Integration of immune cell subtypes across diseases & tissue

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Abstract Single cell and single nucleus-based data have now been generated from many different tissues in the AMP projects as well as blood, CSF, synovial fluid and other biosamples. We have generated an atlas of microglial subtypes1 and are analyzing over 1.8 million transcriptomes from individual nuclei collected from the frontal cortex of 436 participants.2 We have a portfolio of additional single cell projects generating data from additional brain collections, peripheral blood mononuclear cells from healthy subjects and multiple sclerosis (MS) patients, as well as CSF cells from MS, other neuroinflammatory, and older individuals with and without Alzheimer. There are also data from other local and external efforts related to the Human Cell Atlas and related projects that can help to broaden the capture of immune cell states from a variety of tissue environments, context of comorbidities and diverse subjects. However, these resources have yet to be brought together to create a joint reference relating the different immune cell subtypes and cell states together in a single framework to accelerate the translation of insights across the AMP spectrum. Here, we integrate all of these and other emerging data to have a shared framework with which to interpret the cellular composition of immune responses involved in inflammatory, metabolic and neurologic diseases.