Comprehensive analysis of two potential novel SARS-CoV-2 entries, TMPRSS2 and IFITM3, in healthy individuals and cancer patients

NYC metropolitan wastewater reveals links between SARS-CoV-2 amino acid mutations and disease outcomes

Since late 2020, diverse SARS-CoV-2 variants with enhanced infectivity and transmissibility have emerged. In contrast to the focus on amino acid mutations in the spike protein, mutations in non-spike proteins and their associated impacts remain relatively understudied. New York City metropolitan wastewater revealed over 60 % of the most frequently occurring amino acid mutations in regions outside the spike protein. Strikingly, ~50 % of the mutations detected herein remain uncharacterized for functional impacts. Our results suggest that there are several understudied mutations within non-spike proteins N, ORF1a, ORF1b, ORF9b, and ORF9c, that could increase transmissibility, and infectivity among human populations. We also demonstrate significant correlations of P314L, D614G, T95I, G50E, G50R, G204R, R203K, G662S, P10S, and P13L with documented mortality rates, hospitalization rates, and percent positivity suggesting that amino acid mutations are likely to be indicators of COVID-19 infection outcomes.

COVID-19-The Shift of Homeostasis into Oncopathology or Chronic Fibrosis in Terms of Female Reproductive System Involvement

The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus remains a global public health concern due to the systemic nature of the infection and its long-term consequences, many of which remain to be elucidated. SARS-CoV-2 targets endothelial cells and blood vessels, altering the tissue microenvironment, its secretion, immune-cell subpopulations, the extracellular matrix, and the molecular composition and mechanical properties. The female reproductive system has high regenerative potential, but can accumulate damage, including due to SARS-CoV-2. COVID-19 is profibrotic and can change the tissue microenvironment toward an oncogenic niche. This makes COVID-19 and its consequences one of the potential regulators of a homeostasis shift toward oncopathology and fibrosis in the tissues of the female reproductive system. We are looking at SARS-CoV-2-induced changes at all levels in the female reproductive system.

Molecular mechanisms involved in pathogenicity of SARS-CoV-2: Immune evasion and implications for therapeutic strategies

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the outbreak of unusual viral pneumonia that emerged in late 2019 in the city of Wuhan, China. Since then, because of its high transmission and pathogenic potential it spread almost all over the world causing the pandemic, as an extraordinary threat to the world public health. Rapid activation of a well-orchestrated and functional immune system with its both arms innate and adaptive immune response is pivotal to eradication of the disease caused by this coronavirus (COVID-19). Therefore, in this review are summarized the most recent data on complex molecular mechanisms involved in the innate and adaptive immune response to combat COVID-19. In addition to widely used vaccines against SARS-CoV-2, because of the induction of short-lived immunity and appearance of variants of concern (VOCs), there will be also discussed newly developed strategies to target different viral proteins, which are not prone to frequent mutations. Obviously, SARS-CoV-2 cannot evade the effect of these novel drugs and therefore they show a great promise as an antiviral therapy not only in COVID-19 but also in future viral outbreaks.

Comprehensive Analysis of the Novel Omicron Receptor AXL in Cancers

The SARS-CoV-2 is constantly mutating, and the new coronavirus such as Omicron has spread to many countries around the world. Anexelekto (AXL) is a transmembrane protein with biological functions such as promoting cell growth, migration, aggregation, metastasis and adhesion, and plays an important role in cancers and coronavirus disease 2019 (COVID-19). Unlike angiotensin-converting enzyme 2 (ACE2), AXL was highly expressed in respiratory system cells. In this study, we verified the AXL expression in cancer and normal tissues and found AXL expression was strongly correlated with cancer prognosis, tumor mutation burden (TMB), the microsatellite instability (MSI) in most tumor types. Immune infiltration analysis also demonstrated that there was an inextricable link between AXL expression and immune scores in cancer patients, especially in BLCA, BRCA and CESC. The NK-cells, plasmacytoid dendritic cells, myeloid dendritic cells, as one of the important components of the tumor microenvironment, were highly expressed AXL. In addition, AXL-related tumor neoantigens were identified and might provide the novel potential targets for tumor vaccines or SARS-Cov-2 vaccines research in cancer patients.

