# Integrated bioinformatics-based identification of proliferative diabetic retinopathy and idiopathic pulmonary fibrosis: Focus on fibrosis and immune infiltration

**Authors:** Juanhui Cao, Fangyuan Dong, Xianfeng Li, Xuechun Zhu

PMC · DOI: 10.1371/journal.pone.0343398 · PLOS One · 2026-02-23

## TL;DR

This study explores shared fibrosis mechanisms in diabetic retinopathy and pulmonary fibrosis, identifying genes and potential drugs that could help treat both conditions.

## Contribution

The study identifies shared fibrosis-related genes and potential drug candidates for proliferative diabetic retinopathy and idiopathic pulmonary fibrosis.

## Key findings

- 90 fibrosis-related genes were identified through transcriptome analysis.
- Six hub genes and three drug molecules showed strong correlations and potential for diagnosis and treatment.
- Immune activation was found to play a key role in fibrosis progression.

## Abstract

Proliferative diabetic retinopathy (PDR) and idiopathic pulmonary fibrosis (IPF) share the common pathological feature of fibrosis, but the connecting mechanisms are not well – understood. This study aimed to identify potential shared genes and therapeutic drug candidates for fibrosis in both conditions by analyzing transcriptome datasets from the Gene Expression Omnibus (GEO). Differential expression analysis of two training datasets revealed 90 fibrosis – related genes. These genes were then analyzed for gene function enrichment, protein - protein interaction (PPI), transcription factor (TF) network, immune cell infiltration, and drug prediction. The findings underscored the role of immune activation in fibrosis progression. Among the 13 identified hub genes, however, six demonstrated strong correlations and high diagnostic potential upon further validation. The study also pinpointed six drug molecules with significant enrichment values, three of which showed promising results in blind docking simulations. These six genes and three drug molecules serve as potential targets for diagnosing and treating fibrosis in both PDR and IPF, though additional research is necessary to confirm their clinical utility.

## Linked entities

- **Diseases:** proliferative diabetic retinopathy (MONDO:0001660), idiopathic pulmonary fibrosis (MONDO:0800029)

