Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients.

Transcription factor programs mediating the immune response to coronavirus disease 2019 (COVID-19) are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped small RNA sequencing (csRNA-seq), in contrast to capturing steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factor activity and regulatory pathways. Here, we profile transcription initiation in critically ill COVID-19 patients, identifying transcription factor motifs that correlate with clinical lung injury and disease severity. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the cell type, pathway-specific, and combinatorial transcription factor activity. We find evidence of critical roles of regulatory networks, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with COVID-19 susceptibility genetic variants. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.

Survey Outcomes of Lipedema Reduction Surgery in the United States.

BACKGROUND: Lipedema is a loose connective tissue disease affecting the limbs of women, that is difficult to lose by diet, exercise, or bariatric surgery. Publications from Europe demonstrate that lipedema reduction surgery improves quality of life for women with lipedema. There are no comparable studies in the United States (USA). The aim of this study was to collect data from women with lipedema in the USA who have undergone lipedema reduction surgery in the USA to determine if quality of life, pain, and other measures improved after lipedema reduction surgery. METHODS: Subjects were recruited and consented online for a 166-item questionnaire in REDCap. In total, 148 women answered the questionnaire after undergoing lipedema reduction surgery in the USA. Significance set at P < 0.05 was determined by ANOVA, Tukey's multiple comparison test, or paired t-test. RESULTS: Quality of life improved in 84% and pain improved in 86% of patients. Ambulation improved most in lipedema Stage 3 (96%). Weight loss occurred in all stages by 3 months after surgery. Complications included growth of loose connective tissue within and outside treated areas, tissue fibrosis, anemia, blood clots, and lymphedema. CONCLUSIONS: Women with lipedema noticed significant benefits after lipedema reduction surgery in the USA. Prospective studies are needed to assess benefits and complications after lipedema reduction surgery in the USA.

Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19.

The contribution of transcription factors (TFs) and gene regulatory programs in the immune response to COVID-19 and their relationship to disease outcome is not fully understood. Analysis of genome-wide changes in transcription at both promoter-proximal and distal cis-regulatory DNA elements, collectively termed the 'active cistrome,' offers an unbiased assessment of TF activity identifying key pathways regulated in homeostasis or disease. Here, we profiled the active cistrome from peripheral leukocytes of critically ill COVID-19 patients to identify major regulatory programs and their dynamics during SARS-CoV-2 associated acute respiratory distress syndrome (ARDS). We identified TF motifs that track the severity of COVID- 19 lung injury, disease resolution, and outcome. We used unbiased clustering to reveal distinct cistrome subsets delineating the regulation of pathways, cell types, and the combinatorial activity of TFs. We found critical roles for regulatory networks driven by stimulus and lineage determining TFs, showing that STAT and E2F/MYB regulatory programs targeting myeloid cells are activated in patients with poor disease outcomes and associated with single nucleotide genetic variants implicated in COVID-19 susceptibility. Integration with single-cell RNA-seq found that STAT and E2F/MYB activation converged in specific neutrophils subset found in patients with severe disease. Collectively we demonstrate that cistrome analysis facilitates insight into disease mechanisms and provides an unbiased approach to evaluate global changes in transcription factor activity and stratify patient disease severity.