Molecular Landscape of Lung Epithelium Contributes to High Severity and Comorbidities for COVID-19 and Lung Cancer

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The heterogeneous and complex nature of cancer is extensively revealed at molecular, genetic, and tissue microenvironment levels. Currently, co-occurrence of coronavirus disease 2019 (COVID-19) to lung cancer patients and severity of infections by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been understood at preclinical and clinical levels. However, molecular and cellular insights are not discussed in those papers that support the increased COVID-19 severity and comorbidities in several cancer types, including lung cancer patients. Therefore, this perspective highlights the basis of high severity and comorbidities among lung cancer patients infected by COVID-19 with an emphasis on translational aspects.

Role of Genetic Variants and Host Polymorphisms on COVID‐19: From Viral Entrance Mechanisms to Immunological Reactions

Coronavirus disease 2019 (COVID‐19), caused by a highly pathogenic emerging virus, is called severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Knowledge regarding the pathogenesis of this virus is in infancy; however, investigation on the pathogenic mechanisms of the SARS‐CoV‐2 is underway. In COVID‐19, one of the most remarkable characteristics is the wide range of disease manifestation and severity seen across individuals of different ethnic backgrounds and geographical locations. To effectively manage COVID‐19 in the populations, beyond SARS‐CoV‐2 detection, serological response assessment, and analytic techniques, it is critical to obtain knowledge about at‐risk individuals and comprehend the identified variations in the disease's severity in general and also in the populations' levels. Several factors can contribute to variation in disease presentation, including population density, gender and age differences, and comorbid circumstances including diabetes mellitus, hypertension, and obesity. Genetic factors presumably influence SARS‐CoV‐2 infection susceptibility. Besides this, COVID‐19 has also been linked with a higher risk of mortality in men and certain ethnic groups, revealing that host genetic characteristics may affect the individual risk of death. Also, genetic variants involved in pathologic processes, including virus entrance into cells, antiviral immunity, and inflammatory response, are not entirely understood. Regarding SARS‐CoV‐2 infection characteristics, the present review suggests that various genetic polymorphisms influence virus pathogenicity and host immunity, which might have significant implications for understanding and interpreting the matter of genetics in SARS‐CoV‐2 pathogenicity and customized integrative medical care based on population investigation.

Genetic factors presumably influence SARS‐CoV‐2 infection susceptibility.

Genetic variants were involved in the pathologic processes of SARS‐CoV‐2 infection.

Various genetic polymorphisms influence virus pathogenicity and host immunity.

Human leukocyte antigens (HLAs) may play a vital role in SARS‐CoV‐2 susceptibility.

Polymorphisms in several genes such as IL‐6, TMPRSS2, IFITM3, CD26, ACE, and DBP were associated with the COVID‐19 severity.

Interactions of renin-angiotensin system and COVID-19: the importance of daily rhythms in ACE2, ADAM17 and TMPRSS2 expression

Angiotensin-converting enzyme 2 (ACE2) was identified as a molecule that mediates the cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several membrane molecules of the host cell must cooperate in this process. While ACE2 serves in a membrane receptor-mediating interaction with the surface spike (S) glycoprotein of SARS-CoV-2 located on the virus envelope, enzyme A disintegrin and metalloproteinase 17 (ADAM17) regulates ACE2 availability on the membrane and transmembrane protease serine 2 (TMPRSS2) facilitates virus-cell membrane fusion. Interestingly, ACE2, ADAM17 and TMPRSS2 show a daily rhythm of expression in at least some mammalian tissue. The circadian system can also modulate COVID-19 progression via circadian control of the immune system (direct, as well as melatonin-mediated) and blood coagulation. Virus/ACE2 interaction causes ACE2 internalization into the cell, which is associated with suppressed activity of ACE2. As a major role of ACE2 is to form vasodilatory angiotensin 1-7 from angiotensin II (Ang II), suppressed ACE2 levels in the lung can contribute to secondary COVID-19 complications caused by up-regulated, pro-inflammatory vasoconstrictor Ang II. This is supported by the positive association of hypertension and negative COVID-19 prognosis although this relationship is dependent on numerous comorbidities. Hypertension treatment with inhibitors of renin-angiotensin system does not negatively influence prognosis of COVID-19 patients. It seems that tissue susceptibility to SARS-CoV-2 shows negative correlation to ACE2 expression. However, in lungs of infected patient, a high ACE2 expression is associated with better outcome, compared to low ACE2 expression. Manipulation of soluble ACE2 levels is a promising COVID-19 therapeutic strategy.

