# Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS–chemokine–myeloid axis

**Authors:** Bruno Beernaert, Rose L. Jady-Clark, Parin Shah, Erik Ramon-Gil, Nora M. Lawson, Zack D. Brodtman, Somnath Tagore, Frederik Stihler, Alfie S. Carter, Shannique Clarke, Tong Liu, Winston M. Zhu, Juliet E. Martin, Erkin Erdal, Alistair Easton, Leticia Campo, Molly Browne, Stephen Ash, Rabial Q. Raja, Nicola Waddell, Tom Crosby, Simon R. Lord, Derek A. Mann, Ignacio Melero, Carlos E. de Andrea, Andréa E. Tijhuis, Floris Foijer, Ester M. Hammond, Kadir C. Akdemir, Jack Leslie, Benjamin Izar, Eileen E. Parkes

PMC · DOI: 10.1126/sciadv.aeb1611 · 2026-03-11

## TL;DR

Chromosomal instability in esophageal cancer promotes tumor growth by triggering inflammation through a specific immune pathway.

## Contribution

The study reveals a novel CIN-driven cGAS–chemokine–myeloid axis that promotes immunosuppression in esophageal adenocarcinoma.

## Key findings

- CIN drives expression of myeloid-attracting chemokines like CXCL8 in EAC.
- High CIN correlates with poor patient outcomes and disrupted cGAS–STING signaling.
- CIN activates innate immune responses that lead to tumor-promoting inflammation.

## Abstract

Chromosomal instability (CIN), a pervasive feature of esophageal adenocarcinoma (EAC), drives tumor aggressiveness and metastasis. CIN stimulates the cGAS–STING pathway, typically linked to antitumor immunity. However, despite the high CIN burden in EAC, the cGAS–STING pathway remains largely intact. To address this paradox, we interrogated multiple esophageal cancer models, finding myeloid-attracting chemokines—with CXCL8 as a prominent hit—as conserved CIN-driven targets in EAC. Using multiplexed immunofluorescence microscopy, we quantified ongoing CIN in human EAC tumors by measuring cGAS-positive micronuclei, validated by whole-genome sequencing. Coupling in situ CIN detection with single-nucleus RNA sequencing and multiplex immunophenotyping of human EAC, we link CIN to tumor-intrinsic innate immune activation, CXCL8 expression, and myeloid cell–mediated immunosuppression. In patients with EAC, CINhigh, myeloid-dominated tumors correlate with poor outcomes and aberrant cGAS–STING signaling. These insights explain the counterintuitive maintenance of cGAS–STING and highlight the disruption of the CIN–cGAS–inflammation axis as a potential therapeutic strategy in EAC.

Chromosomal chaos rewires immune defense into tumor-promoting inflammation.

## Linked entities

- **Genes:** CGAS (cyclic GMP-AMP synthase) [NCBI Gene 115004], STING1 (stimulator of interferon response cGAMP interactor 1) [NCBI Gene 340061], CXCL8 (C-X-C motif chemokine ligand 8) [NCBI Gene 3576]
- **Diseases:** esophageal adenocarcinoma (MONDO:0005028)

