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1.
Pharmacol Ther ; 260: 108670, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38823489

ABSTRACT

Advances in cancer therapeutics have improved patient survival rates. However, cancer survivors may suffer from adverse events either at the time of therapy or later in life. Cardiovascular diseases (CVD) represent a clinically important, but mechanistically understudied complication, which interfere with the continuation of best-possible care, induce life-threatening risks, and/or lead to long-term morbidity. These concerns are exacerbated by the fact that targeted therapies and immunotherapies are frequently combined with radiotherapy, which induces durable inflammatory and immunogenic responses, thereby providing a fertile ground for the development of CVDs. Stressed and dying irradiated cells produce 'danger' signals including, but not limited to, major histocompatibility complexes, cell-adhesion molecules, proinflammatory cytokines, and damage-associated molecular patterns. These factors activate intercellular signaling pathways which have potentially detrimental effects on the heart tissue homeostasis. Herein, we present the clinical crosstalk between cancer and heart diseases, describe how it is potentiated by cancer therapies, and highlight the multifactorial nature of the underlying mechanisms. We particularly focus on radiotherapy, as a case known to often induce cardiovascular complications even decades after treatment. We provide evidence that the secretome of irradiated tumors entails factors that exert systemic, remote effects on the cardiac tissue, potentially predisposing it to CVDs. We suggest how diverse disciplines can utilize pertinent state-of-the-art methods in feasible experimental workflows, to shed light on the molecular mechanisms of radiotherapy-related cardiotoxicity at the organismal level and untangle the desirable immunogenic properties of cancer therapies from their detrimental effects on heart tissue. Results of such highly collaborative efforts hold promise to be translated to next-generation regimens that maximize tumor control, minimize cardiovascular complications, and support quality of life in cancer survivors.


Subject(s)
Cardiotoxicity , Neoplasms , Radiotherapy , Humans , Neoplasms/radiotherapy , Neoplasms/drug therapy , Cardiotoxicity/etiology , Animals , Radiotherapy/adverse effects , Signal Transduction , Cardiovascular Diseases
2.
Int J Mol Sci ; 25(9)2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38731948

ABSTRACT

Based on the need for radiobiological databases, in this work, we mined experimental ionizing radiation data of human cells treated with X-rays, γ-rays, carbon ions, protons and α-particles, by manually searching the relevant literature in PubMed from 1980 until 2024. In order to calculate normal and tumor cell survival α and ß coefficients of the linear quadratic (LQ) established model, as well as the initial values of the double-strand breaks (DSBs) in DNA, we used WebPlotDigitizer and Python programming language. We also produced complex DNA damage results through the fast Monte Carlo code MCDS in order to complete any missing data. The calculated α/ß values are in good agreement with those valued reported in the literature, where α shows a relatively good association with linear energy transfer (LET), but not ß. In general, a positive correlation between DSBs and LET was observed as far as the experimental values are concerned. Furthermore, we developed a biophysical prediction model by using machine learning, which showed a good performance for α, while it underscored LET as the most important feature for its prediction. In this study, we designed and developed the novel radiobiological 'RadPhysBio' database for the prediction of irradiated cell survival (α and ß coefficients of the LQ model). The incorporation of machine learning and repair models increases the applicability of our results and the spectrum of potential users.


Subject(s)
Cell Survival , DNA Breaks, Double-Stranded , Linear Energy Transfer , Radiation, Ionizing , Radiobiology , Humans , Cell Survival/radiation effects , Radiobiology/methods , DNA Breaks, Double-Stranded/radiation effects , Databases, Factual , Monte Carlo Method
3.
Genes (Basel) ; 14(12)2023 12 17.
Article in English | MEDLINE | ID: mdl-38137049

ABSTRACT

Ionizing radiation can induce different types of DNA lesions, leading to genomic instability and ultimately cell death. Radiation therapy or radiotherapy, a major modality in cancer treatment, harnesses the genotoxic potential of radiation to target and destroy cancer cells. Nevertheless, cancer cells have the capacity to develop resistance to radiation treatment (radioresistance), which poses a major obstacle in the effective management of cancer. It has been shown that administration of platinum-based drugs to cancer patients can increase tumor radiosensitivity, but despite this, it is associated with severe adverse effects. Several lines of evidence support that activation of the DNA damage response and repair machinery in the irradiated cancer cells enhances radioresistance and cellular survival through the efficient repair of DNA lesions. Therefore, targeting of key DNA damage repair factors would render cancer cells vulnerable to the irradiation effects, increase cancer cell killing, and reduce the risk of side effects on healthy tissue. Herein, we have employed a computer-aided drug design approach for generating ab initio a chemical compound with drug-like properties potentially targeting two proteins implicated in multiple DNA repair pathways. The findings of this study could be taken into consideration in clinical decision-making in terms of co-administering radiation with DNA damage repair factor-based drugs.


