Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there has been substantial progress in the pharmacologic treatment and supportive care of patients hospitalized with active COVID-19 infections. To date there have been numerous medications trialed for COVID-19 management. In this review, our objective is to provide a comprehensive review of the primary literature and clinical applications surrounding some of the prominent drugs and medication classes that have been utilized in those suffering from COVID-19 infections. The medications reviewed in this article include: hydroxychloroquine, remdesivir, azithromycin, dexamethasone, melatonin, tocilizumab, ascorbic acid, and zinc. The medication classes reviewed include: anticoagulation, angiotensin converting enzyme inhibitors, angiotensin II receptor blockers, convalescent plasma, non-steroidal anti-inflammatory drugs, human recombinant soluble ACE2, and the BNT162b2 mRNA COVID-19 vaccine. The coronavirus study group of the International Committee on Taxonomy of Viruses had proposed the novel coronavirus disease 2019 (COVID-19) infection be categorized as a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This virus has a similar subgenus as severe acute respiratory syndrome (SARS) and is distantly related to the Middle East respiratory syndrome (MERS).2In this review article, our objective was to provide a review of the primary literature and clinical applications of some prominent drugs and drug classes utilized for the treatment and support of patients with COVID-19 infections. Details surrounding drug applications are detailed and organized by specific medications below. Medications reviewed in this article, include; hydroxychloroquine, remdesivir, azithromycin, dexamethasone, melatonin, tocilizumab, ascorbic acid, and zinc. In addition, the medication classes reviewed, include anticoagulation, angiotensin converting enzyme (ACE) inhibitors, angiotensin II receptor blockers (ARB), convalescent plasma, non-steroidal anti-inflammatory drugs (NSAIDs), human recombinant soluble ACE2, and the BNT162b2 mRNA COVID-19 vaccine.We searched PubMed, MEDLINE, and the Cochrane Library using combinations of words that included specific medication names or drug classes with other keywords, such as “COVID-19,” “SARS-CoV-2,” and “coronavirus.” Additional national databases utilized were the World Health Organization and National Institutes of Health. Expert guidance from reputable and established healthcare groups pertaining to COVID-19 management recommendations were assessed throughout this literature review.2Chloroquine is a 4-aminoquinoline analog, used as the preferred treatment for malaria worldwide. Hydroxychloroquine has an additional hydroxyl group at the molecule’s end chain and is a disease-modifying antirheumatic drug indicated for the treatment of rheumatoid arthritis, lupus, and porphyria cutanea tarda. Early during the COVID-19 pandemic, it was hypothesized that hydroxychloroquine may prove beneficial in treating COVID-19 owing to its immunomodulatory effects and established reduction of cytokine production to allow an anti-inflammatory response against COVID-19 infections.3A multi-center, open label, randomized controlled trial (RCT) in China conducted by Tang et al.An observational study of hydroxychloroquine in New York City hospital systems by Geleris et al.Another multi-centered, double-blinded RCT by Boulware et al.In conclusion, additional safety findings have shown reported cases of serious cardiac events and new cases of methemoglobinemia associated with use of high doses. Furthermore, early data suggesting decreased serum viral load and shedding with hydroxychloroquine were not easily replicated in subsequent studies.7Remdesivir is a nucleoside analog that inhibits viral RNA polymerase and has shown an inhibitory effect on some pathogenic animal and human coronaviruses. The initial place in therapy for remdesivir was reserved for compassionate use in patients with severe COVID-19 infection. This was established on the basis of a multicenter prospective cohort study by Grein et al.As the COVID-19 pandemic became more ubiquitous, the use of remdesivir increased as more studies demonstrated its efficacy. Beigel et al.th day. However, those receiving a five-day course of remdesivir showed a statistically significant difference in clinical status compared with the standard of care.Spinner et al.These findings were adopted into current clinical practice, with a five-day course of remdesivir becoming standard of care treatment for patients hospitalized with moderate to severe COVID-19.Ascorbic acid is theorizedAzithromycin is a macrolide used for treatment of respiratory, enteric, and genitourinary bacterial infections. Although it is currently used in conjunction with other antimicrobials for the management of COVID-19, there are no established clinical RCTs that support its use. Damle et al.In vitro studies have compared the degree to which azithromycin reduces this acidic environment and has shown improved inhibition of viral replication over hydroxychloroquine treatment alone.15Potential mechanisms proposed for azithromycin halting viral replication include blocking endocytosis and the inhibition of viral genetic shedding from lysosomes. Azithromycin is a weak base theorized to raise pH through intracellular accumulation. This pH change prevents viral replication through the inhibition of endosome maturation and function by buffering the acidic environment necessary for removal of the viral capsid resulting in viral replication. A retrospective cohort study18In a multicenter randomized clinical trial published in the Lancet, Furtado et al.Dexamethasone is a synthetic corticosteroid widely used in the treatment of acute and chronic conditions with anti-inflammatory and immunosuppressive properties. Initial guidance from the US Centers for Disease Prevention and Control (CDC) recommended against the use of systemic corticosteroids in SARS-CoV-2 infections on the basis of evidence from earlier MERS and SARS-CoV-1 viruses. Unlike MERS and previous SARS-CoV-1, COVID-19, especially in the critically ill, presents with an innate immune response transitioning into an adaptive immune response. Those patients with poorer outcomes are found to have higher serum viral loads and localized elevations in viral loads in their lungs, especially at the time of death.The RECOVERY Trial25Melatonin is known to have anti-inflammatory properties, free radical scavenging activities, and immunomodulatory functions. It was theorized that melatonin may inhibit tissue damage by causing a decrease in CD147 levels. Notably, SARS-Cov-2 causes tissue damage by increasing the TNF-alpha, MCP-1, and interferon-gamma levels modulated through CD147 cells.27Based on higher mortality rates observed in elderly patients infected with COVID-19, low melatonin levels may be a contributing factor to poor clinical outcomes. There are currently many ongoing clinical trials trying to determine the role of melatonin in patients with COVID-19.Acute respiratory distress syndrome is a devastating complication of COVID-19 infections. Patients who are critically ill with COVID-19 are subject to the development of life-threatening acute systemic inflammatory syndromes characterized by multi-organ failure and cytokine-release syndrome (CRS), marked by elevated levels of the proinflammatory cytokine interleukin 6 (IL-6). In the initial phase of the infection, COVID-19 is thought to antagonize type I INF response in the alveolar epithelial cells of the patient’s airways, leading to rapid viral replication and subsequent activation of numerous inflammatory markers, namely IL-6. This cascade of events causes diffuse alveolar damage within airway epithelium and endothelium causing cellular apoptosis and pulmonary fibrinolysis. This elevation in IL-6 plays a role in the induction of a severe systemic inflammatory response in patients with COVID-19, which leads to the consideration of targeted therapy against this inflammatory marker.29Tocilizumab is a recombinant humanized anti-IL-6 receptor monoclonal antibody that is indicated for the treatment of autoimmune diseases. However, there is increasing evidence suggesting that tocilizumab may reduce mortality in severe COVID-19 pneumonia and CRS. It is hypothesized that blockade of IL-6 receptor may impact cytokine release storm in patients experiencing a systemic hyper-inflammatory response to COVID-19. A retrospective case-control studySeveral single-center studies also suggested clinical improvement in patients with COVID-19 receiving tocilizumab who experienced a hyper-inflammatory systemic response associated with ARDS and/or CRS. A 154-patient cohort in an observational controlled study in Michigan studied severe COVID-19 requiring invasive mechanical ventilation and showed that 78 patients receiving tocilizumab experienced a 45% reduction in hazard of death (hazard ratio 0.55). However, patients receiving tocilizumab had a higher rate of super-infection with bacterial pneumonia (54% versus 26%) but did not show a difference in 28-day mortality compared with those without super-infections.in vitro studies, zinc is being evaluated in clinical trials for possible efficacy in patients with COVID-19.Zinc has been theorizedAlthough the true pathophysiologic mechanism of hypercoagulability in patients with COVID-19 is not concretely defined, studies to date have suggested COVID-19 associated coagulopathy may result from an uncontrolled immunothrombotic response to viral infection with COVID-19.42A retrospective cohort study by Tang et al.45The CHEST PhysiciansKlok et al.SARS-CoV-2 utilizes angiotensin converting enzyme 2 (ACE2) receptors as an entry mechanism into cells. ACE2 is expressed by epithelial cells of the lung, intestines, kidney, and vasculature. Fang et al.47To determine if negative outcomes exist between specific anti-hypertensives, Reynolds et al.Convalescent plasma is collected from patients who have recovered from COVID-19 and which contains polyclonal antibodies thought to provide short-term passive immunity against SARS-Co-V2 virus. Historically, convalescent plasma has been used to treat other viruses with varying degrees of success .Further evaluation of convalescent plasma on mortality was examined in systematic review of 12 studies.55in vitro antiviral activity against SARS-CoV-2. Amici et al.in vitro studies on monkey Vero E6 cells and A72 canine cells, which demonstrated a reduction in viral particle production by blocking viral RNA synthesis. Despite