Computational identification of differentially-expressed genes as suggested novel COVID-19 biomarkers: A bioinformatics analysis of expression profiles.

COVID-19 was declared a pandemic in March 2020, and since then, it has not stopped spreading like wildfire in almost every corner of the world, despite the many efforts made to stem its spread. SARS-CoV-2 has one of the biggest genomes among RNA viruses and presents unique characteristics that differentiate it from other coronaviruses, making it even more challenging to find a cure or vaccine that is efficient enough. This work aims, using RNA sequencing (RNA-Seq) data, to evaluate whether the expression of specific human genes in the host can vary in different grades of disease severity and to determine the molecular origins of the differences in response to SARS-CoV-2 infection in different patients. In addition to quantifying gene expression, data coming from RNA-Seq allow for the discovery of new transcripts, the identification of alternative splicing events, the detection of allele-specific expression, and the detection of post-transcriptional alterations. For this reason, we performed differential expression analysis on different expression profiles of COVID-19 patients, using RNA-Seq data coming from NCBI public repository, and we obtained the lists of all differentially expressed genes (DEGs) emerging from 7 experimental conditions. We performed a Gene Set Enrichment Analysis (GSEA) on these genes to find possible correlations between DEGs and known disease phenotypes. We mainly focused on DEGs coming out from the analysis of the contrasts involving severe conditions to infer any possible relation between a worsening of the clinical picture and an over-representation of specific genes. Based on the obtained results, this study indicates a small group of genes that result up-regulated in the severe form of the disease. EXOSC5, MESD, REXO2, and TRMT2A genes are not differentially expressed or not present in the other conditions, being for that reason, good biomarkers candidates for the severe form of COVID-19 disease. The use of specific over-expressed genes, whether up-regulated or down-regulated, which have an individual role in each different condition of COVID-19 as a biomarker, can assist in early diagnosis.

Corrigendum: Cardio-oncology in the COVID Era (Co & Co): The never-ending story.

[This corrects the article DOI: 10.3389/fcvm.2022.821193.].

ANMCO POSITION PAPER: cardio-oncology in the COVID era (CO and CO).

The COVID-19 pandemic and its impact on patients with cancer and cardiovascular disease have confirmed the particular vulnerability of these populations. Indeed, not only a higher risk of contracting the infection has been reported but also an increased occurrence of a more severe course and unfavourable outcome. Beyond the direct consequences of COVID-19 infection, the pandemic has an enormous impact on global health systems. Screening programmes and non-urgent tests have been postponed; clinical trials have suffered a setback. Similarly, in the area of cardiology care, a significant decline in STEMI accesses and an increase in cases of late presenting heart attacks with increased mortality and complication rates have been reported. Health care systems must therefore get ready to tackle the 'rebound effect' that will likely show a relative increase in the short- and medium-term incidence of diseases such as heart failure, myocardial infarction, arrhythmias, and cardio- and cerebrovascular complications. Scientific societies are taking action to provide general guidance and recommendations aimed at mitigating the unfavourable outcomes of this pandemic emergency. Cardio-oncology, as an emerging discipline, is more flexible in modulating care pathways and represents a beacon of innovation in the development of multi-specialty patient management. In the era of the COVID-19 pandemic, cardio-oncology has rapidly modified its clinical care pathways and implemented flexible monitoring protocols that include targeted use of cardiac imaging, increased use of biomarkers, and telemedicine systems. The goal of these strategic adjustments is to minimize the risk of infection for providers and patients while maintaining standards of care for the treatment of oncologic and cardiovascular diseases. The aim of this document is to evaluate the impact of the pandemic on the management of cardio-oncologic patients with the-state-of-the-art knowledge about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease (COVID-19) in order to optimize medical strategies during and after the pandemic.

Cardio-Oncology in the COVID Era (Co & Co): The Never Ending Story.

The pathophysiology of some non-communicable diseases (NCDs) such as hypertension, cardiovascular disease (CVD), diabetes, and cancer includes an alteration of the endothelial function. COVID-19 is a pulmonary and vascular disease with a negative impact on patients whose damaged endothelium is particularly vulnerable. The peculiar SARS-CoV-2-induced "endothelitis" triggers an intriguing immune-thrombosis that affects both the venous and arterial vascular beds. An increased liability for infection and an increased likelihood of a worse outcome have been observed during the pandemic in patients with active cancer and in cancer survivors. "Overlapping commonalities" between COVID-19 and Cardio-Oncology have been described that include shared phenotypes of cardiovascular toxicities such as left ventricular dysfunction, ischemic syndromes, conduction disturbances, myocarditis, pericarditis and right ventricular failure; shared pathophysiologic mechanisms such as inflammation, release of cytokines, the renin-angiotensin-aldosterone-pathway, coagulation abnormalities, microthrombosis and endothelial dysfunction. For these features and for the catalyst role of NCDs (mainly CVD and cancer), we should refer to COVID-19 as a "syndemic." Another challenging issue is the persistence of the symptoms, the so-called "long COVID" whose pathogenesis is still uncertain: it may be due to persistent multi-organ viral attacks or to an abnormal immune response. An intensive vaccination campaign is the most successful pharmacological weapon against SARS-CoV-2, but the increasing number of variants has reduced the efficacy of the vaccines in controlling SARS-CoV-2 infections. After a year of vaccinations we have also learned more about efficacy and side-effects of COVID-19 vaccines. An important byproduct of the COVID-19 pandemic has been the rapid expansion of telemedicine platforms across different care settings; this new modality of monitoring cancer patients may be useful even in a post pandemic era. In this paper we analyze the problems that the cardio-oncologists are facing in a pandemic scenario modified by the extensive vaccination campaign and add actionable recommendations derived from the ongoing studies and from the syndemic nature of the infection.

