Fibroblast proliferative capacity predicts prognosis in Idiopathic Pulmonary Fibrosis and identifies PITX1 as a growth-associated gene

This is a preview and has not been published.

Fibroblast proliferative capacity predicts prognosis in Idiopathic Pulmonary Fibrosis and identifies PITX1 as a growth-associated gene

Authors

  • Min Kyung Kim Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan
  • Seung-Lee Park Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan
  • Eun jeong Seo Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan
  • So-Yoon Kim Department of Interdisciplinary Program in Biomedical Science Major, Graduate School, Soonchunhyang University, Asan
  • Jong-Uk Lee Department of Internal Medicine, Soonchunhyang University Bucheon Hospital
  • Sung Woo Park Division of Allergy and Respiratory Medicine, Dept. of Internal Medicine, Soonchunhyang University Bucheon Hospital

Keywords:

Idiopathic pulmonary fibrosis, Fibroblast proliferation, PITX1, Prognosis

Abstract

Background

Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease with poor prognosis. Lung fibroblasts isolated from patients with IPF exhibit enhanced proliferative capacity; however, the molecular determinants linking fibroblast proliferation to clinical outcomes remain incompletely understood.

Methods

Fibroblast growth slopes were measured in primary lung fibroblast derived from patients with IPF and control subjects. Transcriptome microarray data were integrated with fibroblast growth kinetics to identify growth slope–associated genes. Differential expression analysis was performed between IPF and control fibroblasts, and candidate genes were further evaluated at the mRNA and protein levels in lung fibroblasts and bronchoalveolar lavage (BAL) fluids. Associations with clinical outcomes were assessed.

Results

Fibroblasts derived from patients with IPF showed significantly higher growth slope than control fibroblasts, and increased fibroblast growth slope were associated with reduced survival in IPF. Integration of fibroblast growth kinetics with transcriptomic analysis identified a fibroblast growth slope–associated gene signature, from which PITX1 emerged as a disease-relevant candidate gene. PITX1 mRNA and protein levels were elevated in IPF fibroblasts compared with controls. In BAL fluids, PITX1 protein levels were significantly higher in patients with IPF and were associated with clinical outcomes, although they did not correlate with pulmonary function parameters.

Conclusions

Enhanced fibroblast proliferative capacity is associated with poor prognosis in IPF, and PITX1 represents a fibroblast growth slope–associated gene reflecting fibroblast heterogeneity and prognostic relevance. These findings suggest that assessment of fibroblast growth behavior and PITX1 expression may provide insight into disease progression in IPF, although further validation studies are required.

References

1. Lederer, D.J. and F.J. Martinez, Idiopathic Pulmonary Fibrosis. N Engl J Med, 2018. 378(19): p. 1811-1823.

2. Martinez, F.J. and K. Flaherty, Pulmonary function testing in idiopathic interstitial pneumonias. Proc Am Thorac Soc, 2006. 3(4): p. 315-21.

3. Upagupta, C., C. Shimbori, R. Alsilmi, and M. Kolb, Matrix abnormalities in pulmonary fibrosis. Eur Respir Rev, 2018. 27(148).

4. King, T.E., Jr., M.I. Schwarz, K. Brown, et al., Idiopathic pulmonary fibrosis: relationship between histopathologic features and mortality. Am J Respir Crit Care Med, 2001. 164(6): p. 1025-32.

5. Nicholson, A.G., L.G. Fulford, T.V. Colby, et al., The relationship between individual histologic features and disease progression in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med, 2002. 166(2): p. 173-7.

6. Selman, M. and A. Pardo, Alveolar epithelial cell disintegrity and subsequent activation: a key process in pulmonary fibrosis. Am J Respir Crit Care Med, 2012. 186(2): p. 119-21.

7. Epstein Shochet, G., E. Brook, B. Bardenstein-Wald, and D. Shitrit, TGF-β pathway activation by idiopathic pulmonary fibrosis (IPF) fibroblast derived soluble factors is mediated by IL-6 trans-signaling. Respiratory Research, 2020. 21(1): p. 56.

8. Crestani, B., V. Besnard, L. Plantier, K. Borensztajn, and A. Mailleux, Fibroblasts: the missing link between fibrotic lung diseases of different etiologies? Respir Res, 2013. 14(1): p. 81.

9. Renzoni, E.A., D.J. Abraham, S. Howat, et al., Gene expression profiling reveals novel TGFbeta targets in adult lung fibroblasts. Respir Res, 2004. 5(1): p. 24.

