Decoding the neuro-immune mechanisms of achalasia

• Applicant: Flavio Dionisio, Ph.D.
• Subject Area: Immunology ; Bioinformatics and Theoretical Biology ; Virology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 578615260

Achalasia is a rare eosophageal motility disorder characterised by impaired relaxation of the lower oesophageal sphincter (LES) and absent or defective peristalsis in the oesophagus. This impaired motor function is caused by the loss of inhibitory myenteric neurons. As current clinical management options are traumatic and do not fully recover oesophageal motor function, the development of novel therapies is necessary for the treatment of achalasia. Preclinical studies have shown that neural stem cell transplantation in the gut can lead to their migration to the myenteric plexus and restore motor function. However, the causative factor(s) behind enteric neuronal loss are not fully understood. In the current proposal, I aim to identify the main pathophysiological mechanisms of achalasia to ultimately understand the cause of enteric neuronal loss in the LES. Identifying the molecular mechanisms involved in achalasia is crucial for both preventing further neuronal loss and improving the survival and function of transplanted neurons. Myenteric infiltrates show an accumulation of antigen-specific CD8+ T cells and macrophages in LES biopsies of achalasia patients. Although the trigger for this inflammatory reaction is not clearly defined, a viral infection is thought to be the cause. Both viral DNA and anti-viral antibodies have been found in LES biopsies of achalasia patients, but others failed to replicate these findings. In this project, I intend to use sequencing technologies to determine if a viral infection is indeed involved in the pathophysiology of achalasia, and to identify the potentially implicated viral agent(s). Briefly, I will use single nuclei(sn-) RNA- and ATAC-seq to profile LES biopsies from patients with different achalasia types and controls. Then I will use de novo and reference-based bioinformatic approaches to perform an in silico screening for viral transcripts in enteric neurons in the snRNA-seq dataset. If this method is not sensitive enough, I will employ a probe capture method for enrichment of viral RNA transcripts. Macrophages play a key role in viral clearance, neuro-supportive functions and, more importantly, antigen presenting functions to T cells. Hence, I also aim to characterise the crosstalk of macrophages, T cells and enteric neurons in achalasia. Here I will use the snRNA- and snATAC-seq datasets as a basis for performing imaging-based spatial transcriptomics (MERFISH). This will allow me to further describe both the cellular activation states and intercellular communications among these three cell types in achalasia. In conclusion, with this proposal, I will investigate the possibility of viral-mediated neuronal loss and then map the neuro-immune mechanisms of achalasia. This will advance our understanding of the pathophysiological mechanisms of achalasia, potentially paving the way for developing better clinical management options for this disabling disease.

• DFG Programme: Fellowship
• International Connection: Belgium
• Host: Professor Dr. Guy E. Boeckxstaens