Corrigendum: Cardio-Oncology in the COVID Era (Co & Co): The Never Ending Story.

[This corrects the article DOI: 10.3389/fcvm.2022.821193.].

Lung ultrasound in the follow-up of severe COVID-19 pneumonia: six months evaluation and comparison with CT.

While lung ultrasonography (LUS) proved to be a useful diagnostic and prognostic tool in acute phase of COVID 19 pneumonia, its role in detecting long-term pulmonary sequelae has yet to be explored. In our prospective observational study we assessed the potential of LUS in detecting the presence of computed tomography (CT) fibrotic-like changes after 6 months from COVID-19 pneumonia. Patients who were discharged with a diagnosis of severe COVID-19 pneumonia were enrolled. After 6 months from hospital discharge they underwent LUS, chest CT scan and pulmonary function tests. A logistic regression analysis was performed to assess the association between presence of symptoms, LUS score and diffusing capacity for carbon monoxide (DLCO) at 6-month after hospital discharge and CT scan fibrotic-like changes. A second logistic model was performed to assess the value of some predefined baseline factors (age, sex, worst PaO2/FiO2, ventilator support, worst CRP value, worst D-dimer value and worst LUS score during hospitalization) to predict fibrotic-like changes on 6-month CT scan. Seventy-four patients were enrolled in the study. Twenty-four (32%) showed lung abnormalities suitable for fibrotic-like changes. At multivariate logistic regression analysis LUS score after 6 months from acute disease was significantly associated with fibrotic-like pattern on CT scan. The second logistic model showed that D-dimer value was the only baseline predictive variable of fibrotic-like changes at multivariate analysis. LUS performed after 6 months from severe COVID-19 pneumonia may be a promising tool for detection and follow-up of pulmonary fibrotic sequelae.

Model verification tools: a computational framework for verification assessment of mechanistic agent-based models.

BACKGROUND: Nowadays, the inception of computer modeling and simulation in life science is a matter of fact. This is one of the reasons why regulatory authorities are open in considering in silico trials evidence for the assessment of safeness and efficacy of medicinal products. In this context, mechanistic Agent-Based Models are increasingly used. Unfortunately, there is still a lack of consensus in the verification assessment of Agent-Based Models for regulatory approval needs. VV&UQ is an ASME standard specifically suited for the verification, validation, and uncertainty quantification of medical devices. However, it can also be adapted for the verification assessment of in silico trials for medicinal products. RESULTS: Here, we propose a set of automatic tools for the mechanistic Agent-Based Model verification assessment. As a working example, we applied the verification framework to an Agent-Based Model in silico trial used in the COVID-19 context. CONCLUSIONS: Using the described verification computational workflow allows researchers and practitioners to easily perform verification steps to prove Agent-Based Models robustness and correctness that provide strong evidence for further regulatory requirements.

A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets.

The COVID-19 pandemic has highlighted the need to come out with quick interventional solutions that can now be obtained through the application of different bioinformatics software to actively improve the success rate. Technological advances in fields such as computer modeling and simulation are enriching the discovery, development, assessment and monitoring for better prevention, diagnosis, treatment and scientific evidence generation of specific therapeutic strategies. The combined use of both molecular prediction tools and computer simulation in the development or regulatory evaluation of a medical intervention, are making the difference to better predict the efficacy and safety of new vaccines. An integrated bioinformatics pipeline that merges the prediction power of different software that act at different scales for evaluating the elicited response of human immune system against every pathogen is proposed. As a working example, we applied this problem solving protocol to predict the cross-reactivity of pre-existing vaccination interventions against SARS-CoV-2.

[ANMCO Position paper: Cardio-oncology in the COVID-19 era]. / Position paper ANMCO: Cardio-oncologia in era COVID-19.

