
4:116–122. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Humphrey W, Dalke A and Schulten K: VMD:
Visual molecular dynamics. J Mol Graph. 14:33–38. 27–28. 1996.
View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Rosignoli S and Paiardini A: Boosting the
full potential of PyMOL with structural biology plugins.
Biomolecules. 12:17642022. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Moberly JG, Bernards MT and Waynant KV:
Key features and updates for origin 2018. J Cheminform. 10:52018.
View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Kumari R, Kumar R; Open Source Drug
Discovery Consortium; Lynn A: g_mmpbsa-a GROMACS tool for
high-throughput MM-PBSA calculations. J Chem Inf Model.
54:1951–1962. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Martinez Molina D, Jafari R,
Ignatushchenko M, Seki T, Larsson EA, Dan C, Sreekumar L, Cao Y and
Nordlund P: Monitoring drug target engagement in cells and tissues
using the cellular thermal shift assay. Science. 341:84–87. 2013.
View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Tan BX, Brown CJ, Ferrer FJ, Yuen TY, Quah
ST, Chan BH, Jansson AE, Teo HL, Nordlund P and Lane DP: Assessing
the efficacy of Mdm2/Mdm4-inhibiting stapled peptides using
cellular thermal shift assays. Sci Rep. 5:121162015. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Selman M and Pardo A: Pathogenic
mechanisms in the development of diffuse pulmonary fibrosis. Braz J
Med Biol Res. 29:1117–1126. 1996.PubMed/NCBI
|
|
35
|
Rosser JI, Nagy N, Goel R, Kaber G,
Demirdjian S, Saxena J, Bollyky JB, Frymoyer AR, Pacheco-Navarro
AE, Burgener EB, et al: Oral hymecromone decreases hyaluronan in
human study participants. J Clin Invest. 132:e1579832022.
View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Ghatak S, Markwald RR, Hascall VC, Dowling
W, Lottes RG, Baatz JE, Beeson G, Beeson CC, Perrella MA,
Thannickal VJ and Misra S: Transforming growth factor β1 (TGFβ1)
regulates CD44V6 expression and activity through extracellular
signal-regulated kinase (ERK)-induced EGR1 in pulmonary fibrogenic
fibroblasts. J Biol Chem. 292:10465–10489. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Qin W, Spek CA, Scicluna BP, van der Poll
T and Duitman J: Myeloid DNA methyltransferase3b deficiency
aggravates pulmonary fibrosis by enhancing profibrotic macrophage
activation. Respir Res. 23:1622022. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Liu L, Wu P, Wei Y, Lu M, Ge H, Wang P,
Sun J, Horng T, Liu X, Shen X, et al: TWEAK-Fn14 signaling protects
mice from pulmonary fibrosis by inhibiting fibroblast activation
and recruiting pro-regenerative macrophages. Cell Rep.
44:1152202025. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Zhou JW, Bai Y, Guo JQ, Li YY, Liu YF,
Liang C, Xing YR, Guo HL, Qi TX, Wu J and Hu D: Peroxiredoxin 4 as
a switch regulating PTEN/AKT axis in alveolar macrophages
activation. Signal Transduct Target Ther. 10:3522025. View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Li S, Xu H, Liu S, Hou J, Han Y, Li C, Li
Y, Zheng G, Wei Z, Yang F, et al: Targeting Lp-PLA2 inhibits
profibrotic monocyte-derived macrophages in silicosis through
restoring cardiolipin-mediated mitophagy. Cell Mol Immunol.
22:776–790. 2025. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Kultti A, Pasonen-Seppänen S, Jauhiainen
M, Rilla KJ, Kärnä R, Pyöriä E, Tammi RH and Tammi MI:
4-Methylumbelliferone inhibits hyaluronan synthesis by depletion of
cellular UDP-glucuronic acid and downregulation of hyaluronan
synthase 2 and 3. Exp Cell Res. 315:1914–1923. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
He XY, Zhao WL, Yao LP, Sun P, Cheng G,
Liu YL, Yu Y, Liu Y, Wang TJ, Zhang QY, et al: Orcinol glucoside
targeted p38 as an agonist to promote osteogenesis and protect
glucocorticoid-induced osteoporosis. Phytomedicine. 119:1549532023.
View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Li J, He P, Zhang J and Li N: Orcinol
glucoside improves the depressive-like behaviors of perimenopausal
depression mice through modulating activity of
hypothalamic-pituitary-adrenal/ovary axis and activating
BDNF-TrkB-CREB signaling pathway. Phytother Res. 35:5795–5807.
2021. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Wang X, Li G, Li P, Huang L, Huang J and
Zhai H: Anxiolytic effects of orcinol glucoside and orcinol
monohydrate in mice. Pharm Biol. 53:876–881. 2015. View Article : Google Scholar
|
|
45
|
Nahak P, Gajbhiye RL, Karmakar G, Guha P,
Roy B, Besra SE, Bikov AG, Akentiev AV, Noskov BA, Nag K, et al:
Orcinol glucoside loaded polymer-lipid hybrid nanostructured lipid
carriers: potential cytotoxic agents against gastric, colon and
hepatoma carcinoma cell lines. Pharm Res. 35:1982018. View Article : Google Scholar
|
|
46
|
Nie Y, Dong X, He Y, Yuan T, Han T, Rahman
K, Qin L and Zhang Q: Medicinal plants of genus Curculigo:
Traditional uses and a phytochemical and ethnopharmacological
review. J Ethnopharmacol. 147:547–563. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
47
|
Yang YM, Noureddin M, Liu C, Ohashi K, Kim
SY, Ramnath D, Powell EE, Sweet MJ, Roh YS, Hsin IF, et al:
Hyaluronan synthase 2-mediated hyaluronan production mediates
Notch1 activation and liver fibrosis. Sci Transl Med.
11:eaat92842019. View Article : Google Scholar : PubMed/NCBI
|
|
48
|
Klee S, Picart-Armada S, Wenger K, Birk G,
Quast K, Veyel D, Rist W, Violet C, Luippold A, Haslinger C, et al:
Transcriptomic and proteomic profiling of young and old mice in the
bleomycin model reveals high similarity. Am J Physiol Lung Cell Mol
Physiol. 324:L245–L258. 2023. View Article : Google Scholar : PubMed/NCBI
|