Host factors: Implications in immunopathogenesis of COVID-19

Coronavirus disease 2019 (COVID-19) is a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is more serious in people with underlying diseases, but the cause of healthy people with progressive disease is largely unknown. Host genetic factors such as ACE2 variants, IFITM-3, HLA, TMRSS2, and furin polymorphisms appear to be one of the agents involved in the progression of the COVID-19 and outcome of the disease. This review discusses the general characteristics of SARS-CoV-2, including viral features, receptors, cell entry, clinical findings, and the main human genetic factors that may contribute to the pathogenesis of COVID-19 and get the patients' situation more complex. Further knowledge in this context may help to find a way to prevent and treat this viral pneumonia.

Impact of androgen deprivation therapy on mortality of prostate cancer patients with COVID-19: a propensity score-based analysis

BACKGROUND

Previous studies hypothesized that androgen deprivation therapy (ADT) may reduce severe acute respiratory syndrome coronavirus 2 (SARS-COV2) infectivity. However, it is unknown whether there is an association between ADT and a higher survival in prostate cancer patients with COVID-19.

METHODS

We performed a retrospective analysis of prostate cancer (PC) patients hospitalized to treat COVID-19 in Brazil's public health system. We compared patients with the active use of ADT versus those with non-active ADT, past use. We constructed propensity score models of patients in active versus non-active use of ADT. All variables were used to derive propensity score estimation in both models. In the first model we performed a pair-matched propensity score model between those under active and non-active use of ADT. To the second model we initially performed a multivariate backward elimination process to select variables to a final inverse-weight adjusted with double robust estimation model.

RESULTS

We analyzed 199 PC patients with COVID-19 that received ADT. In total, 52.3% (95/199) of our patients were less than 75 years old, 78.4% (156/199) were on active ADT, and most were using a GnRH analog (80.1%; 125/156). Most of patients were in palliative treatment (89.9%; 179/199). Also, 63.3% of our cohort died from COVID-19. Forty-eight patients under active ADT were pair matched against 48 controls (non-active ADT). All patients (199) were analyzed in the double robust model. ADT active use were not protective factor in both inverse-weight based propensity score (OR 0.70, 95% CI 0.38-1.31, P = 0.263), and pair-matched propensity score (OR 0.67, 95% CI 0.27-1.63, P = 0.374) models. We noticed a significant imbalance in the propensity score of patients in active and those in non-active ADT, with important reductions in the differences after the adjustments.

CONCLUSIONS

The active use of ADT was not associated with a reduced risk of death in patients with COVID-19.

A nomogram predicting severe COVID-19 based on a large study cohort from China

BACKGROUND

The use of accurate prediction tools and early intervention are important for addressing severe coronavirus disease 2019 (COVID-19). However, the prediction models for severe COVID-19 available to date are subject to various biases. This study aimed to construct a nomogram to provide accurate, personalized predictions of the risk of severe COVID-19.