these in vitro findings, there is no clinical evidence to support use of indomethacin in COVID-19.Fang et al.Amidst research and treatment efforts for COVID-19, ACE2 has been identified as a cell surface receptor for SARS-CoV2 needed for virus replication. This receptor is a regulator of the RAAS system and protects organ systems and tissues, namely the lungs, from injury. Subsequently, efforts in drug development targeting ACE2 gained traction, and a novel compound synthesized by Apeiron Biologics in Vienna, Austria, has been developed. This compound, the human recombinant soluble ACE2 (hrsACE2), targets two mechanisms of action in COVID-19 treatment. The first mechanism involves targeted suppression of proteins associated with ACE2, which generally spike when viral loads are high. The second mechanism targets an increase in angiotensin II concentrations and RAAS hyperactivity associated with increased viral load. Targeting and suppressing these cascades theoretically minimizes injury to multiple organ systems including the lungs, kidneys, and heart.58A case report recently published by Zoufaly et al.58The BNT162B2 is a nanoparticle-formulated, nucleoside-modified RNA (modRNA) vaccine that encodes a pre-fusion stabilized, membrane anchored SARS-CoV-2 full length spike protein with two Proline mutations that lock the virus in its pre-fusion confirmation. In a multinational placebo-controlled double-blinded efficacy trial, 43,548 participants aged 16 years or older were randomly assigned in the 1:1 ratio to receive the two dose vaccine 21 days apart or placebo. During the study, two 30 mcg doses elicited high SARS-CoV-2 neutralization antibodies and a robust CD8+ and CD4+ T-cell response. This response showed neutralization exceeding the average titer measured in human convalescent serum panels. Subsequently, the authors demonstrated that the two dose regimen of the BNT162b2 was 95% efficacious at preventing COVID-19 infections. Ten cases of severe COVID-19 were reported after the first injection, nine of which were in the placebo group and one in the BNT162b2 group. Amongst the BNT162b2 group, there were eight reported cases of COVID-19 and 162 reported cases of COVID-19 in the placebo group within seven days after the second dose. The efficacy of the vaccine was observed in all enrolled subjects regardless of ethnicity, sex, race, baseline body mass index, and other comorbidities. The BNT162b2 vaccine reactogenicity profile proved safe with participants having reported short-term local injection site pain or minor systemic responses, such as headaches or subjective fevers. The vaccine safety profile coupled with the efficacy data conferring substantial immune response  was the basis for emergency use authorization of the BNT162b2 vaccine during the phase 2/3 trials.Considering the widespread and devastating impact of COVID-19 infections, developing and trialing medications for management and supportive care of COVID-19 infections is at the forefront of healthcare today.This article is a comprehensive literature review of inpatient COVID-19 management to include antivirals for direct treatment of the COVID-19 viral infection, supportive agents for side effect management, and other medications or medication classes thought to contribute to the overall treatment.The medications reviewed include hydroxychloroquine, remdesivir, azithromycin, dexamethasone, melatonin, tocilizumab, ascorbic acid, and zinc. The medication classes reviewed include anticoagulation, angiotensin converting enzyme inhibitors, angiotensin II receptor blockers, convalescent plasma, non-steroidal anti-inflammatory drugs, human recombinant soluble ACE2, and the BNT162b2 mRNA COVID-19 vaccine.Drug specific literature review and evaluation sheds light on possible benefit or lack thereof for each medication or medication class reviewed.


Poly (adenosine diphosphate-ribose) polymerases (PARPs) are a family of proteins responsible for transferring ADP-ribose groups to target proteins to initiate the ADP-ribosylation, a highly conserved and fundamental post-translational modification in all organisms. PARPs play important roles in various cellular functions, including regulating chromatin structure, transcription, replication, recombination, and DNA repair. Several studies have recently converged on the widespread involvement of PARPs and ADP-Ribosylation reaction in mammalian innate immunity. Here, we provide an overview of the emerging roles of PARPs family and ADP-ribosylation in regulating the host’s innate immune responses involved in cancers, pathogenic infections, and inflammations, which will help discover and design new molecular targets for cancers, pathogenic infections, and inflammations. Innate immunity is an evolutionary conservative defense system that generates prompt immune responses to protect the host from tumorigeneses and pathogenic infections, which depends on the recognition of endogenous damage-associated molecular patterns (DAMPs) or exogenous conserved pathogen-associated molecular patterns (PAMPs) in many microorganisms by host pattern recognition receptors (PRRs), including four main families: Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), cytosolic DNA sensor cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) axis, and the nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs). Innate immunity is characterized by the production of inflammatory mediators and/or type I interferons (IFN-I) and thousands of IFN-induced genes (ISGs).+) to their target proteins. PARPs are the best-understood ARTs, and to date, 17 members of PARPs in humans have been identified. Based on the characteristics of their structural and functional domains, PARPs are broadly categorized as four subfamilies: DNA-dependent PARPs , Tankyrases PARPs (including PARP5a and PARP5b), Macrodomain-containing PARPs , and CCCH (Cys-Cys-Cys-His) zinc finger-containing PARPs   through transferring ADP-ribose groups from nicotinamide adenine dinucleotide (NAD PARP13) . PARPs aDNA damage events caused by intra- and inter-cellular stimuli occur in our bodies’ cells every minute of the day, greatly threatening their genetic integrity. Cells have evolved multiple mechanisms, such as transient cell cycle arrest and DNA repair responses, to maintain genomic stability. The DNA double-strand break (DSB) is the most cytotoxic form of DNA damage, leading to the accumulation of DNA fragments in the cytoplasm, termed cytoplasmic chromatin fragments (CCF), which can be recognized by the nucleic acid sensor cyclic cGAS , 12. AftPARP1 and PARP2 are localized in the nucleus and share approximately 69% homology in their catalytic domains. Both are involved in the early DNA damage response to participate in the DNA repair process , 16. In Viral infection recognition by host innate immunity is the first and the most important event to eliminate viruses. PRRs are a group of proteins employed by the innate immune system to recognize PAMPs or DAMPs to evoke the host’s first-line defense. The recognition function of PRRs is usually activated by special PAMPs from pathogens such as viral glycoproteins and nucleic acids. Recently, PARPs are demonstrated to be involved in regulating antiviral innate immune responses during the virus-host interactions , 22. RIGInterestingly, TRIM25, an E3 ubiquitin ligase responsible for the poly-ubiquitination and activation of RIG-I, was also found to catalyze K48- and K63-linked polyubiquitination of ZAP during SINV infection in 293T cells . AlthougIntriguingly, a recent study identified PARP9 as a noncanonical sensor for RNA virus in dendritic cells during the IFN-I-mediated antiviral process. PARP9 could recognize and bind to viral genomic dsRNA from reovirus or dsRNA poly(I:C), and its antiviral role relied on the activation of the phosphoinositide 3-kinase (PI3K)/AKT3 pathway, but not the MAVS signaling pathway, to produce IFN-I . PI3K isIn addition to participation in the positively regulating antiviral responses, some PARP family members also show potentiality to regulate the production of IFN-I negatively. The aryl hydrocarbon receptor (AhR) is a cytoplasmic receptor/transcription factor modulating several cellular and immunological processes following viral infections. A recent study showed that upon the infection of mouse hepatitis virus strain A59 (MHV-A59), a prototypical coronavirus, in bone marrow-derived macrophages (BMDMs), AhR is activated and contributes to the upregulation of PARP7. Knockdown of PARP7 reduces viral replication and increases IFN expression, suggesting that PARP7 functions as a pro-viral factor during MHV infection . HoweverSimilarly, results from another group also demonstrated that the expression of PARP7 was upregulated following activation of the AhR. While in AhR-deficient MEF cells, upon the infection of vesicular stomatitis virus (VSV), influenza virus, Newcastle disease virus (NDV), Sendai virus (SeV), encephalomyocarditis virus (EMCV), or herpes simplex virus-1 (HSV-1), the antiviral IFN-I responses were stronger than that of wild-type MEF cells . The undIn addition to the PARPs discussed above, more PARPs are involved in the antiviral innate responses. Our recently published review  has specInflammation is an essential immune response that protects the body from pathogenic infections, toxic stimulations, or autoimmune damages. Accordingly, untimely controlled destruction will increase pro-inflammatory mediators, lead to persistent tissue damage, and promote various chronic diseases, including diabetes, cancer, autoimmune diseases, and inflammatory bowel diseases. Therefore, a full understanding of inflammatory responses’ regulatory mechanisms will provide novel insights to treat a range of inflammation-associated diseases.in vivo  stimulated monocytes/macrophages indicates that ADP-ribosylation participates in inflammation. The induction of inflammatory cytokines tumor necrosis factor-α (TNF-α), IL-1, and IL-6 by LPS were attenuated by PARP inhibitor, indicating that PARPs may play major roles in promoting inflammatory responses through the expression of pro-inflammatory cytokines , 32. Sinin vivo . This stin vivo . A recenin vivo . Howeverin vivo . In macrin vivo , 37. In in vivo , 39.NEMO , also called IKKγ, is required for the activation of the IκB kinase complex by inflammatory stimuli such as TNF-α . The polCells are exposed to diverse stresses, including genotoxic, oxidative, and pathogenic infections. In addition to DDR, PARPs regulate other cellular stress responses, such as SG formation