Subject(s)
Neoplasms , Humans , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/radiotherapy , DNA Repair , Cell Survival/genetics , DNA Damage , Radiation Tolerance/genetics
4.
Article in English | MEDLINE | ID: mdl-37444135

ABSTRACT

Ewing sarcoma is a rare type of cancer that develops in the bones and soft tissues. Drug therapy represents an extensively used modality for the treatment of sarcomas. However, cancer cells tend to develop resistance to antineoplastic agents, thereby posing a major barrier in treatment effectiveness. Thus, there is a need to uncover the molecular mechanisms underlying chemoresistance in sarcomas and, hence, to enhance the anticancer treatment outcome. In this study, a differential gene expression analysis was conducted on high-throughput transcriptomic data of chemoresistant versus chemoresponsive Ewing sarcoma cells. By applying functional enrichment analysis and protein-protein interactions on the differentially expressed genes and their corresponding products, we uncovered genes with a hub role in drug resistance. Granted that non-coding RNA epigenetic regulators play a pivotal role in chemotherapy by targeting genes associated with drug response, we investigated the non-coding RNA molecules that potentially regulate the expression of the detected chemoresistance genes. Of particular importance, some chemoresistance-relevant genes were associated with the autonomic nervous system, suggesting the involvement of the latter in the drug response. The findings of this study could be taken into consideration in the clinical setting for the accurate assessment of drug response in sarcoma patients and the application of tailored therapeutic strategies.


Subject(s)
Antineoplastic Agents , Bone Neoplasms , Sarcoma, Ewing , Sarcoma , Humans , Sarcoma, Ewing/drug therapy , Sarcoma, Ewing/genetics , Sarcoma, Ewing/metabolism , Systems Biology , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Drug Resistance , Bone Neoplasms/drug therapy , Bone Neoplasms/genetics , Cell Line, Tumor
5.
PeerJ ; 11: e15096, 2023.
Article in English | MEDLINE | ID: mdl-36945359

ABSTRACT

Low-grade gliomas (LGG) are central nervous system Grade I tumors, and as they progress they are becoming one of the deadliest brain tumors. There is still great need for timely and accurate diagnosis and prognosis of LGG. Herein, we aimed to identify diagnostic and prognostic biomarkers associated with LGG, by employing diverse computational approaches. For this purpose, differential gene expression analysis on high-throughput transcriptomics data of LGG versus corresponding healthy brain tissue, derived from TCGA and GTEx, respectively, was performed. Weighted gene co-expression network analysis of the detected differentially expressed genes was carried out in order to identify modules of co-expressed genes significantly correlated with LGG clinical traits. The genes comprising these modules were further used to construct gene co-expression and protein-protein interaction networks. Based on the network analyses, we derived a consensus of eighteen hub genes, namely, CD74, CD86, CDC25A, CYBB, HLA-DMA, ITGB2, KIF11, KIFC1, LAPTM5, LMNB1, MKI67, NCKAP1L, NUSAP1, SLC7A7, TBXAS1, TOP2A, TYROBP, and WDFY4. All detected hub genes were up-regulated in LGG, and were also associated with unfavorable prognosis in LGG patients. The findings of this study could be applicable in the clinical setting for diagnosing and monitoring LGG.


Subject(s)
Brain Neoplasms , Glioma , Humans , Prognosis , Neoplasm Grading , Glioma/diagnosis , Brain Neoplasms/diagnosis , Gene Expression Profiling , Membrane Proteins/genetics , Amino Acid Transport System y+L/genetics
6.
PeerJ ; 11: e15099, 2023.
Article in English | MEDLINE | ID: mdl-36949761