The COVID-19 pandemic and its impact on patients with cancer and cardiovascular disease have confirmed the particular vulnerability of this population. Indeed, not only a higher risk of contracting the infection has been reported, but also an increased occurrence of a more severe course and unfavorable outcome. Beyond the direct consequences of COVID-19, the pandemic has an enormous impact on global health systems. Screening programs and non-urgent tests have been postponed; clinical trials have suffered a setback. Similarly, in the area of cardiology care, a significant decline in ST-elevation myocardial infarction accesses and an increase in cases of late presenting heart attacks with increased mortality and complication rates have been reported. Health care systems must therefore get ready to tackle the "rebound effect" that will likely show a relative increase in the short and medium term incidence of diseases such as heart failure, myocardial infarction, arrhythmias and cardio- and cerebrovascular complications. Scientific societies are taking action to provide general guidance and recommendations aimed at mitigating the unfavorable outcomes of this pandemic emergency. Cardio-oncology, as an emerging discipline, is more flexible in modulating care pathways and represents a beacon of innovation in the development of multi-specialty patient management. In the era of the COVID-19 pandemic, cardio-oncology has rapidly modified its clinical care pathways and implemented flexible monitoring protocols that include targeted use of cardiac imaging, increased use of biomarkers, and telemedicine systems. The goal of these strategic adjustments is to minimize the risk of infection for providers and patients while maintaining standards of care for the treatment of oncologic and cardiovascular diseases. The aim of this position paper is to evaluate the impact of the COVID-19 pandemic on the management of cardio-oncologic patients with the-state-of-the-art knowledge about SARS-CoV-2 and COVID-19 in order to optimize medical strategies during and after the pandemic.

Immune-checkpoint inhibitors from cancer to COVID­19: A promising avenue for the treatment of patients with COVID­19 (Review).

The severe acute respiratory syndrome associated coronavirus­2 (SARS­CoV­2) poses a threat to human life worldwide. Since early March, 2020, coronavirus disease 2019 (COVID­19), characterized by an acute and often severe form of pneumonia, has been declared a pandemic. This has led to a boom in biomedical research studies at all stages of the pipeline, from the in vitro to the clinical phase. In line with this global effort, known drugs, currently used for the treatment of other pathologies, including antivirals, immunomodulating compounds and antibodies, are currently used off­label for the treatment of COVID­19, in association with the supportive standard care. Yet, no effective treatments have been identified. A new hope stems from medical oncology and relies on the use of immune­checkpoint inhibitors (ICIs). In particular, amongst the ICIs, antibodies able to block the programmed death­1 (PD­1)/PD ligand-1 (PD­L1) pathway have revealed a hidden potential. In fact, patients with severe and critical COVID­19, even prior to the appearance of acute respiratory distress syndrome, exhibit lymphocytopenia and suffer from T­cell exhaustion, which may lead to viral sepsis and an increased mortality rate. It has been observed that cancer patients, who usually are immunocompromised, may restore their anti­tumoral immune response when treated with ICIs. Moreover, viral-infected mice and humans, exhibit a T­cell exhaustion, which is also observed following SARS­CoV­2 infection. Importantly, when treated with anti­PD­1 and anti­PD­L1 antibodies, they restore their T­cell competence and efficiently counteract the viral infection. Based on these observations, four clinical trials are currently open, to examine the efficacy of anti­PD­1 antibody administration to both cancer and non­cancer individuals affected by COVID­19. The results may prove the hypothesis that restoring exhausted T­cells may be a winning strategy to beat SARS­CoV­2 infection.

In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform.

BACKGROUND: SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects. RESULTS: We present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2. CONCLUSIONS: In silico trials are showing to be powerful weapons in predicting immune responses of potential candidate vaccines. Here, UISS has been extended to be used as an in silico trial platform to speed-up and drive the discovery pipeline of vaccine against SARS-CoV-2.

A multistage combined approach to promote diabetic wound healing in COVID-19 era.

When diabetes mellitus is not properly controlled with drugs and a healthy lifestyle, it exposes patients with advanced peripheral arterial disease or critical limb ischaemia (CLI) to the most serious complications, in particular lower limb ulcers. Surgical or endovascular treatments represent the first line of intervention; in addition, the adequate management of ulcers can guarantee not only a faster wound healing but also the improvement of the patient's prognosis. To speed up this process, negative pressure wound therapy (NPWT), platelet-rich plasma (PRP), and other advanced moist wound dressing have been proposed. During Coronavirus disease 2019 (COVID-19) pandemic, many patients with CLI and diabetes mellitus had difficult access to advanced treatments with a significant reduction in life expectancy. We report the cases of patients with non-healing ulcers and CLI treated with an empiric multistage approach after successful endovascular revascularisation; the postoperative course was eventful in all patients, and foot ulcers are currently in an advanced state of healing. The association between adequate revascularisation, systemic anti-inflammatory, and antibiotic therapy with the multistage advanced medications ensures healing of ulcers, limb salvage, and improvement of patient prognosis.