and UPR Figure 4SGs are non-membrane-bound organelles localized in the cytoplasm. They are aggregates of untranslated messenger ribonucleoproteins (mRNPs) complex to stall the translation initiation . The SG The UPR is a conserved stress response activated when misfolded proteins accumulate in the endoplasmic reticulum (ER), a protective mechanism for cells to maintain cellular homeostasis in response to ER stress. Once the protein homeostasis is broken, UPR activation is initiated by three ER-localized integral membrane proteins, PKR-like Endoplasmic Reticulum Kinase (PERK), Activating Transcription Factor 6 (ATF6), and Inositol-Requiring Enzyme 1 (IRE1), and will promote cell death through apoptosis or autophagy pathway . AccumulThe diverse roles of PARPs implicated in various human diseases have been widely complimented by recent advances that link ADP-ribosylation to stress responses, metabolisms, viral infections, and cancers, in which the PARPs are predicated to be potent therapeutical targets, especially that cancer treatment with PARP inhibitors has received some considerable success. Moreover, recent studies revealed that some members of PARPs are also involved in host-virus interactions. Recent advance implicates the PARPs family as potent antiviral regulators, which would be a promising topic. The current pandemic of coronavirus disease 2019 (COVID-2019), caused by the severe acute respiratory syndrome Coronavirus (SARS-CoV-2), still poses a threat to global public health. Enormous efforts have been devoted to this virus. Recently, a study used MHV as a model coronavirus demonstrated that in human lung cell lines, the infection of SARS-CoV-2 strikingly upregulated the noncanonical MARylating PARP isozymes including PARP7, PARP9, PARP10, PARP11, PARP12, PARP13, and PARP14, and then depressed the cellular NAD metabolome by inducing the expression of enzymes for salvage NAD synthesis from nicotinamide (NAM) and nicotinamide riboside (NR), and reducing other NAD biosynthetic . Given tFurthermore, the latest finding in the recognization of SARS-CoV-2 with a low abundance of CpG dinucleotides by PARP13  may subvMeanwhile, agonists for PARP14 and some other antiviral PARPs seem to be workable by enhancing the host’s IFN-I-mediated antiviral responses. Nevertheless, beyond acting as antiviral regulators, PARPs are involved in multiple cellular activities, especially those that play an important role in promoting inflammation. Therefore, it should be cautious about developing a target therapeutic strategy associated with PARPs regulated innate immune signaling. Furthermore, separation-of-function targeting of PARPs will achieve tailored therapeutic effects. Much more studies are encouraged to reveal the defense mechanisms by PARPs.HZ, Y-DT, GZ, and CS write the draft. CZ review and supervise the manuscript. All authors contributed to the article and approved the submitted version.This article is funded by the National Natural Science Foundation of China (82003043), and the Natural Science Foundation of Jiangxi Province (20202BAB216002).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Development of adaptive immunity after COVID-19 and after vaccination against SARS-CoV-2 is predicated on recognition of viral peptides, presented on HLA class II molecules, by CD4+ T-cells. We capitalised on extensive high-resolution HLA data on twenty five human race/ethnic populations to investigate the role of HLA polymorphism on SARS-CoV-2 immunogenicity at the population and individual level. Within populations, we identify wide inter-individual variability in predicted peptide presentation from structural, non-structural and accessory SARS-CoV-2 proteins, according to individual HLA genotype. However, we find similar potential for anti-SARS-CoV-2 cellular immunity at the population level suggesting that HLA polymorphism is unlikely to account for observed disparities in clinical outcomes after COVID-19 among different race/ethnic groups. Our findings provide important insight on the potential role of HLA polymorphism on development of protective immunity after SARS-CoV-2 infection and after vaccination and a firm basis for further experimental studies in this field. The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019 (COVID-19), has caused an ongoing pandemic with 93,805,612 confirmed cases and 2,026,093 deaths worldwide  utilisiFollowing Hardy-Weinberg equilibrium proportions, multi-locus HLA Class II genotypes were generated by randomly sampling two haplotypes from the same population HLA haplotype frequency distribution. Simulated genotypes were generated for each of the four broad and 21 detailed population groups, with ten replicates at each population of size 1,000, 5,000 and 10,000.For population-based analyses at the haplotype level, we analysed haplotypes up to 99% cumulative coverage within each population. HLA alleles, when examined individually, included all HLA alleles present in any of these selected haplotypes for the four broad and 21 detailed population groups.Peptide binding affinity was assessed for all Class II HLA that featured in haplotypes in any of the ethnic populations studied using NetMHCIIpan v4.0 . PeptidePeptide-HLA scoring models were assessed using scikit-learn  in Pytho+ T-cell recognition and are therefore critical components for an effective adaptive immune response that incorporates humoral (B-cell) and cytotoxic (CD8+ T-cell) arms.The principal objective of our study was to examine whether genetic variation at the HLA loci may influence immune responses, and therefore COVID-19 clinical outcomes or response to vaccination, among patients from different ethnic populations. HLA class II molecules present peptides from exogenous antigens for CD4We analysed peptide binding for all classical HLA class II loci . The main analysis focused on four broad population categories, African Americans (AFA), European Caucasians (CAU), Hispanics (HIS) and Asian/Pacific Islanders (API) and sub-analysis included 21 detailed population subgroups of these broad categories. To account for linkage disequilibrium between HLA class II loci, we analysed HLA haplotypes rather than assuming allele frequencies were independent at each locus. HLA haplotype frequencies were estimated utilising HLA genotype data obtained from a cohort of approximately 8.9 million donors  at the population level may reflect disparities in capacity for effective anti-SARS-CoV-2 immunity which could in turn influence response to vaccination or underpin observed variability in COVID-19 clinical outcomes among different ethnic populations. To investigate this hypothesis, we examined viral proteome presentation by HLA class II, accounting for the distribution of HLA haplotypes in a population. This analysis showed that the overall capacity for HLA peptide presentation, at the whole SARS-CoV-2 proteome level, among the four broad ethnic populations examined was remarkably similar . These observations were confirmed  using more stringent thresholds for defining HLA class II peptide presentation (data not shown). In further analysis, we considered immune reactivity against the Receptor Binding Domain (RBD) of Spike glycoprotein, as it represents a proposed target of coronavirus subunit vaccines currently in clinical trials  with wide variation in predicted RBD specific peptide presentation  and humoral adaptive immune responses after viral infection and after vaccination. In this computational study, we investigated the role of HLA on SARS-CoV-2 immunogenicity at the individual and at the population level, considering population-specific HLA allele, haplotype, and genotype frequencies. We accounted for genetic polymorphism and for HLA linkage disequilibrium in twenty five ethnic populations by capitalising on, to our knowledge, the most extensive HLA haplotype frequency information to date to predict SARS-CoV-2 specific CD4+ T-cell epitopes covering the entire viral proteome. We find that the overall capacity for anti SARS-CoV-2 cellular immunity according to HLA class II genotype is similar at the population level across all ethnic groups examined. However, we identify wide inter-individual variability in predicted CD4+ T-cell reactivity against every SARS-CoV-2 protein according to expressed HLA genotype. We predict robust immune reactivity against the SARS-CoV-2 Spike protein, the basis for the majority of current vaccination efforts, both at the population and at the individual level regardless of population origin. Finally, we provide comprehensive maps of SARS-CoV-2 proteome immunogenicity accounting for population coverage in ethnic groups.Recognition of SARS-CoV-2 peptides in the context of HLA class II molecules is essential for CD4+ T-cells have been associated with lessened COVID-19 severity and that high frequency of Spike-specific CD4+ T-cell responses were observed in patients who had recovered from COVID-19  is likely required to reduce COVID-19 severity, with the cellular response being key for both initiating the adaptive response and for controlling the acute infection  and genetic factors , 49. Noncination , 56–61. cination , 60, 62.+ T-cell activation; peptide recognition is complex and incompletely understood and is influenced by many factors, including relative expression of individual viral proteins  / Be The Match  and DataHC, VK, AL and LG contributed to definition of the central question and solutions. HC developed and implemented the peptide-HLA prediction models, the HLA, haplotype and population analysis and the algorithm validation with advice and supervision from AL and VK. LG performed the HLA population frequency computation, calculated the Haplotype frequency distributions, generated simulated populations and performed the statistical analysis on simulated populations. VK conceived and supervised the work and wrote the manuscript. All authors contributed to the article and approved the submitted version.The research presented in this manuscript has received funding from the NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation at the University of Cambridge, from the NIHR Cambridge Biomedical Research Centre and from an NIHR Fellowship . We gratefully acknowledge funding from an MRC Clinical Research Training Fellowship to HC (MR/S006745/1). VL acknowledges funding as a P.I. Terasaki Scholar. AL acknowledges funding by the Member States of the European Molecular Biology Laboratory (EMBL).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


