# Spatial single-cell multiomics reveals peripheral immune dysfunction in Parkinson’s and inflammatory bowel disease

**Authors:** MacKenzie L. Bolen, Marc Buendia, Ji Shi, Hannah Staley, Jennifer M. Kachergus, Philip A. Efron, Gwoncheol Park, Ravinder Nagpal, Stephan D. Alvarez, Qing-Shan Xue, Nikolaus R. McFarland, Ellen M. Zimmermann, Christopher E. Forsmark, Kelly B. Menees, Azucena Salas, E. Aubrey Thompson, Malú Gámez Tansey

PMC · DOI: 10.1038/s41531-025-01199-2 · NPJ Parkinson's Disease · 2026-01-16

## TL;DR

This study uses advanced imaging to show gut inflammation linked to Parkinson’s and IBD, suggesting immune dysfunction starts in the gut.

## Contribution

The study introduces spatial single-cell multiomics to reveal immune dysfunction in peripheral tissues in Parkinson’s and IBD.

## Key findings

- Inflammatory injury in gut epithelial cells is linked to iron mishandling in both PD and IBD.
- Parallel RNA and protein dysregulation in gut epithelium is observed in PD and IBD samples.
- CCL22 protein depletion in plasma (PD) and stool (IBD) suggests systemic immune dysfunction.

## Abstract

Parkinson’s disease (PD) is the fastest-growing neurodegenerative disease in the world1. Gastrointestinal (GI) dysfunction can occur decades before motor impairments and in up to 80% of individuals living with PD2–4. We investigated peripheral relationships that may underlie mechanisms along the gut–blood axis that contribute to PD progression. Single-cell multiomic spatial molecular imaging (SMI) of colonic tissue localized and identified inflammatory injury within epithelial cells that appear to be associated with iron mishandling in both inflammatory bowel disease (IBD) and PD biosamples. We found that both the single-cell SMI of RNA and protein revealed parallel cross-modal dysregulation in the gut epithelium, in both IBD and PD biosamples. These data are accompanied by plasma (PD) and stool (IBD) protein depletion of CCL22. Our findings suggest iron mishandling along the gut barrier likely contributes to systemic inflammation, which may be one catalyst that primes circulating immune cells to body-first PD progression.

## Linked entities

- **Proteins:** CCL22 (C-C motif chemokine ligand 22)
- **Chemicals:** iron (PubChem CID 23925)
- **Diseases:** Parkinson’s disease (MONDO:0005180), inflammatory bowel disease (MONDO:0005265)

