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1. Epigenetic Evolution of ACE2 and IL-6 Genes: Non-Canonical Interferon-Stimulated Genes Correlate to COVID-19 Susceptibility in Vertebrates

   https://doi.org/10.3390/genes12020154  

   Sang, Eric R. ; Tian, Yun ; Miller, Laura C. ; Sang, Yongming ( February 2021 , Genes)

   The current novel coronavirus disease (COVID-19) has spread globally within a matter of months. The virus establishes a success in balancing its deadliness and contagiousness, and causes substantial differences in susceptibility and disease progression in people of different ages, genders and pre-existing comorbidities. These host factors are subjected to epigenetic regulation; therefore, relevant analyses on some key genes underlying COVID-19 pathogenesis were performed to longitudinally decipher their epigenetic correlation to COVID-19 susceptibility. The genes of host angiotensin-converting enzyme 2 (ACE2, as the major virus receptor) and interleukin (IL)-6 (a key immuno-pathological factor triggering cytokine storm) were shown to evince active epigenetic evolution via histone modification and cis/trans-factors interaction across different vertebrate species. Extensive analyses revealed that ACE2 ad IL-6 genes are among a subset of non-canonical interferon-stimulated genes (non-ISGs), which have been designated for their unconventional responses to interferons (IFNs) and inflammatory stimuli through an epigenetic cascade. Furthermore, significantly higher positive histone modification markers and position weight matrix (PWM) scores of key cis-elements corresponding to inflammatory and IFN signaling, were discovered in both ACE2 and IL6 gene promoters across representative COVID-19-susceptible species compared to unsusceptible ones. The findings characterize ACE2 and IL-6 genes as non-ISGs that respond differently to inflammatorymore »and IFN signaling from the canonical ISGs. The epigenetic properties ACE2 and IL-6 genes may serve as biomarkers to longitudinally predict COVID-19 susceptibility in vertebrates and partially explain COVID-19 inequality in people of different subgroups.« less
2. Patient-specific COVID-19 resource utilization prediction using fusion AI model

   https://doi.org/10.1038/s41746-021-00461-0  

   Tariq, Amara ; Celi, Leo Anthony ; Newsome, Janice M. ; Purkayastha, Saptarshi ; Bhatia, Neal Kumar ; Trivedi, Hari ; Gichoya, Judy Wawira ; Banerjee, Imon ( June 2021 , npj Digital Medicine)

   The strain on healthcare resources brought forth by the recent COVID-19 pandemic has highlighted the need for efficient resource planning and allocation through the prediction of future consumption. Machine learning can predict resource utilization such as the need for hospitalization based on past medical data stored in electronic medical records (EMR). We conducted this study on 3194 patients (46% male with mean age 56.7 (±16.8), 56% African American, 7% Hispanic) flagged as COVID-19 positive cases in 12 centers under Emory Healthcare network from February 2020 to September 2020, to assess whether a COVID-19 positive patient’s need for hospitalization can be predicted at the time of RT-PCR test using the EMR data prior to the test. Five main modalities of EMR, i.e., demographics, medication, past medical procedures, comorbidities, and laboratory results, were used as features for predictive modeling, both individually and fused together using late, middle, and early fusion. Models were evaluated in terms of precision, recall, F1-score (within 95% confidence interval). The early fusion model is the most effective predictor with 84% overall F1-score [CI 82.1–86.1]. The predictive performance of the model drops by 6 % when using recent clinical data while omitting the long-term medical history. Feature importancemore »analysis indicates that history of cardiovascular disease, emergency room visits in the past year prior to testing, and demographic factors are predictive of the disease trajectory. We conclude that fusion modeling using medical history and current treatment data can forecast the need for hospitalization for patients infected with COVID-19 at the time of the RT-PCR test.

