Highlights
– The largest GWAS of idiopathic achalasia (IA) to date (4,602 cases, 10,766 controls) identifies dominant class II HLA effects, including an HLA-DQB1 8–amino-acid insertion (PQGPPPAG) with OR 2.45 (p=3.27×10−68).
– Independent amino-acid signals at HLA-DQA1 (positions 41 and 130), HLA-DQB1 (position 45) and HLA-DRB1 (position 86) indicate complex HLA class II involvement.
– Non-HLA risk alleles include a functional PTPN22 amino-acid substitution, a regulatory variant reducing expression of TNFSF8/TNFSF15/TNC in immune cells, and a locus near ZNF365.
– Integration with single-cell RNA-sequencing of the myenteric plexus highlights a memory FOS+Tc4+CD8+ T-cell population as central to disease biology (p=2.50×10−19); polygenic risk scores (PRS) permit genetic stratification and IA shows partial genetic overlap with Crohn’s disease (rg=0.335).
Background and clinical significance
Idiopathic achalasia (IA) is a rare, chronic oesophageal motility disorder caused by progressive loss of inhibitory neurons in the myenteric (Auerbach) plexus, leading to failure of lower oesophageal sphincter relaxation and aperistalsis. Clinically, patients present with dysphagia, regurgitation, chest pain and weight loss. Treatments (pneumatic dilation, laparoscopic Heller myotomy, per‑oral endoscopic myotomy) address the mechanical obstruction but do not reverse neuronal loss. The underlying aetiology has long been debated; accumulating clinicopathological and immunopathological data have suggested immune-mediated neuronal injury in many patients, but direct genetic evidence has been lacking.
Identification of genetic risk factors provides multiple benefits: it can confirm immune mechanisms, nominate specific molecular pathways for functional study, enable patient stratification by genetic risk, and potentially identify targets for disease-modifying therapy. The study by Grover et al. (Gut, 2025) reports the first well-powered genome‑wide association study (GWAS) in IA and integrates genetic findings with single‑cell transcriptomic maps of the myenteric plexus to link loci to cell types.
Study design and methods
Grover and colleagues performed a GWAS in 4,602 European-ancestry patients with idiopathic achalasia and 10,766 ethnically matched controls. The primary analyses included single-marker association testing across the genome, detailed HLA imputation and amino-acid mapping in the HLA class II region, conditional analyses to resolve independent signals, and fine-mapping of non-HLA loci. They constructed polygenic risk scores (PRS) to assess genetic stratification, used cross-trait LD score regression to estimate genetic correlation with other immune-mediated conditions, and integrated GWAS summary statistics with single-cell RNA-sequencing (scRNA-seq) data from the human myenteric plexus to identify candidate effector cell types and pathways. Statistical thresholds adhered to standard genome-wide significance (p<5×10−8) and employed omnibus tests for amino-acid position associations.
Key methodological references that underpin the analytic approach include LD score regression to estimate genetic correlation and partition confounding (Bulik‑Sullivan et al., 2015) and emerging methods that integrate GWAS with cell-type transcriptomes to map disease biology to specific cell populations (Skene & Grant, 2016; Finucane et al., 2015).
Key findings
1. Dominant and complex HLA class II signal
The most striking result was a strong association within the HLA class II region. A single nucleotide polymorphism (SNP) in HLA-DQB1 that produces an 8–amino-acid insertion (PQGPPPAG) conveyed the largest effect (p=3.27×10−68; OR=2.45). Conditional analyses within the HLA locus revealed multiple independent amino-acid associations: HLA‑DQA1 positions 41 and 130, HLA‑DQB1 position 45, and HLA‑DRB1 position 86 (omnibus p<5×10−8 for each), indicating a structurally complex class II–mediated risk architecture rather than a single tag allele.
Interpretation: class II HLA molecules present peptides to CD4+ T cells and shape adaptive immune recognition. These results provide strong genetic evidence that antigen presentation and adaptive immunity are central to IA pathogenesis. The presence of multiple independent amino-acid signals implies that peptide-binding properties and T‑cell recognition are likely important determinants of susceptibility.
2. Non‑HLA loci with immune relevance
Outside the HLA, three independent genome‑wide significant loci were reported. One encodes an amino‑acid substitution in PTPN22, a well-established immune regulator associated with multiple autoimmune diseases (e.g., rheumatoid arthritis, type 1 diabetes). The PTPN22 variant points to altered TCR (T‑cell receptor) signalling thresholds as a plausible pathogenic mechanism in IA; PTPN22 R620W has been shown to modulate T-cell activation and tolerance (Begovich et al., 2004).
A second risk variant was associated with decreased expression of TNFSF8, TNFSF15 and TNC in immune cells. TNFSF15 (also known as TL1A) has prior links to gut inflammation and inflammatory bowel disease; reduced or altered expression of this TNF superfamily signalling axis could plausibly modify mucosal/neuronal immune responses in the oesophagus.
The third locus lies near ZNF365; while the precise cellular mechanism remains unresolved, ZNF365 has appeared in GWASs of inflammatory conditions and may influence immune cell function or genomic stability.
