Flow Cytometry of Immune Cells From Human Pancreas Lymphatic, Mesentery Lymphatic, and Splenic Tissues in the Context of Type 1 Diabetes

Summary:
Type 1 diabetes (T1D) is caused by the autoimmune destruction of insulin-producing pancreatic beta cells, leading to life-long dependence on exogenous insulin. Profiling immune cells that infiltrate islets would be invaluable to understanding how beta cell destruction occurs. However, human pancreatic samples demonstrating active infiltration and beta cell destruction are rare. Alternatively, peri-pancreatic lymph nodes (pLNs) or other secondary lymphoid organs may harbor immune cells which participate in memory responses that drive T1D autoimmunity. To study the immune response throughout T1D onset and disease, lymphocytes from pLNs, mesenteric lymph nodes (mesLNs), the spleen, and from blood were collected from human T1D, auto-antibody positive (AAb+), and normal donors (NDs) enrolled in the Human Pancreas Analysis Program (HPAP). Tissue immune cell identity and phenotype was analyzed using a high parameter flow cytometry panel. Please see a pre-print containing figures generated from this analyzed data at https://www.biorxiv.org/content/10.1101/2024.04.23.590798v2 as well as in a forthcoming peer-reviewed publication. Code associated with generation of these figures can be found at https://github.com/betts-lab/hpap-tissue-citeseq.

Overall design:
All samples are human secondary lymphoid tissue mononuclear cells and blood leukocytes/peripheral blood mononuclear cells acquired through the Human Pancreas Analysis Program (HPAP). The samples are derived fresh mononuclear cells purified from either pancreatic lymph nodes (pLN), mesenteric lymph nodes (mesLNs), the spleen, or blood. Additionally, there are samples derived from lymphocytes that egressed out of ex vivo cultured pancreas islets (“Islet Sup”) that were not included in the analysis contained in the pre-print (see link above) and subsequent peer-reviewed publication. Samples from 18 non-diabetic autoantibody negative (ND), 10 non-diabetic auto-antibody positive (AAb+), and 18 type 1 diabetic (T1D) donors are included in the dataset. 

Contents:

FCS_files.zip - a ZIP file containing all FCS flow cytometry files used to analyze immune perturbations in human pancreas lymphatic tissue before and after Type 1 Diabetes. There are additional FCS files of peripheral blood mononuclear cells, whole blood leukocytes, and lymphocytes that egressed out of ex vivo cultured pancreas islets (“Islet Sup”) that were not included in the analysis contained in the pre-print (see link above) and subsequent peer-reviewed publication.

Lineage_MasterV3.csv - a CSV file containing cell population frequencies for gates drawn on the FCS files in this submission. This data was used to generate flow cytometry figures in the pre-print (see link above) and subsequent peer-reviewed publication. This file also contains some limited donor metadata.

Metadata.zip - a ZIP file containing two files. The first, donor_metadata.zip, is a detailed clinical data metadata sheet for all donors in the database. The second, HLAgrs.csv, contains Type 1 Diabetes risk scores calculated using the HLA component of the Type 1 Diabetes polygenic risk score, GRS2. These data were used to generate some of the flow cytometry figures in the pre-print (see link above) and subsequent peer-reviewed publication.