Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings (preprint)

Gene set analysis methods rely on knowledge-based representations of genetic interactions in the form of both gene set collections and protein-protein interaction (PPI) networks. Explicit representations of genetic interactions often fail to capture complex interdependencies among genes, limiting the analytic power of such methods. Here we propose an extension of gene set enrichment analysis to a latent feature space reflecting PPI network topology, called gene set proximity analysis (GSPA). Compared with existing methods, GSPA provides improved ability to identify disease-associated pathways in disease-matched gene expression datasets, while improving reproducibility of enrichment statistics for similar gene sets. GSPA is statistically straightforward, reducing to classical gene set enrichment through a single user-defined parameter. We apply our method to identify novel drug associations with SARS-CoV-2 viral entry. Finally, we validate our drug association predictions through retrospective clinical analysis of claims data from 8 million patients, supporting a role for gabapentin as a risk factor and metformin as a protective factor for COVID-19 hospitalization.

CRISPRa screening with real world evidence identifies potassium channels as neuronal entry factors and druggable targets for SARS-CoV-2 (preprint)

Although vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been successful, there are no good treatments for those who are actively infected and potentially suffer from diverse neurological symptoms. While SARS-CoV-2 primarily infects the respiratory tract, clinical evidence indicates that cells from sensory organs, brain, and heart are also susceptible to infection. An understanding of factors critical for viral infection in these tissues may help identify novel therapeutics. To discover host factors involved in SARS-CoV-2 viral entry, we performed CRISPR activation (CRISPRa) screens targeting all 6000+ human membrane proteins in cells with and without overexpression of ACE2 using Spike-pseudotyped lentiviruses. We identified both novel as well as previously validated host factors. Notably, we used replication-competent SARS-CoV-2 to validate new viral-entry promoting genes, including potassium channel KCNA6, protease LGMN, and MHC-II component HLA-DPB1. We found that the overexpression of KCNA6 led to a marked increase in infection even in cells with undetectable levels of ACE2 expression. Our analysis of human olfactory neuroepithelium scRNA-seq data revealed that OLIG2+ cells--previously identified as sites of infection in COVID-19 autopsy studies--have high KCNA6 expression and minimal levels of ACE2, suggesting that the presence of KCNA6 may explain sensory/neuronal aspects of COVID-19 symptoms. Further, we demonstrate that FDA-approved compound dalfampridine, an inhibitor of KCNA-family potassium channels, suppresses viral entry in a dosage-dependent manner. Finally, we identified common prescription drugs likely to modulate the top screen hits. We then performed a retrospective analysis of insurance claims of ~8 million patients and found a clinical association between screen-identified drug classes, particularly those targeting potassium channels, and COVID-19 severity. We have thus identified the potassium channel KCNA6 as a SARS-CoV-2 host factor, expanded our understanding of potential viral tropism, and identified promising targets for drug repurposing and development.

Pharmacogenomic and drug interaction risk associations with hospital length of stay among Medicare Advantage members with COVID-19 (preprint)

Importance: COVID-19 has severely impacted older populations and strained healthcare resources, with many patients requiring long periods of hospitalization. Reducing the hospital length of stay (LOS) reduces patient and hospital burden. Given that adverse drug reactions are known to prolong LOS, unmanaged pharmacogenomic risk and drug interactions among COVID-19 patients may be a risk factor for longer hospital stays. Objective: The objective of this study was to determine if pharmacogenomic and drug interaction risks were associated with longer lengths of stay among high-risk patients hospitalized with COVID-19. Design: Retrospective cohort study of medical and pharmacy claims Setting: Administrative database from a large U.S. health insurance company Participants: Medicare Advantage members with a first COVID-19 hospitalization between January 2020 and June 2020, who did not die during the stay. Exposures: (1) Pharmacogenetic interaction probability (PIP) of [≤]25% (low), 26%-50% (moderate), or >50% (high), which indicate the likelihood that one or more clinically actionable gene-drug or gene-drug-drug interactions would be identified with testing; (2) drug-drug interaction (DDI) severity of minimal, minor, moderate, major, or contraindicated, which indicate the severity of an interaction between two or more active medications. Main Outcomes and Measures: The primary outcome was hospital length of stay. Results were stratified by hierarchical condition categories (HCC) counts and chronic conditions. Results: A total of 6,025 patients hospitalized with COVID-19 were included in the study. Patients with moderate or high PIP were hospitalized for 9% (CI: 4%-15%; p < 0.001) and 16% longer (CI: 8%-24%; p < 0.001), respectively, compared to those with low PIP, whereas RAF score was not associated with LOS. High PIP was significantly associated with 12%-22% longer lengths of stay compared to low PIP in patients with hypertension, hyperlipidemia, diabetes, or COPD. Finally, among patients with 2 or 3 HCCs, a 10% longer length of stay was observed among patients with moderate or more severe DDI compared to minimal or minor DDI. Conclusions and Relevance: Proactively mitigating pharmacogenomic risk has the potential to reduce length of stay in patients hospitalized with COVID-19 especially those with COPD, diabetes, hyperlipidemia, and hypertension.