In developing countries where point-of-care testing is limited, providers rely on clinical judgement to discriminate between viral and bacterial respiratory infections. We performed a cross-sectional cohort study of hospitalized Jordanian children to evaluate antibiotic use for respiratory syncytial virus (RSV) infections.Admitting diagnoses from a prior viral surveillance cohort of hospitalized Jordanian children were dichotomized into suspected viral-like, non-pulmonary bacterial-like, and pulmonary bacterial-like infection. Stratifying by sex, we performed a polytomous logistic regression adjusting for age, underlying medical condition, maternal education, and region of residence to estimate prevalence odds ratios (PORs) for antibiotic use during hospitalization. Sensitivity and specificity of admission diagnoses and research laboratory results were compared.Children with a suspected viral-like admission diagnosis, compared to those with suspected non-pulmonary bacterial-like, were 88% and 86% less likely to be administered an empiric/first-line antibiotic . There were slight differences by sex with males having a lower prevalence than females in being administered an expanded coverage antibiotic; but they had a higher prevalence of macrolide administration than males with non-pulmonary bacterial-like infection. Overall, children with RSV had a 34% probability (sensitivity) of being assigned to a suspected viral-like diagnosis; whereas RSV-negative children had a 76% probability (specificity) of being assigned to a suspected pulmonary bacterial-like diagnosis.Hospitalized children with a suspected viral-like admission diagnosis were less likely to receive an empiric/first-line and expanded coverage antibiotic compared to suspected non-pulmonary and pulmonary infections; however, when evaluating the accuracy of admission diagnosis to RSV-laboratory results there were considerable misclassifications. These results highlight the need for developing antibiotic interventions for Jordan and the rest of the Middle East. Respiratory viruses are the leading cause of lower respiratory tract infections in young children worldwide, with respiratory syncytial virus (RSV) as the most common . SymptomPatterns of antimicrobial prescriptions are well characterized in the United States; however, few studies have been conducted to assess prescribing practices in the Middle East. In Jordan, only two studies have evaluated antibiotic prescribing among children with respiratory infections. One evaluated the proportions of antibiotics prescriptions to children seen at an emergency department ; and theTo establish antibiotic stewardship strategies and guidelines for hospitalized pediatric patients in Jordan, additional research on the antibiotic use in diagnostic resource-limited settings are needed. Our primary goal of this study was to evaluate the association of clinical admission diagnoses and antibiotic administration practices in children less than two years who presented with fever and/or respiratory symptoms and were hospitalized at a government-run hospital in Amman, Jordan, where point-of-care viral testing is lacking. Based on our previous research, 64% of children hospitalized in Jordan with a virus had RSV detected in their respiratory specimen . Thus asWe conducted a cross-sectional cohort study from our main three-year prospective respiratory viral surveillance study at Al-Bashir Hospital, in Amman Jordan (population > 2 million), which is one of three government hospitals in Jordan ,11. ChilTM  database [After we obtained informed consent from the parents/guardian of an eligible child, we conducted an interview collecting information on demographics, family history, social history , maternal education, delivery method, prenatal care, and region of residence . Trained research personnel administered interviews in Arabic using a standardized questionnaire and recorded responses in English ,11. Medidatabase .®, Remel, USA), aliquoted into MagMAXTM Lysis/Binding Solution Concentrate , snap-frozen, stored at -70°C, and shipped on dry ice to Nashville, TN, USA [Trained research personnel collected a nasal and throat swab; and both were combined into transport medium  pulmonary bacterial-like infection , and non-pulmonary bacterial-like infection . Children with a both a symptom diagnosis  and a condition diagnosis , were categorized by their condition status. Those with conflicting or no admitting diagnoses were excluded from the analysis.As many admission diagnoses can be of viral and/or bacterial origin, we categorized children with an admission diagnoses that may warrant empiric antibiotic therapy into either the suspected non-pulmonary or pulmonary bacterial-like illness group. Our reasoning for this classification was to emulate the challenges physicians in Jordan face without laboratory diagnostic testing.The primary outcome of our study is defined as the administration of at least one antibiotic throughout the individual’s hospitalization course. Antibiotics were categorized into four levels: 1) None administered; 2) Empiric/first-line ; 3) Macrolides ; and 4) Expanded coverage . The administration of antibiotics were retrospectively collected through medical chart abstractions for all enrolled children.2 test for categorical variables. Potential confounders were identified using a priori knowledge and the 10% change-in-estimate criterion. We evaluated potential effect measure modification by sex. Statistically significant differences  in each stratum were evaluated on the multiplicative scale with the likelihood ratio test. Polytomous logistic regression adjusting for spline-coded age, underlying medical conditions, maternal education, and region of residence were conducted to estimate the prevalence odds ratios (aPORs) and 95% confidence intervals (CIs) for the administration of empiric/first-line, macrolides, or expanded coverage antibiotics during hospitalization (compared to no antibiotic administration). Sensitivity and specificity were calculated to evaluate the accuracy of admission diagnosis in classifying the causative pathogen  and further applied to virus-positive vs. virus-negative. Statistical significance was based on two-tailed tests with α = 5%. All analyses were conducted using statistical software StataIC 16.0 .Differences in demographic and clinical characteristics of children were evaluated using simple linear regression with robust standard errors for continuous variables and Pearson χFig 1). The final study population represents 99% (n = 3153) of children enrolled into our parent study [Fig 1).From March 2010 to March 2013, 3168 children were enrolled and 15 (0.5%) were excluded from this analysis: nine had no admission diagnosis and five had diagnoses that were not decipherable between suspected viral- and bacterial-like infection (nt study . The mosTable 1) compared to children with suspected pulmonary or non-pulmonary bacterial-like infection. In contrast, children with suspected pulmonary or non-pulmonary bacterial-like infection had a higher frequency of fever , a longer hospitalization stay, more likely admitted to ICU. Children in the non-pulmonary bacterial-like infection group had the highest frequency of clinical laboratory confirmed bacterial infection  with the majority being urinary tract infections (Table 1). Approximately 40% of our cohort had a parent or legal guardian report antibiotic use prior to hospitalization .Of the 685 children with a suspected viral-like infection, 61% had RSV detected from their research laboratory specimen. These children were primarily male, had a median mean age of 5.8 months (SD: 4.7), and 89 (13.0%) had history of an underlying medical condition. Children with a viral-like infection most often reported cough (95%), wheezing (88%), and shortness of breath (85%); and were more likely have RSV detected by research RT-qPCR testing . Compared to children with a suspected non-pulmonary bacterial-like infection, children with a suspected viral-like and pulmonary bacterial-like infection were more frequently prescribed one antibiotic  and had a shorter median therapy duration .Overall, 505 (74%) children with a suspected viral-like infection were administered at least one antibiotic during their hospitalization, of which 497 (98%) had no documentation of a concominant bacterial infection. Empiric/first-line antibiotics were the most common antibiotics administered during our study period . Whereas, non-pulmonary bacterial-like infections had the highest percentage with 84% given an antibiotic. Of the macrolides and expanded coverage antibiotics administered, macrolides were more often given to children with viral-like (27%) and pulmonary bacterial-like (66%) diagnoses, whereas expanded coverage antibiotics were often administered to those in the non-pulmonary bacterial-like group (38%)  and an 95% and 91% lower prevalence of being administered an expanded coverage antibiotic  than those who presented with a suspected non-pulmonary bacterial-like infection (Table 2). Alternatively, males with a suspected viral-like infection had two-fold increased prevalence odds  of being administered a macrolide than males with a non-pulmonary bacterial-like infection. Whereas a significant association was not observed for macrolide administration in female children with a viral-like infection. Compared to non-pulmonary bacterial-like infections, both males and females with suspected pulmonary bacterial-like infection had a respective 19-fold and 16-fold increased prevalence odds of being administered a macrolide .Overall, both male and female children who presented to Al-Bashir Hospital with a suspected viral-like infection had an 88% and 86% lower prevalence of being administered an empiric/first-line antibiotic during their hospitalization . Comparatively, among children who were RSV-negative, 76% were diagnosed with a suspected pulmonary bacterial-like infection upon admission (specificity). However, the sensitivity and specificity between non-pulmonary bacterial-like and suspected viral-like admission diagnoses and RT-qPCR RSV results had better diagnostic accuracy . When further evaluating the sensitivity and specificity comparing virus-positive to virus-negative, our results were similar (Table 3).When comparing pulmonary bacterial-like admission diagnosis to research RT-qPCR viral results, there was a 34% (sensitivity) probability the admitting clinician would diagnose a child with RSV as a suspected viral-like infection given the child was RSV-positive based on their RT-qPCR results Click here for additional data file.