## Full-text entities

- **Genes:** TAFAZZIN (tafazzin, phospholipid-lysophospholipid transacylase) [NCBI Gene 6901] {aka BTHS, CMD3A, EFE, EFE2, G4.5, LVNCX}, COL15A1 (collagen type XV alpha 1 chain) [NCBI Gene 1306], MIR29B1 (microRNA 29b-1) [NCBI Gene 407024] {aka MIRN29B1, miR-29b, miRNA29B1, mir-29b-1}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, FOXL1 (forkhead box L1) [NCBI Gene 2300] {aka FKH6, FKHL11, FREAC7, OTSC11}, ACVR1C (activin A receptor type 1C) [NCBI Gene 130399] {aka ACVRLK7, ALK7}, KDR (kinase insert domain receptor) [NCBI Gene 3791] {aka CD309, FLK1, VEGFR, VEGFR2}, STAT3 (signal transducer and activator of transcription 3) [NCBI Gene 6774] {aka ADMIO, ADMIO1, APRF, HIES}, COL5A2 (collagen type V alpha 2 chain) [NCBI Gene 1290] {aka EDSC, EDSCL2}, FBN1 (fibrillin 1) [NCBI Gene 2200] {aka ACMICD, ECTOL1, FBN, GPHYSD2, MASS, MFLS}, GATA3 (GATA binding protein 3) [NCBI Gene 2625] {aka HDR, HDRS}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, POSTN (periostin) [NCBI Gene 10631] {aka OSF-2, OSF2, PDLPOSTN, PN}, STAT1 (signal transducer and activator of transcription 1) [NCBI Gene 6772] {aka CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, COL1A2 (collagen type I alpha 2 chain) [NCBI Gene 1278] {aka EDSARTH2, EDSCV, OI4}, THBS2 (thrombospondin 2) [NCBI Gene 7058] {aka EDSCLL3, TSP2}, ACVR1B (activin A receptor type 1B) [NCBI Gene 91] {aka ACTRIB, ACVRLK4, ALK4, SKR2}, MIRLET7C (microRNA let-7c) [NCBI Gene 406885] {aka LET7C, MIRNLET7C, hsa-let-7c, let-7c}, FOXC1 (forkhead box C1) [NCBI Gene 2296] {aka ARA, ASGD3, FKHL7, FREAC-3, FREAC3, IGDA}, MIRLET7I (microRNA let-7i) [NCBI Gene 406891] {aka LET7I, MIRNLET7I, hsa-let-7i, let-7i}, MIRLET7E (microRNA let-7e) [NCBI Gene 406887] {aka LET7E, MIRNLET7E, hsa-let-7e, let-7e}, MIRLET7G (microRNA let-7g) [NCBI Gene 406890] {aka LET7G, MIRNLET7G, hsa-let-7g, let-7g}, COL3A1 (collagen type III alpha 1 chain) [NCBI Gene 1281] {aka EDS4A, EDSVASC, PMGEDSV}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, BGN (biglycan) [NCBI Gene 633] {aka DSPG1, MRLS, PG-S1, PGI, SEMDX, SLRR1A}, YY1AP1 (YY1 associated protein 1) [NCBI Gene 55249] {aka GRNG, HCCA1, HCCA2, YY1AP}, COL1A1 (collagen type I alpha 1 chain) [NCBI Gene 1277] {aka CAFYD, EDSARTH1, EDSC, OI1, OI2, OI3}, RHO (rhodopsin) [NCBI Gene 6010] {aka CSNBAD1, OPN2, RP4}, PDR [NCBI Gene 5171], IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, YY1 (YY1 transcription factor) [NCBI Gene 7528] {aka DELTA, GADEVS, INO80S, NF-E1, UCRBP, YIN-YANG-1}, COL5A1 (collagen type V alpha 1 chain) [NCBI Gene 1289] {aka EDSC, EDSCL1, FMDMF}, COL6A1 (collagen type VI alpha 1 chain) [NCBI Gene 1291] {aka BTHLM1, BTHLM1A, OPLL, UCHMD1, UCHMD1A}, F3 (coagulation factor III, tissue factor) [NCBI Gene 2152] {aka CD142, TF, TFA}, COL4A2 (collagen type IV alpha 2 chain) [NCBI Gene 1284] {aka BSVD2, BSVD2A, BSVD2B, ICH, POREN2}, TGFBR1 (transforming growth factor beta receptor 1) [NCBI Gene 7046] {aka AAT5, ACVRLK4, ALK-5, ALK5, ESS1, LDS1}, COL6A2 (collagen type VI alpha 2 chain) [NCBI Gene 1292] {aka BTHLM1, BTHLM1B, PP3610, UCMD1, UCMD1B}, MIRLET7B (microRNA let-7b) [NCBI Gene 406884] {aka LET7B, MIRNLET7B, hsa-let-7b, let-7b}, POU2F2 (POU class 2 homeobox 2) [NCBI Gene 5452] {aka OCT2, OTF2, Oct-2}
- **Diseases:** lung cancer (MESH:D008175), diabetes (MESH:D003920), cancer (MESH:D009369), oesophageal carcinoma (MESH:D000077277), fibrotic diseases (MESH:D004194), gastroesophageal reflux disease (MESH:D005764), osteosarcoma (MESH:D012516), inflammation (MESH:D007249), fibrosis (MESH:D005355), vision loss (MESH:D014786), fibrotic disorders (MESH:D009358), hypoxia (MESH:D000860), PDR (OMIM:603933), IPF (MESH:D054990), DR (MESH:D003930), amoebiasis (MESH:D000562), colon cancer (MESH:D015179), immune dysregulation (OMIM:614878), liver cancer (MESH:D006528), retinoblastoma (MESH:D012175), interstitial lung disease (MESH:D017563), pulmonary fibrosis (MESH:D011658)
- **Chemicals:** Panobinostat (MESH:D000077767), BRD-K24017250 (-), bruceantin (MESH:C002550), hydrogen (MESH:D006859), SB-431542 (MESH:C459179)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** G4112F

## Full text

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## Figures

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## References

66 references — full list in the complete paper: https://tomesphere.com/paper/PMC12928582/full.md

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Source: https://tomesphere.com/paper/PMC12928582