## Full-text entities

- **Genes:** MAP1LC3A (microtubule associated protein 1 light chain 3 alpha) [NCBI Gene 84557] {aka ATG8E, LC3, LC3A, MAP1ALC3, MAP1BLC3}, CCL5 (C-C motif chemokine ligand 5) [NCBI Gene 6352] {aka D17S136E, RANTES, SCYA5, SIS-delta, SISd, TCP228}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, STAT1 (signal transducer and activator of transcription 1) [NCBI Gene 6772] {aka CANDF7, IMD31A, IMD31B, IMD31C, ISGF-3, STAT91}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, STING1 (stimulator of interferon response cGAMP interactor 1) [NCBI Gene 340061] {aka ERIS, MITA, MPYS, NET23, SAVI, STING}, CCL3 (C-C motif chemokine ligand 3) [NCBI Gene 6348] {aka G0S19-1, LD78, LD78ALPHA, MIP-1-alpha, MIP1A, SCI}, PPBP (pro-platelet basic protein) [NCBI Gene 5473] {aka B-TG1, Beta-TG, CTAP-III, CTAP3, CTAPIII, CXCL7}, IDO1 (indoleamine 2,3-dioxygenase 1) [NCBI Gene 3620] {aka IDO, IDO-1, INDO}, BLNK (B cell linker) [NCBI Gene 29760] {aka AGM4, BASH, BLNK-S, LY57, SLP-65, SLP65}, OAS3 (2'-5'-oligoadenylate synthetase 3) [NCBI Gene 4940] {aka p100, p100OAS}, CD68 (CD68 molecule) [NCBI Gene 968] {aka GP110, LAMP4, SCARD1}, IRF1 (interferon regulatory factor 1) [NCBI Gene 3659] {aka IMD117, IRF-1, MAR}, IFNA8 (interferon alpha 8) [NCBI Gene 3445] {aka IFN-alphaB}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, CXCL8 (C-X-C motif chemokine ligand 8) [NCBI Gene 3576] {aka GCP-1, GCP1, IL8, LECT, LUCT, LYNAP}, CD163 (CD163 molecule) [NCBI Gene 9332] {aka M130, MM130, SCARI1}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, ZFAND2A (zinc finger AN1-type containing 2A) [NCBI Gene 90637] {aka AIRAP}, CXCR2 (C-X-C motif chemokine receptor 2) [NCBI Gene 3579] {aka CD182, CDw128b, CMKAR2, IL8R2, IL8RA, IL8RB}, CCL2 (C-C motif chemokine ligand 2) [NCBI Gene 6347] {aka GDCF-2, HC11, HSMCR30, MCAF, MCP-1, MCP1}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, CXCL1 (C-X-C motif chemokine ligand 1) [NCBI Gene 2919] {aka FSP, GRO1, GROa, MGSA, MGSA-a, NAP-3}, RIGI (RNA sensor RIG-I) [NCBI Gene 23586] {aka DDX58, RIG-I, RIG1, RLR-1, SGMRT2}, IFIH1 (interferon induced with helicase C domain 1) [NCBI Gene 64135] {aka AGS7, Hlcd, IDDM19, IMD95, MDA-5, MDA5}, CSF3 (colony stimulating factor 3) [NCBI Gene 1440] {aka C17orf33, CSF3OS, GCSF}, CXCL3 (C-X-C motif chemokine ligand 3) [NCBI Gene 2921] {aka CINC-2b, GRO3, GROg, MIP-2b, MIP2B, SCYB3}, CBLIF (cobalamin binding intrinsic factor) [NCBI Gene 2694] {aka GIF, IF, IFMH, INF, TCN3}, PF4 (platelet factor 4) [NCBI Gene 5196] {aka CXCL4, PF-4, SCYB4}, IFIT2 (interferon induced protein with tetratricopeptide repeats 2) [NCBI Gene 3433] {aka G10P2, GARG-39, IFI-54, IFI-54K, IFI54, IFIT-2}, MYC (MYC proto-oncogene, bHLH transcription factor) [NCBI Gene 4609] {aka MRTL, MYCC, bHLHe39, c-Myc}, IFNA1 (interferon alpha 1) [NCBI Gene 3439] {aka IFL, IFN, IFN-ALPHA, IFN-alphaD, IFNA13, IFNA@}, CHAC1 (ChaC glutathione specific gamma-glutamylcyclotransferase 1) [NCBI Gene 79094], CXCL2 (C-X-C motif chemokine ligand 2) [NCBI Gene 2920] {aka CINC-2a, GRO2, GROb, MGSA-b, MIP-2a, MIP2}, TRIM16 (tripartite motif containing 16) [NCBI Gene 10626] {aka EBBP}, CCL4 (C-C motif chemokine ligand 4) [NCBI Gene 6351] {aka ACT2, AT744.1, G-26, HC21, LAG-1, LAG1}, CXCL6 (C-X-C motif chemokine ligand 6) [NCBI Gene 6372] {aka CKA-3, GCP-2, GCP2, SCYB6}, HIF1A (hypoxia inducible factor 1 subunit alpha) [NCBI Gene 3091] {aka HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, EIF2AK2 (eukaryotic translation initiation factor 2 alpha kinase 2) [NCBI Gene 5610] {aka PKR, PPP1R83, PRKR}, FUT4 (fucosyltransferase 4) [NCBI Gene 2526] {aka CD15, ELFT, FCT3A, FUC-TIV, FUTIV, LeX}, CCL7 (C-C motif chemokine ligand 7) [NCBI Gene 6354] {aka FIC, MARC, MCP-3, MCP3, NC28, SCYA6}, CD274 (CD274 molecule) [NCBI Gene 29126] {aka ADMIO5, B7-H, B7H1, PD-L1, PDCD1L1, PDCD1LG1}, ITGAX (integrin subunit alpha X) [NCBI Gene 3687] {aka CD11C, SLEB6}, ITGAM (integrin subunit alpha M) [NCBI Gene 3684] {aka CD11B, CR3A, HNA-4, MAC-1, MAC1A, MO1A}, CD47 (CD47 molecule) [NCBI Gene 961] {aka IAP, MER6, OA3}, ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1) [NCBI Gene 5167] {aka ARHR2, COLED, M6S1, NPP1, NPPS, PC-1}, CSF1 (colony stimulating factor 1) [NCBI Gene 1435] {aka CSF-1, MCSF, PG-M-CSF}, CGAS (cyclic GMP-AMP synthase) [NCBI Gene 115004] {aka C6orf150, D4, MB21D1, h-cGAS}, CXCL5 (C-X-C motif chemokine ligand 5) [NCBI Gene 6374] {aka ENA-78, SCYB5}, MPO (myeloperoxidase) [NCBI Gene 4353], CD14 (CD14 molecule) [NCBI Gene 929], CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, MRC1 (mannose receptor C-type 1) [NCBI Gene 4360] {aka CD206, CLEC13D, CLEC13DL, MMR, MRC1L1, bA541I19.1}, USP18 (ubiquitin specific peptidase 18) [NCBI Gene 11274] {aka ISG43, PTORCH2, UBP43}, MAP1LC3B (microtubule associated protein 1 light chain 3 beta) [NCBI Gene 81631] {aka ATG8F, LC3B, MAP1A/1BLC3, MAP1LC3B-a}, TTK (TTK protein kinase) [NCBI Gene 7272] {aka CT96, ESK, MPH1, MPS1, MPS1L1, PYT}, TF (transferrin) [NCBI Gene 7018] {aka HEL-S-71p, PRO1557, PRO2086, TFQTL1}, ALB (albumin) [NCBI Gene 280717]
- **Diseases:** MN (MESH:D048629), dysplastic (MESH:D004416), stomach adenocarcinoma (MESH:D013274), esophageal squamous cell carcinoma (MESH:D000077277), EAC (MESH:D000230), Tumors (MESH:D009369), TRUE (MESH:C565693), BE (MESH:D001471), prostate cancer (MESH:D011471), Inflammatory (MESH:D007249), sepsis (MESH:D018805), aneuploid tumor (MESH:D000782), necrotic (MESH:D009336), CIN (MESH:D043171), EAC tumor (MESH:D004938), hepatocellular cancer (MESH:D006528), breast cancer (MESH:D001943), neutropenia (MESH:D009503), metastasis (MESH:D009362), SCT (MESH:C535780)
- **Chemicals:** reparixin (MESH:C490707), ethanol (MESH:D000431), adenine (MESH:D000225), SDS (MESH:D012967), CaCl2 (MESH:D002122), water (MESH:D014867), polyacrylamide (MESH:C016679), MCDB-153 (MESH:C112696), streptomycin (MESH:D013307), Triton X-100 (MESH:D017830), agar (MESH:D000362), hydrocortisone (MESH:D006854), xylene (MESH:D014992), salt (MESH:D012492), diethyl pyrocarbonate (MESH:D004047), WST-8 (MESH:C476329), NaCl (MESH:D012965), adenosine (MESH:D000241), paraffin (MESH:D010232), MgCl2 (MESH:D015636), 4',6-diamidino-2-phenylindole (MESH:C007293), DMSO (MESH:D004121), Nutlin-3 (MESH:C482205), Tween (MESH:D011136), paraformaldehyde (MESH:C003043), polybrene (MESH:D006583), l-glutamine (MESH:D005973), bicinchoninic acid (MESH:C047117), reversine (MESH:C484369), CO2 (MESH:D002245), ampicillin (MESH:D000667), Alexa Fluor 488 (MESH:C000711379), selenium (MESH:D012643), oil (MESH:D009821), 2-mercaptoethanol (MESH:D008623), Lipofectamine 2000 (MESH:C086724), cGAMP (MESH:C584311), puromycin (MESH:D011691), penicillin (MESH:D010406), NA (MESH:D012964), phenol red (MESH:D010637), Hoechst (-), hydrogen peroxide (MESH:D006861)
- **Species:** Mycoplasma (genus) [taxon 2093], Mus musculus (house mouse, species) [taxon 10090], Escherichia coli (E. coli, species) [taxon 562], Bos taurus (bovine, species) [taxon 9913], Homo sapiens (human, species) [taxon 9606]
- **Cell lines:** OACM5.1C — Homo sapiens (Human), Esophageal adenocarcinoma, Cancer cell line (CVCL_1842), BE — Homo sapiens (Human), Barrett adenocarcinoma, Cancer cell line (CVCL_JY35), ESO-51 — Homo sapiens (Human), Esophageal adenocarcinoma, Cancer cell line (CVCL_2036), ESO-26 — Homo sapiens (Human), Gastroesophageal junction adenocarcinoma, Cancer cell line (CVCL_2035), HEK) 293T — Homo sapiens (Human), Transformed cell line (CVCL_0063), hTERT — Homo sapiens (Human), Telomerase immortalized cell line (CVCL_EE25), OE33 — Homo sapiens (Human), Barrett adenocarcinoma, Cancer cell line (CVCL_0471), CP-C — Homo sapiens (Human), Barrett esophagus, Telomerase immortalized cell line (CVCL_C453), SK-GT-4 — Homo sapiens (Human), Esophageal adenocarcinoma, Cancer cell line (CVCL_2195), Cas9 — Homo sapiens (Human), Transformed cell line (CVCL_UR28), EAC — Homo sapiens (Human), Barrett adenocarcinoma, Cancer cell line (CVCL_8098), OE19 — Homo sapiens (Human), Esophageal adenocarcinoma, Cancer cell line (CVCL_1622), CP-A — Anabas testudineus (Climbing perch), Spontaneously immortalized cell line (CVCL_6F78), RPE-1 — Homo sapiens (Human), Telomerase immortalized cell line (CVCL_4388), FLO-1 — Homo sapiens (Human), Barrett adenocarcinoma, Cancer cell line (CVCL_2045), KYAE-1 — Homo sapiens (Human), Esophageal adenocarcinoma, Cancer cell line (CVCL_1825)

## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12978254/full.md

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Source: https://tomesphere.com/paper/PMC12978254