Globally, lung cancer is the leading cause of cancer-related death. The majority of non-small cell lung cancer (NSCLC) tumours express epidermal growth factor receptor (EGFR), which allows for precise and targeted therapy in these patients. The dysregulation of EGFR in solid epithelial cancers has two distinct mechanisms: either a kinase-activating mutation in EGFR (EGFR-mutant) and/or an overexpression of wild-type EGFR (wt-EGFR). The underlying mechanism of EGFR dysregulation influences the efficacy of anti-EGFR therapy as well as the nature of resistance patterns and secondary mutations. This review will critically analyse the mechanisms of EGFR expression in NSCLC, its relevance to currently approved targeted treatment options, and the complex nature of secondary mutations and intrinsic and acquired resistance patterns in NSCLC. Lung cancer is the leading cause of cancer-related mortality amongst both men and women, accounting for approximately 25% of all cancer deaths globally . There aEGFR was the first oncogenic target discovered in NSCLC and is present in over 60% of patients ,8,9. TheThe EGFR belongs to the ErbB family of tyrosine kinase receptors, which comprises four family members: EGFR/HER1/erbB1, HER2/erbB2/neu, HER3/erb3, and HER4/erb4 . Each faGrowth factors that bind to ErbB receptors belong to the EGF-family and are typically secreted in an autocrine and paracrine fashion . The binEGFR is located on chromosome 7 short arm q22 . Mature Six ligands , amphiregulin, betacellulin, heregulin, and heparin-binding EGF) are known to bind to EGFR. . These lThree main signalling pathways are activated downstream of EGFR: the Ras/Raf/Mitogen-activated protein kinases (MAPK) pathway, the phosphatidylinositol 3-kinase (PI3K)/AKT8 virus oncogene cellular homolog the (AKT)/Mammalian target of rapamycin (mTOR) pathway and the signal transducer and activator of the transcription (STAT) pathway ,28. In tThe PI3K/AKT/mTOR pathway is involved in cellular metabolism and motility ,29. PI3KThe STAT pathway was first identified as part of the intracellular signalling pathway of cytokine receptors ,30. STATThere are three main mechanisms leading to EGFR activation: increased EGFR expression in malignant cells, increased ligand production, and the presence of EGFR-activating mutations  32]. Al. Al32]. Dysregulated EGFR signalling is a well-established phenotype in NSCLC . It can The “classical” EGFR mutations consist of a deletion in exon 19 and a single amino acid substitution L858R in exon 21 and account for 47% and 41% of the EGFR mutations in NSCLC, respectively . Rare muAnti-EGFR therapies consist of either monoclonal antibodies (mAbs) that are directed at the extracellular portion of the EGFR or small molecule tyrosine kinase inhibitors (TKIs) that target the intracellular protein kinase domain. TKIs inhibit receptor signalling by competitively blocking the binding of ATP to the cytoplasmic domain of the EGFR. These medications are associated with a high objective response rate, ranging from 50–77% ,81,82,83The best characterised mutations that confer sensitivity to EGFR-TKI therapy are located in exon 19  and exon 21 (L858R) . These cIn patients with EGFR-mutant NSCLC, the Riesa Pan-Asia Study (IPASS) was the first to demonstrate a significant improvement in 12-month progression-free survival (PFS) with gefitinib, 24.9%, compared to chemotherapy, 6.7% . In contThe role of TKIs in patients with wt-EGFR NSCLC is controversial. Due to the results of the IPASS and TORCH trials, which demonstrated inferior survival compared to chemotherapy, first-line TKI therapy is not recommended in this population ,102,103.Consecutive analysis revealed that while 75% of patients with the common TKI-sensitive L858R or 19del mutations respond to first-generation TKIs, an acquired resistance developed that limited PFS to less than 12 months ,113,114.Secondary EGFR mutations are the predominant mechanism of acquired resistance to first- and second-generation TKIs. Furthermore, the T790M mutation is solely attributed to 60% of acquired resistance cases with a presentation of indolent disease progression ,184,185.The T790M variant prompted the development of further TKI generations to address treatment resistance. While second-generation TKIs were unable to inhibit T790M-EGFR in vivo at clinical concentrations despite promising preclinical data, the third-generation agent osimertinib was successful at achieving inhibition ,195,196.The appearance of secondary mutations or the loss of the T790M clone that occurs with the emergence of acquired resistance can guide further targeted therapy. For resistance that emerges with de novo L474P or G724S mutations, recent reports demonstrate the clinical efficacy of second-generation afatinib rescue therapy. The L474P mutation in the N-terminal of the βchain results in hydrophobic-centre conformational changes and constitutive kinase activation that was managed with afatinib with a much improved PFS of 24 months at the time of publication . SimilarThe emergence of EGFR-mutant clones that display clinical resistance to all current TKI generations indicate the need for further drug development. Specifically, G796 residue mutations display clinical resistance to all TKIs via steric hindrance, even with the loss of a concurrent cis T790M mutation in the resistant clone at the time of disease progression ,146. SimThe C797S mutation is a variant with no current treatment options, yet novel inhibitors demonstrate a proof-of-concept for future mutation-specific targeted therapy. Resistance to third generation TKIs is mediated by impaired osimertinib binding to the C797 residue within the ATP-binding cleft . When thResistance to targeted kinase therapy emerges through signalling aberrations downstream of the initiating EGFR-mutation. These signalling aberrations emerge in post-treatment tumour biopsies and are attributed to resistance to all TKI generations via activation of mitogen-activated protein kinase kinase (MEK)/extracellular signal regulated kinase (ERK), and Akt/mTOR pathways. Within the Akt/mTOR pathway, mutations have been demonstrated in patient-derived tumours within PIK3CA, PTEN, and AKT1 that lead to increased Akt phosphorylation, mTOR-mediated survival signalling, and early disease progression ,164,165.Enhancement of alternative pathways is demonstrated to induce resistance to targeted kinase therapy by bypassing EGFR to activate MEK/ERK and AKT/mTOR signalling. MET signalling is a well-described pathway in which amplification or protein overactivation phosphorylates ErbB3 and bypasses EGFR to activate Akt . MET ampThe heterogeneity of non-small cell lung cancer is evident in the diverse genetic and cellular mechanisms of acquired resistance. Histologic transformation represents the progression of a primary or secondary tumour to either a small cell or squamous cell carcinoma . The traTherapeutic mAbs are used in the treatment of cancers by binding to the specific target cell antigens responsible for growth and differentiation. Anti-EGFR mAbs bind to the surface of EGFR via an antigen-binding fragment (Fab) and competitively block the binding of EGF . AntibodUnfortunately, despite their success in other cancer types, such as colorectal carcinoma and head and neck SCC , mAb theEGFR-targeting therapies have dramatically altered the treatment landscape of a number of cancers. The underlying mechanism of EGFR overexpression has a significant impact on treatment response and the development of resistance. In cancers such as head and neck, where the majority of tumours overexpress EGFR, antibodies inducing effects such as ADCP and ADCC are clinically relevant. In NSCLC, a therapeutic approach is differentiated with regard to mutant-EGFR and the development of resistance to anti-EGFR therapy through various mechanisms including gene line polymorphisms, secondary EGFR mutations, enhancement of alternate signalling pathways, and downstream signalling pathway protein mutations. Further research into these mechanisms of resistance and the nature of EGFR expression will allow the development of superior therapeutic techniques to help improve the outcomes of patients with NSCLC. The approach to EGFR targeting in each cancer thus depends on the type of EGFR dysregulation specific to each tumour type.Granted patents: PAT-02100-JP-01; 2015-538212; PAT-02100-GB-01; 13848409.2; PAT-02100-DE-01; 60 2013059561.5; PAT-02100-AU-02; 2013334493; PAT-02100-US-01 14/438440; PAT-02100-JP-01 2015-538212.


The Coronavirus-2019 (COVID-19) pandemic has disproportionally affected communities of color and older adults in the United States. Nursing homes (NHs) have reported over 130,000 COVID-19 deaths  circa March 2021, a high share of the nation’s total death count (CMS COVID-19 NH Data). These inequities partially driven by barriers to care, segregation and structural racism have resulted in the unequal impact of COVID-19 across NHs . In this presentation, I will describe NHs that disproportionally care for minority residents and the effect of NH composition on COVID-19-related mortality and outcomes. In 2020, minority older adults were less likely to have access to high quality facilities. From June – August, NHs with a high proportion of minority residents reported higher COVID-19 mortality rates per 1000 residents. Equal access to high quality of care across the life-course among racial and ethnic groups is needed.


Correction to: Diabetologia10.1007/s00125-021-05392-9The following sentence in the Discussion was inappropriately changed to a definite statement during editing: ‘Considering the mechanism of action of PB-119, which is similar to exenatide QW, PB-119 also showed superior efficacy compared with available OADs.’The journal would like to revert back to the authors’ original phrasing as follows:‘Considering the mechanism of action of PB-119, which is similar to exenatide QW, PB-119 could also reveal superior efficacy in comparison with available OADs.’The original article has been corrected.