## Full-text entities

- **Genes:** NDUFB1 (NADH:ubiquinone oxidoreductase subunit B1) [NCBI Gene 4707] {aka CI-MNLL, CI-SGDH, MNLL}, CCL22 (C-C motif chemokine ligand 22) [NCBI Gene 6367] {aka A-152E5.1, ABCD-1, DC/B-CK, MDC, SCYA22, STCP-1}, CTLA4 (cytotoxic T-lymphocyte associated protein 4) [NCBI Gene 1493] {aka ALPS5, CD, CD152, CELIAC3, CTLA-4, GRD4}, SNCA (synuclein alpha) [NCBI Gene 6622] {aka NACP, PARK1, PARK4, PD1}, IL1B (interleukin 1 beta) [NCBI Gene 3553] {aka IL-1, IL1-BETA, IL1F2, IL1beta}, ITPKB (inositol-trisphosphate 3-kinase B) [NCBI Gene 3707] {aka IP3-3KB, IP3K, IP3K-B, IP3KB, PIG37}, HAVCR2 (hepatitis A virus cellular receptor 2) [NCBI Gene 84868] {aka CD366, HAVcr-2, KIM-3, SPTCL, TIM3, TIMD-3}, RAB8A (RAB8A, member RAS oncogene family) [NCBI Gene 4218] {aka MEL, RAB8}, GZMA (granzyme A) [NCBI Gene 3001] {aka CTLA3, HFSP}, CCL20 (C-C motif chemokine ligand 20) [NCBI Gene 6364] {aka CKb4, Exodus, LARC, MIP-3-alpha, MIP-3a, MIP3A}, CCL11 (C-C motif chemokine ligand 11) [NCBI Gene 6356] {aka SCYA11}, HAMP (hepcidin antimicrobial peptide) [NCBI Gene 57817] {aka HEPC, HFE2B, LEAP1, PLTR}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, LAG3 (lymphocyte activating 3) [NCBI Gene 3902] {aka CD223}, IL6 (interleukin 6) [NCBI Gene 3569] {aka BSF-2, BSF2, CDF, HGF, HSF, IFN-beta-2}, TF (transferrin) [NCBI Gene 7018] {aka HEL-S-71p, PRO1557, PRO2086, TFQTL1}, LOC102723407 (immunoglobulin heavy variable 4-38-2-like) [NCBI Gene 102723407] {aka IGHV4, IGHV4-30, IGHV4-38-2, IGHV4-39, IGHV4-b, IGVH4-39}, CCL26 (C-C motif chemokine ligand 26) [NCBI Gene 10344] {aka IMAC, MIP-4a, MIP-4alpha, SCYA26, TSC-1}, SLC40A1 (solute carrier family 40 member 1) [NCBI Gene 30061] {aka FPN, FPN1, HFE4, IREG1, MST079, MSTP079}, CRIP1 (cysteine rich protein 1) [NCBI Gene 1396] {aka CRHP, CRIP, CRP-1, CRP1}, SLC6A4 (solute carrier family 6 member 4) [NCBI Gene 6532] {aka 5-HTT, 5-HTTLPR, 5HTT, HTT, OCD1, SERT}, TIMP1 (TIMP metallopeptidase inhibitor 1) [NCBI Gene 7076] {aka CLGI, EPA, EPO, HCI, TIMP, TIMP-1}, IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, FOS (Fos proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 2353] {aka AP-1, C-FOS, p55}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, PINK1 (PTEN induced kinase 1) [NCBI Gene 65018] {aka BRPK, PARK6}, PYY (peptide YY) [NCBI Gene 5697] {aka PYY-I, PYY1}, Ccl22 (C-C motif chemokine ligand 22) [NCBI Gene 20299] {aka ABCD-1, DCBCK, MDC, Scya22}, MT2A (metallothionein 2A) [NCBI Gene 4502] {aka MT-2, MT-II, MT2}, CLDN4 (claudin 4) [NCBI Gene 1364] {aka CPE-R, CPER, CPETR, CPETR1, WBSCR8, hCPE-R}, LGALS3 (galectin 3) [NCBI Gene 3958] {aka CBP35, GAL3, GALBP, GALIG, L31, LGALS2}, CHGA (chromogranin A) [NCBI Gene 1113] {aka CGA, PHE5, PHES}, F3 (coagulation factor III, tissue factor) [NCBI Gene 2152] {aka CD142, TF, TFA}, SLC11A2 (solute carrier family 11 member 2) [NCBI Gene 4891] {aka AHMIO1, DCT1, DMT1, NRAMP2}, CXCL8 (C-X-C motif chemokine ligand 8) [NCBI Gene 3576] {aka GCP-1, GCP1, IL8, LECT, LUCT, LYNAP}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, IREB2 (iron responsive element binding protein 2) [NCBI Gene 3658] {aka ACO3, IRE-BP 2, IRE-BP2, IRP2, IRP2AD, NDCAMA}, FTH1 (ferritin heavy chain 1) [NCBI Gene 2495] {aka FHC, FTH, FTHL6, HFE5, NBIA9, PIG15}, TNFRSF18 (TNF receptor superfamily member 18) [NCBI Gene 8784] {aka AITR, CD357, ENERGEN, GITR, GITR-D}, CD68 (CD68 molecule) [NCBI Gene 968] {aka GP110, LAMP4, SCARD1}
- **Diseases:** endocrine dysfunction (MESH:D004700), neurodegenerative disease (MESH:D019636), systemic (MESH:D015619), immune dysregulation (OMIM:614878), gut) (MESH:C536735), inflamed (MESH:C531841), autonomic dysfunction (MESH:D001342), colitis (MESH:D003092), Crohn's disease (MESH:D003424), Iron dysregulation (MESH:D000090463), infection (MESH:D007239), TMA (MESH:D017695), iron overload (MESH:D019190), autoimmune dysfunction (MESH:D001327), IBD (MESH:D015212), Neurological Diseases (MESH:D020271), cytotoxic (MESH:D064420), age-related disease (MESH:D010024), cancer (MESH:D009369), movement disorder (MESH:D009069), anosmia (MESH:D000857), ulcerative colitis (MESH:D003093), motor (MESH:D000068079), sleep (MESH:D012893), Gut dysfunction (MESH:C535334), immune (MESH:D007154), constipation (MESH:D003248), Chronic (MESH:D002908), GI dysfunction (MESH:D005767), Inflammatory (MESH:D007249), NHC (MESH:D000067329), PD (MESH:D010300), necrotic (MESH:D009336)
- **Chemicals:** DAPI (MESH:C007293), lipid (MESH:D008055), formalin (MESH:D005557), SCFA (MESH:D005232), iron (MESH:D007501), metal (MESH:D008670), CosMx (-), carbohydrates (MESH:D002241), oxygen (MESH:D010100), paraffin (MESH:D010232)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], gut metagenome (species) [taxon 749906], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** K15067M

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12847817/full.md

## References

3 references — full list in the complete paper: https://tomesphere.com/paper/PMC12847817/full.md

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Source: https://tomesphere.com/paper/PMC12847817