Research On Immunological Characteristics Of Parkinson’s Disease Based On Single Cell Multi-omics Data

Parkinson’s disease(PD)is the second most common neurodegenerative disorder in the aging population after Alzheimer’s disease(AD).It is estimated that PD affects 1.7 percent of population over the age of 65 years.With the accelerating process of population aging,PD has become one of the most serious problems faced by geriatric medicine.The pathological hallmark of PD is the abnormal aggregation of alpha-synuclein(α-Syn)to form Lewy bodies,leading to the progressive death of dopaminergic neurons.At present,there is no cure for PD.Existing treatments aim to reduce the effects of the symptoms,but can not prevent the progression of the disease.Neuroinflammation,as an important factor associated with the progression of PD,has attracted much attention over the past 30 years.Uncovering the characteristics of adaptive immune response in PD not only helps to understand the occurrence and development of the disease,but also brings hope for the development of immunomodulatory drugs and immunotherapy strategies.In this study,we performed single-cell transcriptome and V(D)J sequencing,and conducted integrative analyses to decode composition,function and lineage relationship of T and B cells in the blood of PD to gain insight into the immunological characteristics of the adaptive immune response in PD.First,we constructed a cloud-based single-cell transcriptome data analysis platform SC2 Cloud to facilitate the analysis of single-cell sequencing data in this study.SC2 Cloud is compatible with widely used single-cell platforms such as 10 X Genomics,Drop-seq,Smart-seq,and Smart-seq2,and can analyze human and mouse single cell sequencing data.SC2 Cloud covers the main contents of single-cell transcriptome analysis,including quality control of raw sequencing data,mapping and constructing the expression matrix,cell quality control and expression data cleaning,confounding factors and batch effect removal,dimensionality reduction,unsupervised clustering,and pseudo-time analysis,which can meet the analysis needs of most users.In order to further reveal the heterogeneity of peripheral blood B cells and the characteristics of humoral immune response in PD patients,we conduct single-cell RNA and BCR sequencing to systematically characterize the cellular composition,immunoglobulin isotypes,preferential V and J gene segments and clonal expansion of peripheral B lymphocytes in PD patients.We observed significant increase of unswitched memory B cells and significant decrease of na?ve B cells in PD patients compared to healthy controls.We discovered increased IgG and IgA isotypes and more frequent class switch recombination events in PD patients compared to healthy controls.We also observed PD-related HLA genes HLA-DRB5,HLA-DQA2,HLADPB1 and BCR-induced activation of the AP-1 transcription factor up-regulated in PD patients,suggesting that B cells are activated and their antigen-presenting ability is enhanced in PD patients.Moreover,the preferential V and J gene fragments of B cell receptors in PD patients identified in this study also further provide the evidence of convergent selection in PD.In order to further reveal the heterogeneity of peripheral blood T cells and the characteristics of cellular immune response in PD patients,we performed single-cell transcriptome and TCR sequencing,and conducted integrative analyses to decode composition,function and lineage relationship of T cells in the blood of PD.Compared to healthy controls,the proportion of CD8+ T cells was significantly increased and the proportion of CD4+ T cells was significantly decreased in the blood of PD patients.We identified a distinct cluster of terminal effector CD8+ T cells significantly clonally expanded in PD patients,which derived from central memory CD8+ T cells by TCR-dependent activation and upregulated both cell adhesion,migration,survival and toxicity markers.Notably,we reported a group of cytotoxic CD4+ T cells(CD4 CTLs)significantly clonally expanded in PD patients,and TCR shared evidence confirmed that they originated from Th1 cells,and may be involved in central nervous system inflammation.To deeply reveal the molecular basis of "public T cell response" in PD patients,we systematically analyzed the diversity and antigen recognition specificity of T cell receptors in the blood and cerebrospinal fluid of PD patients using HLA typing and single-cell TCR sequencing.We observed that T cell diversity in the blood and cerebrospinal fluid of PD patients was significantly lower than that of healthy controls.Through TCR clustering and MHC-peptide prediction,we identified a series of PDspecific TCR groups and potential autoantigenic peptides.Two of the antigenic peptides "KTKEGVLYVGSKTKE" and "GKTKEGVLYVGSKTK" have been reported to drive helper and cytotoxic T cell responses in PD patients.In conclusion,this study systematically analyzed the characteristics of the adaptive immune response in peripheral blood of PD patients using single-cell sequencing technology,and revealed the molecular basis of public T cell responses in the blood and cerebrospinal fluid of PD patients.This study deepens the understanding of the adaptive immune response in Parkinson’s disease,provides a set of meaningful targets that may guide the development of effective immunotherapy strategies.