Triple-negative breast cancer (TNBC) has been associated with worse prognoses due to the limited treatment options. Thus, there is a need to characterise new biomarkers or treatment targets to improve patient outcomes. Cancer testis antigens (CTAs) are a group of antigens that are preferentially expressed in tumours and exhibit strong immunogenicity, as such, CTAs hold great promise as potential treatment targets and biomarkers in cancer. Previous reports have implicated roles for CTAs in different subtypes of breast cancer, including TNBC. Multiple clinical trials are in progress investigating CTAs as treatment targets in various cancers. This review aims to discuss the roles of CTAs in TNBC and discuss the potential applications and benefits of incorporating CTAs in clinical practice. Breast cancer cells commonly express tumour-associated antigens that can induce immune responses to eradicate the tumour. Triple-negative breast cancer (TNBC) is a form of breast cancer lacking the expression of hormone receptors and cerbB2 (HER2) and tends to be more aggressive and associated with poorer prognoses due to the limited treatment options. Characterisation of biomarkers or treatment targets is thus of great significance in revealing additional therapeutic options. Cancer-testis antigens (CTAs) are tumour-associated antigens that have garnered strong attention as potential clinical biomarkers in targeted immunotherapy due to their cancer-restricted expressions and robust immunogenicity. Previous clinical studies reported that CTAs correlated with negative hormonal status, advanced tumour behaviour and a poor prognosis in a variety of cancers. Various studies also demonstrated the oncogenic potential of CTAs in cell proliferation by inhibiting cell death and inducing metastasis. Multiple clinical trials are in progress to evaluate the role of CTAs as treatment targets in various cancers. CTAs hold great promise as potential treatment targets and biomarkers in cancer, and further research could be conducted on elucidating the mechanism of actions of CTAs in breast cancer or combination therapy with other immune modulators. In the current review, we summarise the current understandings of CTAs in TNBC, addressing the role and utility of CTAs in TNBC, as well as discussing the potential applications and advantage of incorporating CTAs in clinical practise.  Breast cancer is a heterogeneous disease that can be classified based on the clinical, morphological and biological characteristics ,2. TriplClinical outcomes in breast cancer based on disease-free survival (DFS) and overall survival (OS) have been enhanced over the years by incorporating different factors, such as molecular classification, as well as other clinical parameters, such as menopausal status, performance status and the stage of the disease, in treatment algorithms ,6. DespiMAGEA1 caused resistant tumour cell clones to be sensitised to killing by autologous cytotoxic T-lymphocytes . Up. Up49]. Receptor tyrosine kinase-like orphan receptor 2 (ROR2), a novel Wnt receptor, belongs to the tyrosine kinase receptor family, which is important in regulating skeletal and neuronal development, cell migration and cell polarity  76]. Br. Br76]. Sperm protein associated with the nucleus X-linked (SPANX) is a CTA with a role in spermatogenesis  77]. Hi. Hi77]. A-kinase anchoring proteins (AKAP) are a group of CTAs involved in sperm function  78]. AK. AK78]. The CTA New York oesophageal squamous cell carcinoma-1 (NY-ESO-1), also known as cancer-testis antigen 1B (CTAG1B), is immunogenic and reportedly induces specific B-cell and T-cell immunity in patients with NY-ESO-1-expressing cancers . NY-ESO-CTAs have been involved in various processes of tumourigenesis and metastasis, such as epithelial-mesenchymal transition (EMT), proliferation, apoptosis and invasion . MAGE-A Preferentially expressed antigen of melanoma (PRAME) encodes a membrane-bound protein that promotes autologous cytotoxic T-cell-mediated immune responses  82]. An. An82]. SPANX-A/C/D was discovered as an important factor for the metastasis of breast cancer cells; it was hypothesised to act via interactions with components of the cytoskeleton at the inner nuclear membrane and is required to produce actin-rich cellular protrusions during modelling of the extracellular matrix . Sperm-a2H2)n sub-family of zinc-finger proteins and is predominantly found in the nucleus where it interacts with proteins involved in gene-regulatory activity (TRIM27) gene encodes the RING finger protein (RFP), a member of the tripartite motif family that is involved in gene regulation [TRIM27 was reported in TNBC compared to normal breast tissue using data from The Cancer Genome Atlas (TCGA) [Zinc-finger protein 165 (ZNF165) is a member of the SCAN-(Cactivity  27]. ZN. ZN2H2)nTSP50) is an oncogene that promotes breast cancer survival, invasion and metastasis via the activation of the NF-κB signalling pathway , or mastermind-like domain containing 1 (MAMLD1), was expressed in 65% of TNBC . CX. CXCXorfSperm protein 17 (SP17) is involved in various stages of spermiogenesis, and aberrant SP17 expression has been linked to cancers such as ovarian, oesophagus, central nervous system, multiple myeloma and esthesioneuroblastoma  85,86,8,88,89,90Wilms tumour antigen (WT-1) is a transcription factor containing four zinc-finger motifs at the C-terminus and a proline or glutamine-rich DNA-binding domain at the N-terminus . Out of As summarised in Multiple laboratories have utilised mIHC/IF to evaluate biomarkers in several cancers. Systematic review and meta-analysis of tumour patients from 8135 patients revealed that mIHC/IF had superior diagnostic accuracy in predicting clinical response to anti-PD-1/PD-L1 therapy than PD-L1 IHC, tumour mutational burden or gene expression profiling . An optiAdvances in next-generation sequencing (NGS) technology have identified unrecognised gene expressions and somatic mutations in TNBC samples, thus allowing refinement of TNBC subtypes at the genomic level and the possibility of identifying novel targets for personalised therapy . Using aCurrent evidence suggests that CTAs are a common feature of TNBC and may correlate with prognosis of patients with TNBC. At present, TNBC samples are not routinely screened for CTAs expressions. The expression and characteristics of CTAs in TNBC provide exciting possibilities to enhance current screening, diagnosis and treatment methods . We propCTAs such as NY-ESO-1, MAGE, MSLN, SPANXB1, PRAME, ZNF165, TRIM27, KK-LC-1, SP17 and WT-1 were found to be enriched in TNBC compared to non-TNBC tissue . The speSome trials involving NY-ESO-1 showed promising results. LV305, a third-generation lentivirus-based vector, enhances expression of NY-ESO-1 in dendritic cells, and is tested in clinical trial against several tumour types such as sarcoma, ovarian, melanoma and lung cancers . InductiMembers of the MAGE-A family have been developed for T-cell therapy with favourable results. In a Phase I study involving HLA-DPB1*0401-restricted T-cell receptors (TCRs) that was designed to specifically recognise MAGE-A3 antigen, complete remission was seen in a patient with metastatic cervical cancer, and partial remission was seen in 3 patients . The adoCTA1A and CTA1B expression in lung cancer using data from TCGA database showed higher expression of these CTAs in Asians compared to non-Asians [At present, there is limited information on the effect of race or ethnicity on the expression of CTAs in TNBC. NY-ESO-1 and MAGE are the most studied, with several reports involving TNBC patient samples from different continents, races and ethnicities. However, there are currently no reports directly comparing the impact of race and ethnicity on CTAs in TNBC. Analyses of n-Asians . More stFurther research could be performed to analyse expressions of CTAs with different immune infiltrates and correlate with clinicopathological characteristics, given the growing evidence of CTA having immunogenic and oncogenic properties in TNBC and promoting tumourigenesis or invasiveness . SeveralA key aspect for investigation is whether CTAs are abnormally expressed in breast tissue before malignancy occurs and if they could be used as potential biomarkers for TNBC. This would help clinicians to identify women at high risk for cancer development, thus improving screening protocols for the early detection of TNBC .TNBC frequently expresses CTAs, and some CTA expression correlates with overall survival and prognosis. CTAs show biased expression in cancer and robust immunogenicity, thus serving as ideal targets for cancer immunotherapy. Multiple clinical trials have been conducted or are currently on-going to investigate the role of CTAs as treatment targets in advanced cancers, such as TBNC. Further research could be conducted to delineate the mechanism of action of CTAs in TNBC, increasing the efficacy of CTAs or in combination with other immunotherapies, identifying patients that would benefit most from the treatment and devising better drug delivery. With the collation of more data, CTAs may also be incorporated in routine screening protocols for TNBC.


On November 20, 2020, this report was posted online as an MMWR Early Release.During August 7–16, 2020, a motorcycle rally was held in western South Dakota that attracted approximately 460,000 persons from across the United States to numerous indoor and outdoor events over a 10-day period. During August–September 2020, the Minnesota Department of Health (MDH) investigated a coronavirus disease 2019 (COVID-19) outbreak associated with the rally in Minnesota residents. Fifty-one primary event-associated cases were identified, and 35 secondary or tertiary cases occurred among household, social, and workplace contacts, for a total of 86 cases; four patients were hospitalized, and one died. Approximately one third (34%) of 87 counties in Minnesota had at least one primary, secondary, or tertiary case associated with this rally. Genomic sequencing supported the associations with the motorcycle rally. These findings support current recommendations for mask use, physical distancing, reducing the number of attendees at gatherings, isolation for patients with COVID-19, and quarantine for close contacts to slow the spread of SARS-CoV-2 . Reverse transcription–polymerase chain reaction testing for SARS-CoV-2, the virus that causes COVID-19, was used to confirm cases. All confirmed cases among Minnesota residents were reported to MDH. MDH or local public health department staff members interviewed patients with confirmed SARS-CoV-2 infection to identify exposures and persons who might have been in contact with patients during their infectious period (2 days before through 10 days after symptom onset).Secondary and tertiary cases were identified from case interview data. Confirmed secondary cases were defined as laboratory-confirmed infections in persons who did not attend the rally but who received SARS-CoV-2–positive test results after having contact with a person who had a primary case during their infectious period. Tertiary cases were laboratory-confirmed cases in persons who had contact with a person who had a secondary case during their infectious period. Likely event-associated secondary cases were confirmed infections in patients who had contact with a person who had symptoms of COVID-19 and had attended the motorcycle rally but who were not tested. Likely event-associated tertiary cases were confirmed infections in patients who had contact with persons who had a likely event-associated secondary case during their infectious period.To investigate genomic similarity among COVID-19 cases, available SARS-CoV-2 RNA-positive clinical specimens were obtained from clinical laboratories, and whole genome sequencing was conducted at the MDH Public Health Laboratory on 38 specimens using previously described methods  primary event-associated cases,Forty-one (80%) interviewed patients with primary event-associated COVID-19 reported having close contactAmong the 35 patients with confirmed or likely event-associated secondary/tertiary COVID-19, 25 (71%) were symptomatic, with symptom onset dates during August 12–29 . The medSpecimens were obtained from 52 (60%) patients. Among these, 38 (73%) specimens (23 [61%] from primary and 15 [39%] from secondary and tertiary cases) were successfully sequenced, covering at least 98% of the SARS-CoV-2 genome. Six genetically similar clusters with known epidemiologic links were identified , five of which demonstrated secondary or secondary and tertiary transmission. Cluster A  includedOn August 5, MDH recommended through media events that motorcycle rally attendees quarantine for 14 days upon return and be tested 5–7 days later even if they were asymptomatic. Attendees and their close contacts with confirmed COVID-19 were instructed to self-isolate. Contacts of patients with confirmed COVID-19 were instructed to quarantine.Eighty-six Minnesota COVID-19 cases were associated with the South Dakota motorcycle rally; approximately one third of counties in Minnesota reported at least one case epidemiologically linked to this event. These findings highlight the far-reaching effects that gatherings in one area might have on another area. The motorcycle rally was held in a neighboring state that did not have policies regarding event size and mask use, underscoring the implications of policies within and across jurisdictions. The findings suggest that this rally not only had a direct impact on the health of attendees, but also led to subsequent SARS-CoV-2 transmission among household, social, and workplace contacts of rally attendees upon their return to Minnesota. Whole genome sequencing results supported the finding of secondary and tertiary transmission associated with this rally.The findings in this report are subject to at least three limitations. First, despite in-depth epidemiologic investigation, the findings represent an underestimate of the motorcycle rally’s impact in Minnesota and did not capture the impact within South Dakota or other states. Case interviews were voluntary, and patients could choose not to respond to certain questions. Ten patients reported having close contacts but refused to disclose additional details regarding these contacts. Therefore, it was not possible to identify all contacts of patients who attended the rally. Second, attendees and their contacts might not have been tested for SARS-CoV-2. Two rally attendees indicated that their contacts had COVID-19–like symptoms but did not plan to be tested. As such, the findings underrepresent the number of cases, close contacts, and secondary and tertiary cases. Finally, only 52 specimens were received at the MDH Public Health Laboratory because many testing laboratories do not retain or store specimens long-term. Among these specimens, only 38 were successfully sequenced. The lack of whole genome sequencing data from all cases hindered establishment of complete genetic relatedness for epidemiologic investigation.A large event in a neighboring state triggered chains of SARS-CoV-2 transmission within Minnesota. Other studies have shown that chains of transmission associated with gatherings are not uncommon within the United States (Gatherings present an opportunity for rapid spread of COVID-19.Following a 10-day motorcycle rally in South Dakota attended by approximately 460,000 persons, 51 confirmed primary event-associated cases, 21 secondary cases, and five tertiary cases were identified in Minnesota residents. An additional nine likely rally-associated secondary or tertiary cases occurred. Four patients were hospitalized, and one died. Genomic sequencing supported the associations with the motorcycle rally.The impact of gatherings as a source of virus transmission underscores the importance of reducing the number of attendees at gatherings, using face masks, and encouraging physical distancing to prevent ongoing transmission of SARS-CoV-2. Furthermore, these findings demonstrate the rationale for consistent mitigation measures across states.