SARS-CoV-2 infection and risk of clinical sequelae during the post-acute phase: a retrospective cohort study (preprint)

Objective: Clinical sequelae have not been well characterized during the post-acute phase of SARS-CoV-2 among adults 18 to 65 years old, and this study sought to fill that gap by evaluating excess risk and relative hazards for developing incident clinical sequelae during the post-acute phase. Design: Retrospective cohort study including three propensity-matched groups. Setting: This study merged three data sources from a large United States health plan: a large national administrative claims database, an outpatient lab testing database, and an inpatient hospital admissions database. Participants: Individuals 18 to 65 years old with continuous health plan enrollment from January 2019 to date of SARS-CoV-2 diagnosis. Three comparator groups were identified and propensity-score matched to individuals infected with SARS-CoV-2: a 2020 comparator group, a historical 2019 comparator group and a historical comparator group with viral lower respiratory tract illness (vLRTI). Main outcome measures: Over 50 clinical sequelae during the post-acute phase (index date + 21 days) were ascertained using ICD-10 codes. Excess risk due to SARS-CoV-2 during the 4 months following the acute phase of illness and hazard ratios with 95% Bonferroni-corrected confidence intervals were calculated. Results: This study found 14% of adults [≤]65 years of age who were infected with SARS-CoV-2 (n=193113) had at least one new clinical sequelae that required medical attention during the post-acute phase of illness. When considering risk for specific sequelae attributable to SARS-Cov-2 infection during the post-acute phase, clinical outcomes including chronic respiratory failure, cardiac arrythmia, hypercoagulability, encephalopathy, peripheral neuropathy, amnesia (memory difficulty), diabetes, liver test abnormalities, myocarditis, anxiety and fatigue were significantly elevated compared to the three propensity-matched comparator groups (2020, 2019, vLRTI). Significant risk differences due to SARS-CoV-2 infection ranged from 0.02 to 2.26 per 100 people and hazard ratios ranged from 1.24 to 25.65 when compared to the 2020 comparator group. Conclusions: Our results confirm excess risk for developing clinical sequelae due to SARS-CoV-2 during the post-acute phase, including specific types of sequelae less commonly seen among other viral illnesses. Although individuals who were older, had pre-existing conditions, and were hospitalized due to COVID-19 were at greatest excess risk, younger adults ([≤]50 years), adults who did not have pre-existing conditions or adults who were not hospitalized due to COVID-19 were still at elevated risk for developing new clinical sequelae. The elevated risk for incident sequelae during the post-acute phase is relevant for healthcare planning.

Association of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers with the Risk of Hospitalization and Death in Hypertensive Patients with Coronavirus Disease-19 (preprint)

BackgroundWhether angiotensin-converting enzyme (ACE) Inhibitors and angiotensin receptor blockers (ARBs) mitigate or exacerbate SARS-CoV-2 infection remains uncertain. In a national study, we evaluated the association of ACE inhibitors and ARB with coronavirus disease-19 (COVID-19) hospitalization and mortality among individuals with hypertension. MethodsAmong Medicare Advantage and commercially insured individuals, we identified 2,263 people with hypertension, receiving [≥]1 antihypertensive agents, and who had a positive outpatient SARS-CoV-2 test (outpatient cohort). In a propensity score-matched analysis, we determined the association of ACE inhibitors and ARBs with the risk of hospitalization for COVID-19. In a second study of 7,933 individuals with hypertension who were hospitalized with COVID-19 (inpatient cohort), we tested the association of these medications with in-hospital mortality. We stratified all our assessments by insurance groups. ResultsAmong individuals in the outpatient and inpatient cohorts, 31.9% and 29.8%, respectively, used ACE inhibitors and 32.3% and 28.1% used ARBs. In the outpatient study, over a median 30.0 (19.0 - 40.0) days after testing positive, 12.7% were hospitalized for COVID-19. In propensity score-matched analyses, neither ACE inhibitors (HR, 0.77 [0.53, 1.13], P = 0.18), nor ARBs (HR, 0.88 [0.61, 1.26], P = 0.48), were significantly associated with risk of hospitalization. In analyses stratified by insurance group, ACE inhibitors, but not ARBs, were associated with a significant lower risk of hospitalization in the Medicare group (HR, 0.61 [0.41, 0.93], P = 0.02), but not the commercially insured group (HR: 2.14 [0.82, 5.60], P = 0.12; P-interaction 0.09). In the inpatient study, 14.2% died, 59.5% survived to discharge, and 26.3% had an ongoing hospitalization. In propensity score-matched analyses, neither use of ACE inhibitor (0.97 [0.81, 1.16]; P = 0.74) nor ARB (1.15 [0.95, 1.38]; P = 0.15) was associated with risk of in-hospital mortality, in total or in the stratified analyses. ConclusionsThe use of ACE inhibitors and ARBs was not associated with the risk of hospitalization or mortality among those infected with SARS-CoV-2. However, there was a nearly 40% lower risk of hospitalization with the use of ACE inhibitors in the Medicare population. This finding merits a clinical trial to evaluate the potential role of ACE inhibitors in reducing the risk of hospitalization among older individuals, who are at an elevated risk of adverse outcomes with the infection.