@article {97, title = {The GTEx Consortium atlas of genetic regulatory effects across human tissues.}, journal = {Science}, volume = {369}, year = {2020}, month = {2020 09 11}, pages = {1318-1330}, abstract = {

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the version 8 data, examining 15,201 RNA-sequencing samples from 49 tissues of 838 postmortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the underlying molecular mechanisms and their contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large diversity of tissues, we provide insights into the tissue specificity of genetic effects and show that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues.

}, keywords = {Datasets as Topic, Disease, Female, Gene Expression Regulation, Genome-Wide Association Study, Humans, Male, Organ Specificity, Quantitative Trait Loci, Sequence Analysis, RNA}, issn = {1095-9203}, doi = {10.1126/science.aaz1776} } @article {109, title = {RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares.}, journal = {N Engl J Med}, volume = {383}, year = {2020}, month = {2020 07 16}, pages = {218-228}, abstract = {

BACKGROUND: Rheumatoid arthritis, like many inflammatory diseases, is characterized by episodes of quiescence and exacerbation (flares). The molecular events leading to flares are unknown.

METHODS: We established a clinical and technical protocol for repeated home collection of blood in patients with rheumatoid arthritis to allow for longitudinal RNA sequencing (RNA-seq). Specimens were obtained from 364 time points during eight flares over a period of 4 years in our index patient, as well as from 235 time points during flares in three additional patients. We identified transcripts that were differentially expressed before flares and compared these with data from synovial single-cell RNA-seq. Flow cytometry and sorted-blood-cell RNA-seq in additional patients were used to validate the findings.

RESULTS: Consistent changes were observed in blood transcriptional profiles 1 to 2 weeks before a rheumatoid arthritis flare. B-cell activation was followed by expansion of circulating CD45-CD31-PDPN+ preinflammatory mesenchymal, or PRIME, cells in the blood from patients with rheumatoid arthritis; these cells shared features of inflammatory synovial fibroblasts. Levels of circulating PRIME cells decreased during flares in all 4 patients, and flow cytometry and sorted-cell RNA-seq confirmed the presence of PRIME cells in 19 additional patients with rheumatoid arthritis.

CONCLUSIONS: Longitudinal genomic analysis of rheumatoid arthritis flares revealed PRIME cells in the blood during the period before a flare and suggested a model in which these cells become activated by B cells in the weeks before a flare and subsequently migrate out of the blood into the synovium. (Funded by the National Institutes of Health and others.).

}, keywords = {Adult, Arthritis, Rheumatoid, B-Lymphocytes, Female, Fibroblasts, Flow Cytometry, Gene Expression, Humans, Male, Mesenchymal Stem Cells, Middle Aged, Patient Acuity, Sequence Analysis, RNA, Surveys and Questionnaires, Symptom Flare Up, Synovial Fluid}, issn = {1533-4406}, doi = {10.1056/NEJMoa2004114}, author = {Orange, Dana E and Yao, Vicky and Sawicka, Kirsty and Fak, John and Frank, Mayu O and Parveen, Salina and Blach{\`e}re, Nathalie E and Hale, Caryn and Zhang, Fan and Raychaudhuri, Soumya and Troyanskaya, Olga G and Darnell, Robert B} } @article {26, title = {Simultaneous epitope and transcriptome measurement in single cells.}, journal = {Nat Methods}, volume = {14}, year = {2017}, month = {2017 Sep}, pages = {865-868}, abstract = {

High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout. CITE-seq is compatible with existing single-cell sequencing approaches and scales readily with throughput increases.

}, keywords = {Epitope Mapping, Epitopes, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA, Tissue Array Analysis, Transcriptome}, issn = {1548-7105}, doi = {10.1038/nmeth.4380}, author = {Stoeckius, Marlon and Hafemeister, Christoph and Stephenson, William and Houck-Loomis, Brian and Chattopadhyay, Pratip K and Swerdlow, Harold and Satija, Rahul and Smibert, Peter} }