Notably, we observed that the communication probabilities of NRXN3–NLGN1, NEGR1–NEGR1 and CNTN1–NRCAM interactions were more significant (p-value < 0.01) between these three cells (D2-MSN, ENDO_Rbfox1High and AST_Meg3High) (Figure S10C), suggesting that MPTP induced huge cell communication network changes between these three PD-risk clusters by increasing NRXN3–NLGN1, NRXN1–NLGN1 and NEGR1–NEGR1 expression and enhancing the NRXN and NEGR signaling pathways. Here, NRXN3 is linked to Parkinson disease.