10. Lindahl, G.E., C.J. Stock, X. Shi-Wen, et al., Microarray profiling reveals suppressed interferon stimulated gene program in fibroblasts from scleroderma-associated interstitial lung disease. Respir Res, 2013. 14(1): p. 80.

11. Peng, R., S. Sridhar, G. Tyagi, et al., Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: a model for "active" disease. PLoS One, 2013. 8(4): p. e59348.

12. Vuga, L.J., A. Ben-Yehudah, E. Kovkarova-Naumovski, et al., WNT5A is a regulator of fibroblast proliferation and resistance to apoptosis. Am J Respir Cell Mol Biol, 2009. 41(5): p. 583-9.

13. Beisang, D.J., K. Smith, L. Yang, et al., Single-cell RNA sequencing reveals that lung mesenchymal progenitor cells in IPF exhibit pathological features early in their differentiation trajectory. Scientific Reports, 2020. 10(1): p. 11162.

14. Uhal, B.D., The role of apoptosis in pulmonary fibrosis. European Respiratory Review, 2008. 17(109): p. 138-144.

15. Moodley, Y.P., P. Caterina, A.K. Scaffidi, et al., Comparison of the morphological and biochemical changes in normal human lung fibroblasts and fibroblasts derived from lungs of patients with idiopathic pulmonary fibrosis during FasL-induced apoptosis. J Pathol, 2004. 202(4): p. 486-95.

16. Moodley, Y.P., N.L. Misso, A.K. Scaffidi, et al., Inverse effects of interleukin-6 on apoptosis of fibroblasts from pulmonary fibrosis and normal lungs. Am J Respir Cell Mol Biol, 2003. 29(4): p. 490-8.

17. Raghu, G., H.R. Collard, J.J. Egan, et al., An official ATS/ERS/JRS/ALAT statement: idiopathic pulmonary fibrosis: evidence-based guidelines for diagnosis and management. Am J Respir Crit Care Med, 2011. 183(6): p. 788-824.

18. Raghu, G., M. Remy-Jardin, J.L. Myers, et al., Diagnosis of Idiopathic Pulmonary Fibrosis. An Official ATS/ERS/JRS/ALAT Clinical Practice Guideline. Am J Respir Crit Care Med, 2018. 198(5): p. e44-e68.

19. Lee, J.U., H.S. Cheong, E.Y. Shim, et al., Gene profile of fibroblasts identify relation of CCL8 with idiopathic pulmonary fibrosis. Respir Res, 2017. 18(1): p. 3.

20. Lee, J.U., J.H. Son, E.Y. Shim, et al., Global DNA Methylation Pattern of Fibroblasts in Idiopathic Pulmonary Fibrosis. DNA Cell Biol, 2019. 38(9): p. 905-914.

21. Mosmann, T., Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. J Immunol Methods, 1983. 65(1-2): p. 55-63.

22. Zhang, B., D. Schmoyer, S. Kirov, and J. Snoddy, GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics, 2004. 5: p. 16.

23. Liao, Y., J. Wang, E.J. Jaehnig, Z. Shi, and B. Zhang, WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. Nucleic Acids Res, 2019. 47(W1): p. W199-w205.

24. Livak, K.J. and T.D. Schmittgen, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 2001. 25(4): p. 402-8.

25. Søreide, K., Receiver-operating characteristic curve analysis in diagnostic, prognostic and predictive biomarker research. J Clin Pathol, 2009. 62(1): p. 1-5.

26. Budczies, J., F. Klauschen, B.V. Sinn, et al., Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization. PLoS One, 2012. 7(12): p. e51862.

27. Moodley, Y.P., A.K. Scaffidi, N.L. Misso, et al., Fibroblasts isolated from normal lungs and those with idiopathic pulmonary fibrosis differ in interleukin-6/gp130-mediated cell signaling and proliferation. Am J Pathol, 2003. 163(1): p. 345-54.

28. Robinson, M.D., D.J. McCarthy, and G.K. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010. 26(1): p. 139-40.

29. Habiel, D.M. and C. Hogaboam, Heterogeneity in fibroblast proliferation and survival in idiopathic pulmonary fibrosis. Front Pharmacol, 2014. 5: p. 2.

30. Meneghin, A., E.S. Choi, H.L. Evanoff, et al., TLR9 is expressed in idiopathic interstitial pneumonia and its activation promotes in vitro myofibroblast differentiation. Histochem Cell Biol, 2008. 130(5): p. 979-92.

31. Trujillo, G., A. Meneghin, K.R. Flaherty, et al., TLR9 differentiates rapidly from slowly progressing forms of idiopathic pulmonary fibrosis. Sci Transl Med, 2010. 2(57): p. 57ra82.