Senile osteoporosis (SOP) is a worldwide age-related disease characterized by the loss of bone mass and decrease in bone strength. Bone mesenchymal stem cells (BMSCs) play an important role in the pathology of senile osteoporosis. Abnormal expression and regulation of non-coding RNA (ncRNA) are involved in a variety of human diseases. In the present study, we aimed to identify differentially expressed mRNAs and ncRNAs in senile osteoporosis patient-derived BMSCs via high-throughput transcriptome sequencing in combination with bioinformatics analysis. As a result, 415 mRNAs, 30 lncRNAs, 6 circRNAs and 27 miRNAs were found to be significantly changed in the senile osteoporosis group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were applied to analyze the function of differentially expressed mRNAs and ncRNAs. The circRNA–miRNA–mRNA regulatory network was constructed using the cytoHubba plugin based on the Cytoscape software. Interestingly, circRNA008876-miR-150-5p-mRNA was the sole predicted circRNA-miRNA-mRNA network. The differential expression profile of this ceRNA network was further verified by qRT-PCR. The biological function of this network was validated by overexpression and knockdown experiments. In conclusion, circRNA008876-miR-150-5p-mRNA could be an important ceRNA network involved in senile osteoporosis, which provides potential biomarkers and therapeutic targets for senile osteoporosis. Senile osteoporosis (SOP) is an age-related skeleton disease characterized by decreased bone mass and strength, which may lead to increased risk of fragility fractures . With thin vitro (Non-coding RNAs (ncRNAs) are non-protein coding transcripts served as crucial regulators of gene expression and cell fate , which hin vitro . HoweverTo screen the potential ncRNAs involved in senile osteoporosis and explore their molecular mechanism, we systematically analyze the expression profiles of miRNAs, lncRNAs, circRNAs and mRNAs in BMSCs of senile osteoporosis patients and normal individuals by whole transcriptome sequencing. According to the differentially expressed ncRNAs in the SOP group, we found that circRNA008876-miR-150-5p-mRNA represented the only distinctive ceRNA network, which was further validated by molecular biology experiments including qRT-PCR, western blot, overexpression and knockdown. In conclusion, our study established that circRNA008876-miR-150-5p-mRNA could be an important ceRNA network involved in senile osteoporosis, which provides potential biomarkers and therapeutic targets for senile osteoporosis.2. The third passage of hBMSCs were utilized for whole transcriptome sequencing. DMSO was ordered from Sangon Biotech (A503039). The entire research plan has been approved by the ethics committee of Shenzhen Second People’s Hospital .Human BMSCs (hBMSCs) of senile osteoporosis were isolated from the bone marrow of discarded bone tissue from male senile osteoporosis patients (79 ± 5.6 years) who underwent joint replacement and diagnosed as SOP with bone minerality tests using Dual Energy X-ray Absorptiometry . The norThree SOP patients-derived hBMSCs  and three normal individuals  derived hBMSCs were subjected to whole transcriptome sequencing. Total RNA was extracted from hBMSCs using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. After quantification and integrity of RNA samples were verified, rRNAs were removed from total RNA using Ribo-Zero rRNA Removal Kits (Illumina). Then, RNA libraries were constructed with TruSeq Stranded Total RNA Library Prep Kit (Illumina), and the two libraries were then sequenced on HiSeq-4000 (Illumina).The miRNA binding regions of ncRNA and mRNA were analyzed using miRanda software (version 0.10.80) and Targetscan software (Release 7.2). The DE miRNAs targeting DE lncRNA, circRNA and mRNA were predicted to form the lncRNA/circRNA-miRNA-mRNA networks.www.geneontology.org) in which mRNA were grouped according to biological processes (BPs), cellular components (CCs) and molecular functions (MFs). The related pathways were enriched by KEGG and presented in a scatter plot diagram. We were only interested in biological processes and KEGG pathways showing significance according to the following parameters: p < 0.05, FDR <0.05, and enrichment score >1.5.Gene function related to senile osteoporosis was analyzed by GO annotation derived from Gene Ontology  using 1ug total RNA after gDNA was erased according to the manufacturer’s instructions. Applied Biosystems 7500 Real-Time PCR Systems was applied to perform amplification reaction using SYBR Premix Ex Taq (Takara). HEK293T cells were co-transfected with recombinant plasmids (circRNA BR or circRNA BR Mut) and miR-337-3p mimics or negative control siRNAs (GenePharma). The recombinant plasmids were constructed with psiCHECK™-2 using the primers presented in ALP staining was applied to test the osteogenesis of BMSCs after transfection of overexpressing vector or siRNA of circRNA008876 for 7 days according to the ALP staining kit protocol . Photographs were obtained under microscope (Nikon TE 2000).post hoc test. All results are presented as mean ± SD. p < 0.05 was considered statistically significant.Statistical analyses were performed by the GraphPad Prism 8.0 and SPSS 22.0. Statistical significance of two or more biological replicates were performed by analysis of variance (ANOVA) and RUNX2, ALPL, COL1A1 and SPP1 were significantly reduced in BMSCs from SOP patients as compared to those from normal individuals, indicating the decreased osteogenic differentiation potential of BMSCs in SOP patients (The hBMSCs isolated from SOP patients (passage 0) significantly presented a fibroblastic morphology similar to normal hBMSCs . The surpatients .p value <0.05, 30 lncRNAs (23 upregulated and 7 downregulated), 6 circRNAs (3 upregulated and 3 downregulated), 27 miRNAs (23 upregulated and 4 downregulated) and 415 mRNAs (60 upregulated and 51 downregulated) were identified as differentially expressed (DE) genes between hBMSCs from SOP patients and normal ones. The hierarchical cluster analysis of lncRNA, circRNA, miRNA, and mRNA demonstrated significant differences between hBMSCs from normal (BN) and SOP (BP) groups  groups . CompletWe then performed GO enrichment analysis to reveal the key regulators and vital pathways potentially engaged by DE ncRNAs and mRNA in SOP. The top enriched terms regarding biological process (BP), cellular component (CC), and molecular function (MF) of four categories of RNA were shown in We also utilized the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to categorize the DE ncRNAs-targeted genes and mRNAs. The top 20 pathways of KEGG analysis for each category of DE ncRNAs or mRNAs were shown in Both lncRNA and circRNA are known to sponge miRNAs to prevent their interactions with target mRNAs, thus exhibiting competitive endogenous RNA (ceRNA) activity. To predict the functions of DE ncRNAs and mRNAs and uncover the potential ceRNA networks regulating the osteogenic differentiation of hBMSCs in SOP patients, lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks were constructed by using Targetscan and Miranda softwares.As shown in In the case of circRNA, only one ceRNA network, namely circRNA008876/miR-150-5p, was constructed . Among tRUNX2, ALPL, COL1A1, SPP1, and OSX by qPCR. Overexpression of circRNA008876 significantly upregulated the mRNA level of the osteogenic genes, while inhibition of circRNA008876 decreased their mRNA level  osteoporosis (SOP) is different from estrogen deficiency-induced postmenopausal (type I) osteoporosis (PMOP) caused by the activation of osteoclasts. Whereas the osteogenesis deficiency of hBMSCs represents an important pathogenic factor in senile osteoporosis , the undThe function of miRNA in osteogenesis has been extensively investigated in previous studies. Several up-regulated miRNAs of SOP in our study including miR-124-3p, miR-193a, miR-451a, and miR-144-3p have been proven as negative regulators in osteogenesis . FurtherFor example, lncRNA MEG3-miR-133a-3p axis has been suggested to be involved in PMOP through inhibiting osteogenic differentiation of BMSCs . In addiThe functions of DE ncRNAs and mRNAs in senile osteoporosis pathology was pedicted by GO enrichment  and KEGG pathways analyses. As we known, extracellular matrix mineralization is an essential progress in bone formation . Accordiin vivo pro-osteogenesis effect induced by circRNA008876 overexpression is unclear. To be noted, the abovementioned genes identified in this study, mainly including lncRNAs and circRNAs, did not overlap in previous studies. These results can be attributed to the differences in patients and ethnicity, which need further investigation.In general, the regulatory function of cell differentiation by ncRNAs are mainly through the ceRNA network. In this study, five lncRNA-miRNA-mRNA networks were constructed, among which miR-206, miR-381-3p were down-regulated, while miR-2355-5p, miR-181c-5p, and miR-150-5p were up-regulated. Previous reports suggested that miR-206 and miR-381-3p were able to inhibit osteogenic differentiation of BMSCs , which wIn the present study, we systematically explored the role of differently expressed ncRNAs and mRNAs in hBMSCs isolated from senile osteoporosis patients by whole transcriptome sequencing. The ceRNA regulatory networks of lncRNA/circRNA-miRNA-mRNA were constructed to further investigate the function of ncRNAs in senile osteoporosis. Among them, circRNA008876 was identified as a unique and critical circRNA in the occurrence and development of senile osteoporosis and might serve as a potential diagnostic biomarker for senile osteoporosis. Overall, our findings provide an insight into the molecular mechanisms of senile osteoporosis in the view of ncRNAs, which may offer novel therapeutic targets for clinic treatment of senile osteoporosis.