3. Polygenic risk, genetic correlation and cell‑type mapping
Polygenic risk score analyses indicated that IA patients can be stratified by genetic burden, suggesting potential utility for PRS in research and, ultimately, in clinical risk stratification when combined with other clinical and biomarker data. Cross‑trait LD score regression identified a moderate genetic correlation between IA and Crohn’s disease (rg=0.335), supporting shared immune pathways between IA and other gastrointestinal immune disorders.
By integrating GWAS signals with single-cell transcriptomes from the myenteric plexus, the study nominated a memory FOS+Tc4+CD8+ T‑cell population as central to IA (p=2.50×10−19). This is a critical translational bridge: it links genetic susceptibility to a specific effector cell type present in the affected tissue and suggests that CD8+ memory T cells — potentially cytotoxic or regulatory subsets expressing immediate-early genes such as FOS — may mediate neuronal injury.
Clinical and biological implications
Collectively, the results provide robust genetic confirmation that idiopathic achalasia is, at least in many patients, an immune‑mediated disease with a prominent role for class II antigen presentation and T‑cell biology. The HLA class II signals implicate peptide presentation and CD4+ T‑cell interactions in susceptibility, while the PTPN22 and TNFSF locus findings point to altered T‑cell signalling and TNF superfamily pathways.
For clinicians, these data help to reframe achalasia not only as a neuromuscular disorder but also as an immunological disease in which immunomodulatory interventions might, in principle, be explored. However, current management remains focused on symptomatic and mechanical relief of outflow obstruction. The identification of immune pathways raises the prospect of future trials of targeted immunotherapies, particularly for early-stage disease before irreversible neuronal loss occurs, but this remains speculative pending mechanistic and interventional study.
Expert commentary and limitations
Strengths of the study include its sample size (largest IA GWAS to date), rigorous HLA amino‑acid mapping, integration with tissue‑relevant single‑cell data, and use of complementary genomic methods (conditional analyses, PRS, cross‑trait correlations). These collectively strengthen causal inference that immune mechanisms drive IA susceptibility.
Limitations and caveats: the cohort was restricted to individuals of European ancestry, which may limit generalizability to other populations with different HLA allele frequencies; HLA structural complexity means mapping causal residues remains challenging and functional follow‑up is required. The study design is observational and cannot by itself establish temporal causality between immune activation and neuronal degeneration. The nominated gene targets (e.g., TNFSF15, PTPN22) require mechanistic validation in cellular and animal models, and the role of the identified CD8+ memory subset must be confirmed in independent tissues and by functional assays. Finally, although PRS can stratify risk in aggregate, predictive performance at the individual level will need improvement before clinical application.
Research priorities and translational roadmap
Immediate next steps should include: (1) functional studies to assess how the implicated HLA amino‑acid changes affect peptide binding and T‑cell responses to candidate oesophageal/neuronal antigens; (2) immunophenotyping of oesophageal tissue and peripheral blood in patients stratified by genotype to confirm involvement of the nominated CD8+ memory subset and to define antigen specificities; (3) longitudinal studies to determine whether immune activation precedes neuronal loss and whether genetic risk predicts rate of progression; (4) exploration of TNFSF and PTPN22 pathway modulation in preclinical models as a rationale for early-phase clinical trials.
Conclusion
The first large GWAS in idiopathic achalasia provides compelling genetic evidence for an immune‑mediated aetiopathology centered on HLA class II antigen presentation and T‑cell biology, with corroborating non‑HLA signals (PTPN22, TNFSF loci) and linkage to a specific memory CD8+ T‑cell subtype in the myenteric plexus. These findings reshape understanding of IA, prioritize mechanistic experiments, and open a route toward genetic risk stratification and immune‑targeted therapeutic hypotheses. Translation to clinical practice will require replication in diverse populations, functional validation, and carefully designed interventional studies focused on early disease stages.
Funding and clinicaltrials.gov
The GWAS was conducted with multi‑center academic collaboration; specific funding sources and acknowledgements are detailed in the original Gut publication (Grover et al., 2025). No clinicaltrials.gov identifiers are associated with the GWAS itself; any subsequent trials arising from these findings should be prospectively registered.
References
1. Grover S, Gockel I, Latiano A, et al. First genome-wide association study reveals immune-mediated aetiopathology in idiopathic achalasia. Gut. 2025 Oct 23:gutjnl-2024-334498. doi:10.1136/gutjnl-2024-334498. PMID: 41136183.
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3. Begovich AB, Carlton VE, Honigberg LA, et al. A missense single‑nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Nat Genet. 2004;36(4): 410–415. doi:10.1038/ng1332.
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5. Bulik‑Sullivan BK, Loh PR, Finucane HK, et al. LD Score regression distinguishes confounding from polygenicity in genome‑wide association studies. Nat Genet. 2015;47(3):291–295. doi:10.1038/ng.3211.
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7. Skene NG, Grant SG. Identification of vulnerable cell types in major brain disorders using single cell transcriptomes and expression weighted cell type enrichment. Nat Commun. 2016;7: 10924. doi:10.1038/ncomms10924.
Thumbnail prompt (AI‑ready)
High‑resolution image: cross‑sectional esophagus with highlighted myenteric plexus (warm highlight) overlaid by a translucent DNA double helix and stylized SNP markers; to the right, animated CD8+ T cells (labeled FOS+ memory) interacting with a neuronal cell; clinical-research aesthetic, cool blues and warm highlights, realistic but slightly stylized, 3000×2000px.