Integrating population-level and cell-based signatures for drug repositioning (preprint)

Drug repositioning presents a streamlined and cost-efficient way to expand the range of therapeutic possibilities. Furthermore, drugs with genetic evidence are more likely to progress successfully through clinical trials towards FDA approval. Exploiting these developments, single gene-based drug repositioning methods have been implemented, but approaches leveraging the entire spectrum of molecular signatures are critically underexplored. Most multi-gene-based approaches rely on differential gene expression (DGE) analysis, which is prone to identify the molecular consequence of disease and renders causal inference challenging. We propose a framework TReD (Transcriptome-informed Reversal Distance) that integrates population-level disease signatures robust to reverse causality and cell-based drug-induced transcriptome response profiles. TReD embeds the disease signature and drug profile in a high-dimensional normed space, quantifying the reversal potential of candidate drugs in a disease-related cell screen assay. The robustness is ensured by evaluation in additional cell screens. For an application, we implement the framework to identify potential drugs against COVID-19. Taking transcriptome-wide association study (TWAS) results from four relevant tissues and three DGE results as disease features, we identify 37 drugs showing potential reversal roles in at least four of the seven disease signatures. Notably, over 70% (27/37) of the drugs have been linked to COVID-19 from other studies, and among them, eight drugs are supported by ongoing/completed clinical trials. For example, TReD identifies the well-studied JAK1/JAK2 inhibitor baricitinib, the first FDA-approved immunomodulatory treatment for COVID-19. Novel potential candidates, including enzastaurin, a selective inhibitor of PKC-beta which can be activated by SARS-CoV-2, are also identified. In summary, we propose a comprehensive genetics-anchored framework integrating population-level signatures and cell-based screens that can accelerate the search for new therapeutic strategies.

Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories (preprint)

A series of SARS-CoV-2 variants of concern (VOCs) have evolved in humans during the COVID-19 pandemic: Alpha, Beta, Gamma, Delta, and Omicron. Here, we used global proteomic and genomic analyses during infection to understand the molecular responses driving VOC evolution. We discovered VOC-specific differences in viral RNA and protein expression levels, including for N, Orf6, and Orf9b, and pinpointed several viral mutations responsible. An analysis of the host response to VOC infection and comprehensive interrogation of altered virus-host protein-protein interactions revealed conserved and divergent regulation of biological pathways. For example, regulation of host translation was highly conserved, consistent with suppression of VOC replication in mice using the translation inhibitor plitidepsin. Conversely, modulation of the host inflammatory response was most divergent, where we found Alpha and Beta, but not Omicron BA.1, antagonized interferon stimulated genes (ISGs), a phenotype that correlated with differing levels of Orf6. Additionally, Delta more strongly upregulated proinflammatory genes compared to other VOCs. Systematic comparison of Omicron subvariants revealed BA.5 to have evolved enhanced ISG and proinflammatory gene suppression that similarly correlated with Orf6 expression, effects not seen in BA.4 due to a mutation that disrupts the Orf6-nuclear pore interaction. Our findings describe how VOCs have evolved to fine-tune viral protein expression and protein-protein interactions to evade both innate and adaptive immune responses, offering a likely explanation for increased transmission in humans.

Facemasks and the COVID-19 pandemic: The harm caused by improper use of facemasks is a matter of concern (preprint)

Abstract: The use of facemasks has played an important role in the prevention of COVID-19. However, inappropriate use of facemasks also brings people certain problems. Therefore, the reasonable use of facemasks is a necessary measure to protect oneself and others in the current epidemic prevention and control.

Amygdala connectivity as a predisposing neural feature of stress-induced behaviour during the COVID-2019 outbreak in Hubei (preprint)

The amygdala plays an important role in the regulation of stress and anxiety. However, little is known about the relationship between amygdala connectivity and subsequent stress-induced behavior. The current study investigated whether amygdala connectivity measured before experiencing stress is a predisposing neural feature of subsequent stress-induced behavior while individuals face an emergent and unexpected event like the COVID-19 outbreak. Using an fMRI cohort established before the pandemic in Wuhan, Hubei, we found that resting-state functional connectivity (rsFC) of the right amygdala with the dorsomedial prefrontal cortex (dmPFC) was negatively correlated with the stress-induced behavior of these volunteers during the COVID-2019 outbreak in Hubei. Furthermore, the self-connection of the right amygdala, inferred using dynamic causal modeling, was negatively correlated with stress-induced behavior in this cohort. A significant correlation between the right amygdala-dmPFC rsFC and self-connection of the right amygdala was found. Additionally, after three months of the COVID-19 outbreak in Hubei when the stressor weakened - and in another cohort collected in regions outside Hubei where the individuals experienced a lower level of stress - the relationship between the amygdala-dmPFC rsFC and the stress-induced behavior disappeared. Our findings support that amygdala connectivity is a predisposing neural feature of stress-induced behavior in the COVID-19 outbreak in Hubei, suggesting the amygdala connectivity before stress predicts subsequent behavior while facing an emergent and unexpected event. And thus our findings provide an avenue for identifying individuals vulnerable to stress using intrinsic brain function before stress as an indicator.

