Balancing macrophage activation in health and disease:The epigenetic, transcriptional and immunometabolic insights

Macrophages are crucial components of the innate immune system. Macrophages manifest extreme heterogeneity in response to the local milieu. The plasticity and diversity of macrophages are pivotal for host defense against pathogenic insults and the maintenance of tissue homeostasis. However, dysregulated macrophage activation can lead to acute and chronic inflammatory disorders, such as COVID-19, atherosclerosis, and inflammatory bowel diseases. The activation states of macrophages are shaped by various mechanisms, such as epigenetic modifications, transcriptional regulation, and metabolic alterations. This dissertation provides comprehensive transcriptomic and metabolomic profiles of widely used macrophage models. We build a macrophage activation classifier and identify key regulatory network modules constructed by unbiased approaches. Furthermore, our data delivers insights into targeting metabolic pathways, kinases, and epigenetic enzymes for therapeutic development against various diseases. These findings advance our knowledge in macrophage activation and pathogenesis of different diseases and disorders that can support future studies from basic science to translational medicine and from bench to bedside

COVID-19 salivary protein profile: unravelling molecular aspects of SARS-CoV-2 infection

COVID-19 is the most impacting global pandemic of all time, with over 600 million infected and 6.5 million deaths worldwide, in addition to an unprecedented economic impact. Despite the many advances in scientific knowledge about the disease, much remains to be clarified about the molecular alterations induced by SARS-CoV-2 infection. In this work, we present a hybrid proteomics and in silico interactomics strategy to establish a COVID-19 salivary protein profile. Data are available via ProteomeXchange with identifier PXD036571. The differential proteome was narrowed down by the Partial Least-Squares Discriminant Analysis and enrichment analysis was performed with FunRich. In parallel, OralInt was used to determine interspecies Protein-Protein Interactions between humans and SARS-CoV-2. Five dysregulated biological processes were identified in the COVID-19 proteome profile: Apoptosis, Energy Pathways, Immune Response, Protein Metabolism and Transport. We identified 10 proteins (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10 and PHB2) that had never been associated with SARS-CoV-2 infection, representing new evidence of the impact of COVID-19. Interactomics analysis showed viral influence on the host immune response, mainly through interaction with the degranulation of neutrophils. The virus alters the host’s energy metabolism and interferes with apoptosis mechanisms.info:eu-repo/semantics/publishedVersio

A Novel Prophylaxis Strategy Using Liposomal Vaccine Adjuvant CAF09b Protects against Influenza Virus Disease

The SARS-CoV-2 pandemic caused a massive health and societal crisis, although the fast development of effective vaccines reduced some of the impact. To prepare for future respiratory virus pandemics, a pan-viral prophylaxis could be used to control the initial virus outbreak in the period prior to vaccine approval. The liposomal vaccine adjuvant CAF®09b contains the TLR3 agonist polyinosinic:polycytidylic acid, which induces a type I interferon (IFN-I) response and an antiviral state in the affected tissues. When testing CAF09b liposomes as a potential pan-viral prophylaxis, we observed that intranasal administration of CAF09b liposomes to mice resulted in an influx of innate immune cells into the nose and lungs and upregulation of IFN-I-related gene expression. When CAF09b liposomes were administered prior to challenge with mouse-adapted influenza A/Puerto Rico/8/1934 virus, it protected from severe disease, although the virus was still detectable in the lungs. However, when CAF09b liposomes were administered after influenza challenge, the mice had a similar disease course to controls. In conclusion, CAF09b may be a suitable candidate as a pan-viral prophylactic treatment for epidemic viruses, but must be administered prior to virus exposure to be effective.publishedVersio

Two fatal cases of acute liver failure due to HSV-1 infection in COVID-19 patients following immunomodulatory therapies.

