# A Network‐Based Association of IBD and Colorectal Cancer Using Proteomics Data

**Authors:** Jaiya Dhami, Swarnima Kollampallath Radhakrishnan, Dominic Russ, Sudip Mondal, Abdulrahman Alzarooni, Laura Bravo Merodio, Niharika A. Duggal, Ruchi Gupta, Animesh Acharjee

PMC · DOI: 10.1002/prca.70041 · Proteomics. Clinical Applications · 2026-02-17

## TL;DR

This study explores shared molecular mechanisms between inflammatory bowel disease and colorectal cancer using proteomics data to identify key proteins and pathways.

## Contribution

The study introduces a multi-omics network approach to uncover shared molecular links between IBD and CRC.

## Key findings

- Seven CRC-associated proteins were significantly upregulated in CRC, with six also elevated in IBD.
- AHCY and LCN2 were identified as central hubs linking inflammatory and metabolic pathways.
- NF-κB and GATA2 emerged as key transcriptional regulators confirmed in CRC tissues.

## Abstract

Colorectal cancer (CRC) is a major cause of morbidity and mortality, with chronic inflammation from inflammatory bowel disease (IBD) representing a well‐established risk factor. Clarifying shared molecular mechanisms may facilitate early detection and prevention strategies.

Proteomic data from the UK Biobank were analysed using the Olink proximity extension assay for seven CRC‐associated proteins (TFF3, TFF1, AHCY, RETN, LCN2, SELE and CEACAM5) previously identified via machine learning. Expression levels in CRC and IBD cases were compared with controls. Multilayer interaction networks, incorporating protein–protein, protein–metabolite and transcription factor–protein interactions, were generated using OmicsNet. Findings were validated in the Colonomics transcriptomic dataset.

All seven proteins were significantly upregulated in CRC; six (excluding CEACAM5) were also elevated in IBD. Network analysis identified AHCY and LCN2 as central hubs linking inflammatory and metabolic pathways. NF‐κB and GATA2 emerged as recurrent transcriptional regulators. Colonomics validation confirmed upregulation of AHCY, LCN2 and SELE in CRC tissues.

This multi‐omics network analysis reveals a shared molecular framework between IBD and CRC, with inflammation as a key driver of colorectal carcinogenesis.

## Linked entities

- **Proteins:** TFF3 (trefoil factor 3), TFF1 (trefoil factor 1), AHCY (adenosylhomocysteinase), RETN (resistin), LCN2 (lipocalin 2), SELE (selectin E), CEACAM5 (CEA cell adhesion molecule 5), NFKB1 (nuclear factor kappa B subunit 1), GATA2 (GATA binding protein 2)
- **Diseases:** inflammatory bowel disease (MONDO:0005265), colorectal cancer (MONDO:0005575)