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. (preprint)

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes (preprint)

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.

Discussion on the clinical value of combined detection of SARS-CoV-2 nucleic acid, antigen and antibody

Novel coronavirus (SARS-CoV-2) nucleic acid detection is the gold standard, and antigen-antibody detection is an important auxiliary method for nucleic acid detection. Nucleic acid and antigen detection is direct evidence of early infection in patients, but it cannot indicate whether the patient has been infected before. Antibody testing is indirect evidence of patient infection. Positive IgM indicates acute infection, and positive IgG indicates mid-to-late disease or previous infection. At the same time, antibody testing can be used as an important indicator for evaluating the clinical effects of vaccines and antibody therapeutics. Although antigen detection can be used as direct evidence for early diagnosis, it is not highly sensitive and has not yet been recognized. Therefore, the combined detection of nucleic acid, antigen and antibody can improve the sensitivity and specificity of clinical detection, and provide an important basis for resumption of work and production.

An Optimization Framework to Study the Balance Between Expected Fatalities due to COVID-19 and the Reopening of U.S. Communities (preprint)

As communities reopen following shelter-in-place orders, they are facing two conflicting objectives. The first is to keep the COVID-19 fatality rate down. The second is to revive the U.S. economy and the livelihood of millions of Americans. In this paper, a team of researchers from the Center on Stochastic Modeling, Optimization, & Statistics (COSMOS) at the University of Texas at Arlington, in collaboration with researchers from University of Texas Southwestern Medical Center and Harvard Medical School, has formulated a computationally-efficient optimization framework, referred to as COSMOS COVID-19 Linear Programming (CC19LP), to study the delicate balance between the expected fatality rate and the level of normalcy in the community. Given the disproportionate fatality characteristics of COVID-19 among those in different age groups or with an underlying medical condition or those living with crowding, the key to the CC19LP framework is a focus on "key contacts" that separate individuals at higher risk from the rest of the population. The philosophy of CC19LP lies in maximizing protection of key contacts, so as to shield high-risk individuals from infection. Given the lack of pharmaceutical solutions, i.e., a vaccine or cure, the CC19LP framework minimizes expected fatalities by optimizing the use of non-pharmaceutical interventions, namely COVID-19 testing; personal protective equipment; and social precautions, such as distancing, hand-washing, and face coverings. Low-risk individuals that are not key contacts, including most children, are unrestricted and can choose to participate in pre-pandemic normal activities, which eliminates the need for compliance across the entire population. Consequently, the CC19LP framework demonstrates optimal strategies for protecting high-risk individuals while reopening communities.

SARS-CoV-2 Spike protein hijacks VEGF-A/Neuropilin-1 receptor signaling to induce analgesia (preprint)

Global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues unabated. Binding of SARS-CoV-2s Spike protein to host angiotensin converting enzyme 2 triggers viral entry, but other proteins may participate, including neuropilin-1 receptor (NRP-1). As both Spike protein and vascular endothelial growth factor-A (VEGF-A) - a pronociceptive and angiogenic factor, bind NRP-1, we tested if Spike could block VEGF-A/NRP-1 signaling. VEGF-A-triggered sensory neuronal firing was blocked by Spike protein and NRP-1 inhibitor EG00229. Pro-nociceptive behaviors of VEGF-A were similarly blocked via suppression of spontaneous spinal synaptic activity and reduction of electrogenic currents in sensory neurons. Remarkably, preventing VEGF-A/NRP-1 signaling was antiallodynic in a neuropathic pain model. A silencing of pain via subversion of VEGF-A/NRP-1 signaling may underlie increased disease transmission in asymptomatic individuals. One Sentence SummarySARS-CoV-2s Spike protein promotes analgesia by interfering with VEGF-A/NRP1 pathway, which may affect disease transmission dynamics.