Patients with chronic kidney disease (CKD), including dialysis and transplant patients, are at greater risk of contracting SARS-CoV-2 due to kidney dysfunction and preexisting comorbidities. To date, a specific guideline on managing these high-risk patients infected with COVID-19 has not been established. As the current management of COVID-19 comprises mainly experimental drugs, the authors aim to provide information on dosing adjustments at different stages of kidney dysfunction and notable renal side effects. We performed a nonsystematical review of currently available COVID-19 drugs exploring several different clinical trial databases and search browsers. Several antivirals and monoclonal antibodies used in COVID-19 treatment require dosage adjustments in kidney dysfunction. In a global pandemic setting, nephrologists need to consider the appropriate dosage according to the renal function and closely monitor the side effects of different drug combinations to obtain the optimum therapeutic effect while avoiding further renal damage. Further studies are required to determine the safety and efficacy of these drugs in renal patients. With severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ability to bind with the angiotensin-converting enzyme 2 receptors, the kidney becomes one of the potential target organs. The presence of acute kidney injury (AKI) in COVID-19 is associated with disease severity and poor prognosis . MeanwhiNopsopon et al.  reportedPatients receiving in-center dialysis are at an additional two-fold risk of acquiring SARS-CoV-2 infection, with three to four times more significant risk of COVID-19-related hospitalization than those receiving home dialysis, contributed by increased contact with other patients and medical workers , 11. TheTo date, no clear guidelines exist for the management of COVID-19 in renal patients. The BNT162b2 mRNA and mRNA-1273 vaccines demonstrated promising protective effects and safe use in dialysis and transplant patients . So far,Corticosteroids decrease proinflammatory cytokines and suppress the “cytokine storm” involved in rapid clinical deterioration and death . The RECβ-cyclodextrin (SBECD), renally excreted, and may accumulate with reduced renal function. SBECD is readily eliminated by dialysis, which maintains its accumulation within a generally safe limit [Remdesivir inhibits viral RNA-dependent RNA polymerase (RdRp), leading to premature RNA termination and halting transcription . Severalfe limit . Remdesife limit .Lopinavir/ritonavir (LPN/r) is a protease inhibitor that interferes with normal viral replication and growth. LPN/r has been described to reduce viral load and acute respiratory distress syndrome . HoweverFavipiravir is another RdRp inhibitor currently under investigation for SARS-CoV-2 (NCT04425460 and NCT04336904). Favipiravir resulted in faster viral clearance and radiological improvement with fewer adverse events compared to LPN/r . SeveralDarunavir is a protease inhibitor that has been shown in silico to have high binding activity to SARS-CoV-2 protease. Cobicistat is added to prevent darunavir's inhibition by cytochrome P450 . DarunavDanoprevir/ritonavir is a potent inhibitor of hepatitis C virus protease that is repurposed for COVID-19. The early trial revealed that danoprevir/ritonavir is safe and well-tolerated, reducing viral replication and improving clinical symptoms . The effRibavirin is a guanosine analogue that disrupts RNA translation and viral replication and possesses antiviral activity against SARS-CoV-2 in vitro . RibavirOseltamivir is a prodrug that inhibits viral neuraminidase and is initially administered empirically in the Wuhan outbreak. However, further studies did not find its usefulness against SARS-CoV-2 since it lacks neuraminidase . CurrentAntimalarial agents, chloroquine (CQ) and hydroxychloroquine (HCQ), were among the first repurposed drugs in COVID-19 treatment. Their antiviral properties were related to the interference of SARS-CoV-2 binding to angiotensin-converting enzyme 2, replication and viral entry, as well as inhibition of cytokine release and CD8+ T cell activity . Their eAzithromycin and doxycycline are commonly used antibiotics repurposed as COVID-19 treatment due to their potential antiviral and immunomodulatory properties. The addition of azithromycin to HCQ has a synergistic effect in reducing viral load . HoweverThe FDA issued EUA for several anti-SARS-CoV-2 monoclonal antibodies as a treatment for outpatient mild-to-moderate COVID-19 patients who are at high risk for deterioration to severe disease or requiring hospitalization, including patients with CKD and those receiving immunosuppressive treatments .Bamlanivimab is a monoclonal antibody that binds to the spike protein of SARS-CoV-2 and prevents its entry into host cells. The BLAZE-1 study's interim results showed its benefit in lowering viral load and risk of hospitalization and death . In NoveCasirivimab and imdevimab (REGEN-COV) are recombinant human monoclonal antibodies that work in synergy to inhibit SARS-CoV-2 binding from host cells. REGEN-COV also received EUA to treat nonhospitalized COVID-19 patients. A phase 3 RCT reported a 70% relative reduction in hospitalization or death among outpatient COVID-19 patients . These dSotrovimab is a monoclonal antibody that binds to the spike of SARS-CoV-2 protein and has been granted EUA to treat outpatient mild-to-moderate COVID-19. The COMET-ICE trial reported the efficacy of sotrovimab in reducing the rate of hospitalization or death (80%) among the sotrovimab group compared to controls . No dosaTocilizumab is an antiinterleukin (IL)-6 receptor monoclonal antibody that results in inflammation reduction. An initial pilot study showed significant improvement in ferritin, C-reactive protein, and D-dimer levels after tocilizumab, with early use associated with increased survival in severe COVID-19 . HoweverBaricitinib is an inhibitor of Janus kinase that prevents immune activation and inflammation. As of November 2020, baricitinib, in combination with remdesivir, received EUA as COVID-19 treatment . The ACTα explicitly. Data from the SECURE-IBD [Adalimumab targets tumor necrosis factor (TNF)-CURE-IBD  and COVICURE-IBD  registriCURE-IBD . AdalimuCURE-IBD .Sarilumab is another anti-IL-6 receptor monoclonal antibody that modulates IL-6 levels associated with severe COVID-19 . Its effRenal involvement in COVID-19 presenting with hematuria and proteinuria is an independent predictor of in-hospital mortality . Two cenThe International Society of Peritoneal Dialysis guideline stated that COVID-19 management of PD patients is similar to other patients. Mild-to-moderate patients can continue PD, while severe or critical cases should be temporarily transferred to automated PD or continuous renal replacement therapies or intensify ultrafiltration if the patient decides to remain on PD. In addition, telehealth should be used extensively to communicate with PD patients remotely . Kidney In the setting of a global pandemic, a drug repurposing strategy is necessary to find effective therapy, creating a challenge for nephrologists in managing renal patients infected with COVID-19 due to the potential renal side effects. Most of the drugs in this review are not renally excreted and may be applied in patients with renal dysfunction. However, several antivirals and monoclonal antibody agents, such as remdesivir, favipiravir, ribavirin, oseltamivir, baricitinib, and tofacitinib, are renally eliminated, which require dosage adjustment, and their use is generally contraindicated in eGFR <30 ml/min. The available data did not show an increased risk of renal side effects in patients with AKI, CKD, and those on dialysis receiving remdesivir , 57. As Acute interstitial nephritis (AIN) is often associated with medications including lopinavir/ritonavir, azithromycin, and adalimumab, which warrants close monitoring of renal function timely discontinuation if AIN is suspected –61. Pote