## Full-text entities

- **Genes:** APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, LCN2 (lipocalin 2) [NCBI Gene 3934] {aka 24p3, MSFI, NGAL, p25}, TFF1 (trefoil factor 1) [NCBI Gene 7031] {aka BCEI, D21S21, HP1.A, HPS2, pNR-2, pS2}, REST (RE1 silencing transcription factor) [NCBI Gene 5978] {aka DFNA27, GINGF5, HGF5, NRSF, WT6, XBR}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, FOXF2 (forkhead box F2) [NCBI Gene 2295] {aka FKHL6, FREAC-2, FREAC2}, KRAS (KRAS proto-oncogene, GTPase) [NCBI Gene 3845] {aka 'C-K-RAS, C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A}, TWIST1 (twist family bHLH transcription factor 1) [NCBI Gene 7291] {aka ACS3, BPES2, BPES3, CRS, CRS1, CSO}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, GATA3 (GATA binding protein 3) [NCBI Gene 2625] {aka HDR, HDRS}, STAT3 (signal transducer and activator of transcription 3) [NCBI Gene 6774] {aka ADMIO, ADMIO1, APRF, HIES}, SGTA (small glutamine rich tetratricopeptide repeat co-chaperone alpha) [NCBI Gene 6449] {aka SGT, SGT1, Vpu, alphaSGT, hSGT}, RETN (resistin) [NCBI Gene 56729] {aka ADSF, FIZZ3, RENT, RETN1, RSTN, XCP1}, ATF2 (activating transcription factor 2) [NCBI Gene 1386] {aka CRE-BP1, CREB-2, CREB2, HB16, TREB7}, CEACAM5 (CEA cell adhesion molecule 5) [NCBI Gene 1048] {aka CD66e, CEA}, NLRP3 (NLR family pyrin domain containing 3) [NCBI Gene 114548] {aka AGTAVPRL, AII, AVP, C1orf7, CIAS1, CLR1.1}, TFF3 (trefoil factor 3) [NCBI Gene 7033] {aka ITF, P1B, TFI}, SP1 (Sp1 transcription factor) [NCBI Gene 6667], GATA2 (GATA binding protein 2) [NCBI Gene 2624] {aka DCML, IMD21, MONOMAC, NFE1B}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, UBQLN2 (ubiquilin 2) [NCBI Gene 29978] {aka ALS15, CHAP1, DSK2, HRIHFB2157, N4BP4, PLIC2}, BRAF (B-Raf proto-oncogene, serine/threonine kinase) [NCBI Gene 673] {aka B-RAF1, B-raf, BRAF-1, BRAF1, NS7, RAFB1}, UBQLN1 (ubiquilin 1) [NCBI Gene 29979] {aka DA41, DSK2, PLIC-1, UBQN, XDRP1}, GSDMD (gasdermin D) [NCBI Gene 79792] {aka DF5L, DFNA5L, FKSG10, GSDMDC1}, MIR31 (microRNA 31) [NCBI Gene 407035] {aka MIRN31, hsa-mir-31, miR-31}, AHCY (adenosylhomocysteinase) [NCBI Gene 191] {aka SAHH, adoHcyase}, ESR1 (estrogen receptor 1) [NCBI Gene 2099] {aka ER, ESR, ESRA, ESTRR, Era, NR3A1}, STAT1 (signal transducer and activator of transcription 1) [NCBI Gene 6772] {aka CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91}, SELE (selectin E) [NCBI Gene 6401] {aka CD62E, ELAM, ELAM1, ESEL, LECAM2, selectin-e}, RELA (RELA proto-oncogene, NF-kB subunit) [NCBI Gene 5970] {aka AIF3BL3, CMCU, NFKB3, p65}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}
- **Diseases:** gastrointestinal diseases (MESH:D005767), adenoma-carcinoma (MESH:D000230), colitis (MESH:D003092), stable (MESH:D060050), MSI tumours (MESH:D009369), Crohn's disease (MESH:D003424), cardiovascular disease (MESH:D002318), rectal bleeding (MESH:D012002), II MSS (MESH:D053842), FAP (MESH:D011125), abdominal pain (MESH:D015746), metastasis (MESH:D009362), Chronic inflammation (MESH:D007249), CRC (MESH:D015179), dysplasia (MESH:D015792), II (MESH:C537730), tumorigenic (MESH:D002471), death (MESH:D003643), preneoplastic (MESH:D011230), chronic (MESH:D002908), colon tumour (MESH:D003110), Lynch syndrome (MESH:D003123), CMS1-4 (MESH:D053632), ulcerative colitis (MESH:D003093), CMS (MESH:C536089), precancerous polyps (MESH:D011127), obesity (MESH:D009765), mucosal injury (MESH:D052016), IBD (MESH:D015212), type 2 diabetes (MESH:D003924), aggressive (MESH:D010554), oncogenic (MESH:D000074723), carcinogenesis (MESH:D063646), CIMP (MESH:D007516), adenomas (MESH:D000236)
- **Chemicals:** homocysteine (MESH:D006710), IntAct (-), adenosine (MESH:D000241), alcohol (MESH:D000438), S adenosylhomocysteine (MESH:D012435), aspirin (MESH:D001241), H2O (MESH:D014867), selenohomocysteine (MESH:C002979)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** V600E
- **Cell lines:** SW480 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0546), HCT116 — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_0291)

## Full text

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## Figures

11 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12914161/full.md

## References

74 references — full list in the complete paper: https://tomesphere.com/paper/PMC12914161/full.md

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Source: https://tomesphere.com/paper/PMC12914161