Incidence rate, clinical course and risk factor for recurrent PCR positivity in discharged COVID-19 patients in Guangzhou, China: a prospective cohort study (preprint)

Background: The phenomenon of COVID-19 patients tested positive for SARS-CoV-2 after discharge (redetectable as positive, RP) emerged globally. The data of incidence rate and risk factors for RP event and the clinical features of RP patients may provide recommendations for virus containment and discharge assessment for COVID-19. Methods: The baseline included 285 adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Guangzhou Eighth People's Hospital. We started the Observation on Jan 20, 2020, and acquired all their definite clinical outcome (becoming RP or keeping normal during post-discharge surveillance) by Mar 10, 2020. The dynamic clinical data of patients during observation were prospectively collected and analyzed. Univariate and multivariate-adjusted logistic regression were used to explore the risk factors related to RP events in COVID-19 patients. Results: By March 10, 27 (9.5%) discharged patients had tested positive for SARS-CoV-2 in their nasopharyngeal swab after a median duration of 7·0 days (IQR 5·0-8·0). Age, sex, epidemiological history, clinical symptoms and underlying diseases were similar between RP and non-RP patients (p>0.05). Compared to first admission, RP patients generally had milder clinical symptoms, lower viral load, shorter length of stay and improved pulmonary conditions at readmission (p<0.05). Elder RP patients (≥ 60 years old) were more likely to be symptomatic compared to younger patients (7/8, 87.5% vs. 3/19, 18.8%, p=0.001) at readmission. A prolonged duration of viral shedding (>10 days) during the first hospitalization [adjusted odds ratio [aOR]: 5.82, 95% confidence interval [CI]: 2.50-13.57 for N gene; aOR: 9.64, 95% CI: 3.91-23.73 for ORF gene] and higher Ct value (ORF) in the third week of the first hospitalization (aOR: 0.69; 95% CI: 0.50-0.95) were associated with RP events. Conclusions: RP events occurred in nearly 10% of COVID-19 patients which deserves globally attention. During hospitalization, patients’ low efficiency of viral clearance was a risk factor for RP event. Elderly RP patients were more likely to develop clinical symptoms. To reduce the possibility of reinfection and readmission during the management of COVID-19, more rigorously monitoring on patients’ viral load should be carried out especially in elder patients and later stage of hospitalization.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing (preprint)

An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.

Research on the prevention and control of 2019 novel coronavirus pneumonia for Internet-based hospitals using UTAUT-DST model / 中华医院管理杂志

Thanks to the transmission characteristics of 2019 novel coronavirus pneumonia, Internet-based hospitals can effectively cut off the transmission route via online consulting service. The hospital, leveraging the UTAUT model and DST theory, and advantages of Internet-based hospitals, is deploying step by step such four modules, as "pre-hospital screening", "patient acceptance", "auxiliary diagnosis and treatment", and "prevention and control linkage". These efforts ultimately contribute to an innovative prevention and control pattern against the novel coronary pneumonia for Internet-based hospitals and based on the UTAUT-DST model. This practice proves an initial success, and offers useful references for prevention and control of the NCP and development of other Internet-based hospitals.

AGTR2, One Possible Novel Key Gene for the Entry of 2019-nCoV into Human Cells (preprint)

Recently, it was confirmed that ACE2 is the receptor of 2019-nCoV, the pathogen causing the recent outbreak of severe pneumonia in China. It is confused that ACE2 is widely expressed across a variety of organs and is expressed moderately but not highly in lung, which, however, is the major infected organ. It remains unclear why it is the lung but not other tissues among which ACE2 highly expressed is mainly infected. We hypothesized that there could be some other genes playing key roles in the entry of 2019-nCoV into human cells. Here we found that AGTR2 (angiotensin II receptor type 2), a G-protein coupled receptor, has interaction with ACE2 and is highly expressed in lung with a high tissue specificity. More importantly, simulation of 3D structure based protein-protein interaction reveals that AGTR2 shows a higher binding affinity with the Spike protein of 2019-nCov than ACE2 (energy score: -15.7 vs. -6.9 [kcal/mol]). Given these observations, we suggest that AGTR2 could be a putative novel gene for the the entry of 2019-nCoV into human cells but need further confirmation by biological experiments. Finally, a number of compounds, biologics and traditional Chinese medicine that could decrease the expression level of AGTR2 were predicted.