We reported two fatal cases of acute liver failure secondary to Herpes Simplex Virus 1 infection in COVID-19 patients, following tocilizumab and corticosteroid therapy. Screening for and prompt recognition of Herpes Simplex Virus 1 reactivation in these patients, undergoing immunomodulatory treatment, may have potentially relevant clinical consequences

Anti-IFNαR Mabs for the treatment of systemic lupus erythematosus

INTRODUCTION: The type 1 interferon pathway is known to play a role in the immunopathology of systemic lupus erythematosus (SLE). As a result, biologic agents targeting this pathway have been developed and are currently being investigated in clinical trials. AREAS COVERED: We review the biologic agents which have been developed to antagonize type I interferons in SLE. We focus on anifrolumab, a type I interferon receptor antagonist, and consider the complexities of defining efficacy in SLE clinical trials. EXPERT OPINION: Anifrolumab shows promise as an addition to the SLE therapeutic armamentarium. Despite discordant results between its two phase III studies, there is a convincing suggestion of benefit in both trials to encourage the view that this approach might be effective. Data acquired thus far look particularly useful for cutaneous disease. We await data on its effect on renal, pulmonary, cardiac, and central nervous system involvement, on patient reported outcomes, and its safety and efficacy with long-term use

Saliva as a non-invasive diagnostic tool: COVID-19 and T2DM as case-study

Saliva has nowadays a vast research background of how it can mirror the body's health status. Specific salivary biomarkers have been already suggested for multiple diseases and is particularly useful for detecting infectious diseases. We focused on the importance of having a non-invasive, painless and self-collected fluid to study different aspects of two known pandemic diseases: COVID-19 and Type 2 Diabetes Mellitus. COVID-19 is the most impacting global pandemic of all time requiring frequent testing of populations. The necessity to identify cost-effective strategies for the detection of SARS-CoV-2 outbreak became a priority. Nasopharyngeal samples were considered the sampling golden standard but require a healthcare professional to collect the sample causing discomfort and pain to the patient. As saliva has proved successful in SARS-CoV-2 detection, a pooling strategy could be a good approach to decrease the number of individual tests and hazardous material waste which is also beneficial for the environment. We have tested this strategy on two hundred and seventy-nine saliva samples with pools of 10 and 20 randomized samples through RT-PCR. Cycle Threshold of the genes detected was 29.7. Consecutive reactions analysis of positive samples showed an equivalent cycle threshold average (p 0.05). We concluded that saliva-pool samples allowed effective SARS-CoV-2 screening on 10-sample and 20-sample pools. Our strategy was successfully applied in population-wide testing of more than 2000 individuals, showing that it is possible to use pooled saliva as diagnostic fluid for SARS-CoV-2 infection. The SARS-CoV-2 detection is well established with reliable methodologies including saliva as a detection fluid. In the opposite direction are the molecular alterations induced by this infectious virus which remain elusive. We developed a hybrid proteomics and in silico interactomics strategy to establish a COVID-19 salivary protein profile. The most distinctive proteins between healthy and COVID-19 samples were defined with the Partial Least-Squares Discriminant Analysis and the enrichment analysis was performed with FunRich software. In parallel, Protein-Protein virus-host interactome was identified with OralInt algorithm. Five dysregulated biological processes were identified in the COVID-19 proteome profile: Apoptosis, Energy Pathways, Immune Response, Protein Metabolism, and Transport. We identified 10 proteins (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10, and PHB2) that had never been associated with SARS-CoV-2 infection, representing new evidence for the molecular profile behind COVID-19. Interactomics analysis showed viral influence on the host immune response, mainly through interaction with the degranulation of neutrophils. From our results, we can conclude that the virus also alters the host’s