32. Tran, T.Q. and C. Kioussi, Pitx genes in development and disease. Cell Mol Life Sci, 2021. 78(11): p. 4921-4938.

33. Szeto, D.P., C. Rodriguez-Esteban, A.K. Ryan, et al., Role of the Bicoid-related homeodomain factor Pitx1 in specifying hindlimb morphogenesis and pituitary development. Genes Dev, 1999. 13(4): p. 484-94.

34. Byun, J.S., M. Oh, S. Lee, et al., The transcription factor PITX1 drives astrocyte differentiation by regulating the SOX9 gene. J Biol Chem, 2020. 295(39): p. 13677-13690.

35. Song, X., C. Zhao, L. Jiang, et al., High PITX1 expression in lung adenocarcinoma patients is associated with DNA methylation and poor prognosis. Pathol Res Pract, 2018. 214(12): p. 2046-2053.

36. Shi, B., L. Xu, S. Mao, et al., Abnormal PITX1 gene methylation in adolescent idiopathic scoliosis: a pilot study. BMC Musculoskelet Disord, 2018. 19(1): p. 138.

37. Sailer, V., A. Charpentier, J. Dietrich, et al., Intragenic DNA methylation of PITX1 and the adjacent long non-coding RNA C5orf66-AS1 are prognostic biomarkers in patients with head and neck squamous cell carcinomas. PLoS One, 2018. 13(2): p. e0192742.

38. Zhao, Y., J. Zhao, M. Zhong, et al., The expression and methylation of PITX genes is associated with the prognosis of head and neck squamous cell carcinoma. Front Genet, 2022. 13: p. 982241.

39. Ohira, T., S. Nakagawa, J. Takeshita, H. Aburatani, and H. Kugoh, PITX1 inhibits the growth and proliferation of melanoma cells through regulation of SOX family genes. Sci Rep, 2021. 11(1): p. 18405.

40. Kolfschoten, I.G., B. van Leeuwen, K. Berns, et al., A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity. Cell, 2005. 121(6): p. 849-58.

41. Liu, D.X. and P.E. Lobie, Transcriptional activation of p53 by Pitx1. Cell Death Differ, 2007. 14(11): p. 1893-907.

42. Zhao, J. and Y. Xu, PITX1 plays essential functions in cancer. Front Oncol, 2023. 13: p. 1253238.

43. Karam, N., J.F. Lavoie, B. St-Jacques, et al., Bone-Specific Overexpression of PITX1 Induces Senile Osteoporosis in Mice Through Deficient Self-Renewal of Mesenchymal Progenitors and Wnt Pathway Inhibition. Sci Rep, 2019. 9(1): p. 3544.

44. Zhao, X., P. Huang, G. Li, et al., Overexpression of Pitx1 attenuates the senescence of chondrocytes from osteoarthritis degeneration cartilage-A self-controlled model for studying the etiology and treatment of osteoarthritis. Bone, 2020. 131: p. 115177.

45. Coward, W.R., G. Saini, and G. Jenkins, The pathogenesis of idiopathic pulmonary fibrosis. Ther Adv Respir Dis, 2010. 4(6): p. 367-88.

46. Waters, D.W., K.E.C. Blokland, P.S. Pathinayake, et al., Fibroblast senescence in the pathology of idiopathic pulmonary fibrosis. Am J Physiol Lung Cell Mol Physiol, 2018. 315(2): p. L162-l172.

47. Lin, Y. and Z. Xu, Fibroblast Senescence in Idiopathic Pulmonary Fibrosis. Front Cell Dev Biol, 2020. 8: p. 593283.

How to Cite

1.
Kim MK, Park S-L, Seo E jeong, Kim S-Y, Lee J-U, Park SW. Fibroblast proliferative capacity predicts prognosis in Idiopathic Pulmonary Fibrosis and identifies PITX1 as a growth-associated gene. Sarcoidosis Vasc Diffuse Lung Dis [Internet]. [cited 2026 Jun. 21];43(3):19046. Available from: https://www.mattioli1885journals.com/index.php/sarcoidosis/article/view/19046

Issue

Section

Original Articles: Clinical Research

How to Cite

1.
Kim MK, Park S-L, Seo E jeong, Kim S-Y, Lee J-U, Park SW. Fibroblast proliferative capacity predicts prognosis in Idiopathic Pulmonary Fibrosis and identifies PITX1 as a growth-associated gene. Sarcoidosis Vasc Diffuse Lung Dis [Internet]. [cited 2026 Jun. 21];43(3):19046. Available from: https://www.mattioli1885journals.com/index.php/sarcoidosis/article/view/19046