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3. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

   https://doi.org/10.1038/s41467-021-21361-7  

   Butler, Daniel ; Mozsary, Christopher ; Meydan, Cem ; Foox, Jonathan ; Rosiene, Joel ; Shaiber, Alon ; Danko, David ; Afshinnekoo, Ebrahim ; MacKay, Matthew ; Sedlazeck, Fritz J. ; et al ( December 2021 , Nature Communications)

   Abstract In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin–angiotensin–aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
4. A digital protein microarray for COVID-19 cytokine storm monitoring

   https://doi.org/10.1039/D0LC00678E  

   Song, Yujing ; Ye, Yuxuan ; Su, Shiuan-Haur ; Stephens, Andrew ; Cai, Tao ; Chung, Meng-Ting ; Han, Meilan K. ; Newstead, Michael W. ; Yessayan, Lenar ; Frame, David ; et al ( January 2021 , Lab on a Chip)

   Despite widespread concern regarding cytokine storms leading to severe morbidity in COVID-19, rapid cytokine assays are not routinely available for monitoring critically ill patients. We report the clinical application of a digital protein microarray platform for rapid multiplex quantification of cytokines from critically ill COVID-19 patients admitted to the intensive care unit (ICU) at the University of Michigan Hospital. The platform comprises two low-cost modules: (i) a semi-automated fluidic dispensing/mixing module that can be operated inside a biosafety cabinet to minimize the exposure of the technician to the virus infection and (ii) a 12–12–15 inch compact fluorescence optical scanner for the potential near-bedside readout. The platform enabled daily cytokine analysis in clinical practice with high sensitivity (<0.4 pg mL −1 ), inter-assay repeatability (∼10% CV), and rapid operation providing feedback on the progress of therapy within 4 hours. This test allowed us to perform serial monitoring of two critically ill patients with respiratory failure and to support immunomodulatory therapy using the selective cytopheretic device (SCD). We also observed clear interleukin-6 (IL-6) elevations after receiving tocilizumab (IL-6 inhibitor) while significant cytokine profile variability exists across all critically ill COVID-19 patients and to discover a weak correlation between IL-6 to clinical biomarkers,more »such as ferritin and C-reactive protein (CRP). Our data revealed large subject-to-subject variability in patients' response to COVID-19, reaffirming the need for a personalized strategy guided by rapid cytokine assays.« less
5. Ocular blood flow as a clinical observation: Value, limitations and data analysis

   Harris, A. ( January 2020 , Progress in retinal and eye research)

   Alterations in ocular blood flow have been identified as important risk factors for the onset and progression of numerous diseases of the eye. In particular, several population-based and longitudinal-based studies have provided compelling evidence of hemodynamic biomarkers as independent risk factors for ocular disease throughout several different geographic regions. Despite this evidence, the relative contribution of blood flow to ocular physiology and pathology in synergy with other risk factors and comorbidities (e.g., age, gender, race, diabetes and hypertension) remains uncertain. There is currently no gold standard for assessing all relevant vascular beds in the eye, and the heterogeneous vascular biomarkers derived from multiple ocular imaging technologies are non-interchangeable and difficult to interpret as a whole. As a result of these disease complexities and imaging limitations, standard statistical methods often yield inconsistent results across studies and are unable to quantify or explain a patient's overall risk for ocular disease. Combining mathematical modeling with artificial intelligence holds great promise for advancing data analysis in ophthalmology and enabling individualized risk assessment from diverse, multi-input clinical and demographic biomarkers. Mechanism-driven mathematical modeling makes virtual laboratories available to investigate pathogenic mechanisms, advance diagnostic ability and improve disease management. Artificial intelligence provides a novel method formore »utilizing a vast amount of data from a wide range of patient types to diagnose and monitor ocular disease. This article reviews the state of the art and major unanswered questions related to ocular vascular anatomy and physiology, ocular imaging techniques, clinical findings in glaucoma and other eye diseases, and mechanistic modeling predictions, while laying a path for integrating clinical observations with mathematical models and artificial intelligence. Viable alternatives for integrated data analysis are proposed that aim to overcome the limitations of standard statistical approaches and enable individually tailored precision medicine in ophthalmology.« less