energy metabolism and interferes with apoptosis mechanisms. Type 2 Diabetes Mellitus is a chronic metabolic disease and is a major health risk due to its characteristic long-term complications. It is estimated that about 537 million people live with diabetes worldwide and will continue to increase. Diagnosis and glucose monitoring in diabetes are well established. However, monitoring the many of diabetes complications remains a challenge, compromising patients' prognosis and quality of life. We established a hybrid strategy that identified salivary markers of T2DM and its complications. From the functional analysis we highlight metabolic processes, response to stimulus, immune system processes and signalling as disrupted biological processes by the known relation with T2DM. The enrichment analysis identified 11 deregulated biological processes emphasizing 20 proteins directly related to complications in diabetes. Diabetic retinopathy, metabolic syndrome, insulin resistance, molecular impact of glucose and insulin homeostasis dysregulation, atherosclerosis, diabetic foot ulcer, protein catabolism and salivary gland function are diabetic complication capable of being monitored using saliva. We conclude that saliva has the potential to identify several molecules altered in diabetic patients compared to non-diabetic patients and that may be biomarkers not only of diabetes but also of the different complications of this disease. In conclusion, with this research we have confirmed the potential of saliva as a fluid of interest in both diagnosing and discovering new insights into diseases. Saliva was crucial in demonstrating the flexibility and capacity of its use demonstrated by the development of a reliable detection of SARS-CoV-2, the identification and discussion of molecular aspects of viral infection in and with the host, and the discovery of new markers in the diagnosis and monitoring of Type 2 Diabetes Mellitus.A Saliva tem atualmente um vasto background de investigação sobre como pode espelhar o estado de saúde do corpo. Já foram identificados biomarcadores salivares específicos para múltiplas doenças e são particularmente úteis para a monitorização de medicamentos. A saliva é um tipo de amostra particularmente favorável para a deteção de doenças infeciosas. Trata-se de um fluído não-invasivo, indolor e passível de auto recolha, ideal para estudar diferentes aspetos de duas doenças pandémicas conhecidas: COVID-19 e Diabetes Mellitus Tipo 2. A COVID-19 é uma das pandemias mais impactante de todos os tempos, exigindo testes frequentes às populações. A necessidade de identificar estratégias rentáveis para a deteção do surto de SARS-CoV-2 tornou-se uma prioridade global. As amostras nasofaríngeas foram consideradas como o padrão de amostragem, apesar de requerem um profissional de saúde qualificado para efetuar a colheita além de causar desconforto e dor ao doente. Uma vez que a saliva demonstrou ser bem-sucedida na deteção da SARS-CoV-2, o próximo passo seria criar uma estratégia de pools de amostras com vista a diminuir o número de testes individuais e de resíduos de materiais perigosos, o que também seria benéfico para o ambiente. Esta estratégia foi testada em duzentas e setenta e nove amostras de saliva com pools de 10 e 20 amostras aleatórias. O Cycle-Threshold médio dos genes detetados foi de 29,7. Reações de RT-PCT consecutivas em amostras positivas mostraram reprodutibilidade. A análise de comparação de amostras positivas individualizadas mostrou uma carga viral mediana mais elevada em amostras de saliva comparativamente a amostras nasofaríngeas. Concluímos que as amostras de saliva-pool permitiram um rastreio eficaz da SARS-CoV-2 em pools de 10 e de 20 amostras. Esta estratégia foi aplicada com sucesso em testes populacionais de mais de 2000 indivíduos, mostrando que é possível utilizar saliva em pool como líquido de diagnóstico para a infeção pelo SARS-CoV-2. Está demonstrado que a deteção de SARS-CoV-2 está bem estabelecida e com metodologias fiáveis, incluindo a saliva como fluido de deteção. No entanto as alterações moleculares induzidas por este vírus continuam por desvendar. Desenvolvemos uma estratégia proteómica híbrida para estabelecer um perfil proteico salivar COVID-19. As proteínas que mostram uma maior distinção entre amostras saudáveis e COVID-19 foram definidas através da análise