METHODS

This study was based on a large, multicenter retrospective derivation cohort and a validation cohort. The derivation cohort consisted of 496 patients from Jiangsu Province, China, between January 10, 2020, and March 15, 2020, and the validation cohort contained 105 patients from Huangshi, Hunan Province, China, between January 21, 2020, and February 29, 2020. A nomogram was developed with the selected predictors of severe COVID-19, which were identified by univariate and multivariate logistic regression analyses. We evaluated the discrimination of the nomogram with the area under the receiver operating characteristic curve (AUC) and the calibration of the nomogram with calibration plots and Hosmer-Lemeshow tests.

RESULTS

Three predictors, namely, age, lymphocyte count, and pulmonary opacity score, were selected to develop the nomogram. The nomogram exhibited good discrimination (AUC 0.93, 95% confidence interval [CI] 0.90-0.96 in the derivation cohort; AUC 0.85, 95% CI 0.76-0.93 in the validation cohort) and satisfactory agreement.

CONCLUSIONS

The nomogram was a reliable tool for assessing the probability of severe COVID-19 and may facilitate clinicians stratifying patients and providing early and optimal therapies.

Immunogenetic Predictors of Severe COVID-19

According to an analysis of published data, only 20% of patients with the new coronavirus infection develop severe life-threatening complications. Currently, there are no known biomarkers, the determination of which before the onset of the disease would allow assessing the likelihood of its severe course. The purpose of this literature review was to analyze possible genetic factors characterizing the immune response to the new coronavirus infection that could be associated with the expression of angiotension-converting enzyme 2 (ACE-2) and related proteins as predictors of severe Corona virus disease 2019 (COVID-19). We analyzed original articles published in Medline, PubMed and Scopus databases from December 2019 to November 2020. For searching articles, we used the following keywords: New coronavirus infection, Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), COVID-19, severe course, complications, thrombosis, cytokine storm, ACE-2, biomarkers. In total, 3714 publications were selected using the keywords, of which 8 were in congruence with all the criteria. The literature analysis of the association of immunogenic characteristics and the expression of ACE-2 and related proteins with the development of severe COVID-19 revealed following genetic factors: HLA-B*46:01 genotype, CXCR6 gene hypoexpression, CCR9 gene expression, TLR7, rs150892504 mutations in the ERAP2 gene, overexpression of wild-type ACE-2, TMPRSS2 and its different polymorphisms. Genes, associated with the severe course, are more common among men. According to the analysis data, it can be assumed that there are population differences. However, the diagnostic significance of the markers described must be confirmed with additional clinical studies.

Cross talk between COVID-19 and breast cancer

Cancer patients are more susceptible for COVID-19; however, the prevalence of COVID-19 in different types of cancer is still inconsistent and inconclusive. Here, we delineate the intricate relationship between breast cancer and COVID-19. Breast cancer and COVID-19 share involvement of common comorbidities, hormonal signalling pathways, gender differences, rennin-angiotensin system (RAS), angiotensin-converting enzyme-2 (ACE-2), transmembrane protease serine 2 (TMPRSS2) and dipeptidyl peptidase-IV (DPP-IV). We also shed light on the possible effects of therapeutic modalities of COVID-19 on breast cancer outcomes. Briefly, we conclude that breast cancer patients are more susceptible for COVID-19 in comparison with their normal counterparts. Women are more resistant for the occurrence and severity of COVID-19. Increased expression of ACE2 and TMPRSS2 are being correlated with occurrence and severity of COVID-19, but higher expression of ACE2 and lower expression of TMPRSS2 are prognostic markers for overall and disease free survival in breast cancer. The ACE2 inhibitors and ibuprofen therapies for COVID-19 treatment may aggravate the clinical condition of the breast cancer patients through chemo-resistance and metastasis. Most of the available therapeutic modalities for COVID-19 were also found to exert positive effects on breast cancer outcomes. Besides drugs in clinical trend, TMPRSS2 inhibitors, estrogen supplementation, androgen deprivation and DPP-IV inhibitors may also be used to treat breast cancer patients infected with SARS-CoV-2. However, drug-drug interactions suggest that some of the drugs used for the treatment of COVID-19 may modulate the drug metabolism of anticancer therapies which may leads to adverse drug reaction events.