PLS-DA e de enriquecimento funcional. Paralelamente, foram previstas as interações proteína-proteína entre o vírus e o hospedeiro. Foram identificados cinco processos biológicos desregulados no perfil do proteoma COVID-19: Apoptose, Vias de Energia, Resposta Imune, Metabolismo de Proteínas, e Transporte. Foram identificadas 10 proteínas (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10 e PHB2) que nunca tinham sido associadas à infeção por SARS-CoV-2, representando novas provas do perfil molecular por detrás da COVID-19. A análise de interactómica mostrou influência do vírus na resposta imunitária do hospedeiro, principalmente através da interação com a desgranulação dos neutrófilos. A partir destes resultados, é possível concluir que o vírus altera não só a resposta imune, mas também o metabolismo energético do hospedeiro e interfere com os mecanismos de apoptose. A Diabetes Mellitus Tipo 2 é uma doença metabólica crónica e constitui um risco de saúde importante devido às suas complicações características a longo prazo. Estima-se que cerca de 537 milhões de pessoas vivem com diabetes em todo o mundo e continuarão a aumentar. O diagnóstico e a monitorização da glicose na diabetes estão atualmente bem estabelecidos. Contudo, a monitorização de muitas das complicações da diabetes continua a ser um desafio, comprometendo o prognóstico e a qualidade de vida dos pacientes. Tivemos como objetivo estabelecer uma estratégia híbrida que identificou os marcadores salivares do T2DM e as suas complicações. Da análise funcional destacamos processos metabólicos, resposta a estímulos, processos do sistema imunitário e sinalização como processos biológicos perturbados pela relação conhecida com o T2DM. A análise de enriquecimento identificou 11 processos biológicos desregulamentados em que demos destaque a 20 proteínas diretamente relacionadas com complicações na diabetes. A retinopatia diabética, síndrome metabólica, resistência à insulina, impacto molecular da glicose e desregulação da homeostase da insulina, aterosclerose, úlcera do pé diabético, catabolismo proteico e função da glândula salivar são complicações diabéticas capazes de serem monitorizadas usando saliva. Concluímos que a saliva tem o potencial de identificar proteínas alteradas em doentes diabéticos em comparação com não diabéticos e que podem ser biomarcadores não só da diabetes, mas também das diferentes complicações desta doença. Em conclusão, com esta investigação confirmamos o potencial da saliva como fluido de interesse tanto no diagnóstico como na descoberta de novos insights sobre doenças. A saliva foi crucial para demonstrar a flexibilidade e capacidade de seu uso demonstrada pelo desenvolvimento de uma deteção confiável de SARS-CoV-2, a identificação e discussão de aspetos moleculares da infeção viral no hospedeiro e com o hospedeiro, bem como a descoberta de novos marcadores no diagnóstico e monitorização da Diabetes Mellitus tipo 2

Role of MicroRNA in Cancer Development and Treatment

Many researchers around the world have demonstrated that the expression of miRNAs is dysregulated in different tumors. Such dysregulation is caused by multiple mechanisms, and exposure to different carcinogens causes dysregulated epigenetic changes and defects in the miRNA biogenesis machinery. Cancer cells with abnormal miRNA expression evolve the capability to sustain proliferative signaling, evade growth suppressors, resist cell death, activate invasion and metastasis, and induce angiogenesis. Genome-wide profiling demonstrates that miRNA expression signatures are associated with tumor type, tumor grade and clinical outcomes, so miRNAs could be potential candidates for diagnostic biomarkers, prognostic biomarkers, therapeutic targets and preventive screening programs. Although miRNAs have multiple targets, their function in tumorigenesis is due to their regulation of a few specific targets. After the first detection of altered miRNA in leukemia, microRNAs have been demonstrated to be constantly altered in all cancer. More recently, microRNA has been shown to be altered by exposure to environmental carcinogens, thus driving the whole process of carcinogenesis. Our aim is to provide a rigorous peer review and publish cutting-edge research on the role of microRNA in cancer prevention therapy to educate and inspire the scientific community worldwide