ABSTRACT

Keratins (KRTs) are the intermediate filament-forming proteins of epithelial cells, classified, according to their physicochemical properties, into "soft" and "hard" keratins. They have a key role in several aspects of cancer pathophysiology, including cancer cell invasion and metastasis, and several members of the KRT family serve as diagnostic or prognostic markers. The human genome contains both, functional KRT genes and non-functional KRT pseudogenes, arranged in two uninterrupted clusters on chromosomes 12 and 17. This characteristic renders KRTs ideal for evolutionary studies. Herein, comprehensive phylogenetic analyses of KRT homologous proteins in the genomes of major taxonomic divisions were performed, so as to fill a gap in knowledge regarding the functional implications of keratins in cancer biology among tumor-bearing species. The differential expression profiles of KRTs in diverse types of cancers were investigated by analyzing high-throughput data, as well. Several KRT genes, including the phylogenetically conserved ones, were found to be deregulated across several cancer types and to participate in a common protein-protein interaction network. This indicates that, at least in cancer-bearing species, these genes might have been under similar evolutionary pressure, perhaps to support the same important function(s). In addition, semantic relations between KRTs and cancer were detected through extensive text mining. Therefore, by applying an integrative in silico pipeline, the evolutionary history of KRTs was reconstructed in the context of cancer, and the potential of using non-mammalian species as model organisms in functional studies on human cancer-associated KRT genes was uncovered.


Subject(s)
Biomarkers, Tumor , Keratins , Humans , Keratins/genetics , Phylogeny , Biomarkers, Tumor/genetics , Intermediate Filament Proteins/genetics , Biological Evolution
7.
J Autism Dev Disord ; 53(3): 1091-1106, 2023 Mar.
Article in English | MEDLINE | ID: mdl-35759154

ABSTRACT

Transposable elements (TEs) have been implicated in autism spectrum disorder (ASD). However, our understanding of their roles is far from complete. Herein, we explored de novo TE insertions (dnTEIs) and de novo variants (DNVs) across the genomes of dizygotic twins with ASD and their parents. The neuronal regulatory elements had a tendency to harbor dnTEIs that were shared between twins, but ASD-risk genes had dnTEIs that were unique to each twin. The dnTEIs were 4.6-fold enriched in enhancers that are active in embryonic stem cell (ESC)-neurons (p < 0.001), but DNVs were 1.5-fold enriched in active enhancers of astrocytes (p = 0.0051). Our findings suggest that dnTEIs and DNVs play a role in ASD etiology by disrupting enhancers of neurons and astrocytes.


Subject(s)
Autism Spectrum Disorder , Autistic Disorder , Humans , Autistic Disorder/genetics , Autism Spectrum Disorder/genetics , Twins, Dizygotic
8.
Antioxidants (Basel) ; 11(11)2022 Nov 18.
Article in English | MEDLINE | ID: mdl-36421472

ABSTRACT

Ionizing radiation (IR) is a genuine genotoxic agent and a major modality in cancer treatment. IR disrupts DNA sequences and exerts mutagenic and/or cytotoxic properties that not only alter critical cellular functions but also impact tissues proximal and distal to the irradiated site. Unveiling the molecular events governing the diverse effects of IR at the cellular and organismal levels is relevant for both radiotherapy and radiation protection. Herein, we address changes in the expression of mammalian genes induced after the exposure of a wide range of tissues to various radiation types with distinct biophysical characteristics. First, we constructed a publicly available database, termed RadBioBase, which will be updated at regular intervals. RadBioBase includes comprehensive transcriptomes of mammalian cells across healthy and diseased tissues that respond to a range of radiation types and doses. Pertinent information was derived from a hybrid analysis based on stringent literature mining and transcriptomic studies. An integrative bioinformatics methodology, including functional enrichment analysis and machine learning techniques, was employed to unveil the characteristic biological pathways related to specific radiation types and their association with various diseases. We found that the effects of high linear energy transfer (LET) radiation on cell transcriptomes significantly differ from those caused by low LET and are consistent with immunomodulation, inflammation, oxidative stress responses and cell death. The transcriptome changes also depend on the dose since low doses up to 0.5 Gy are related with cytokine cascades, while higher doses with ROS metabolism. We additionally identified distinct gene signatures for different types of radiation. Overall, our data suggest that different radiation types and doses can trigger distinct trajectories of cell-intrinsic and cell-extrinsic pathways that hold promise to be manipulated toward improving radiotherapy efficiency and reducing systemic radiotoxicities.

9.
PeerJ ; 10: e14149, 2022.
Article in English | MEDLINE | ID: mdl-36213495

ABSTRACT

MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.


Subject(s)
MicroRNAs , Neoplasms , Humans , MicroRNAs/genetics , Systems Biology , Gene Regulatory Networks/genetics , Gene Expression Regulation, Neoplastic/genetics , RNA, Messenger/genetics , Neoplasms/diagnosis
10.
Cancer Metastasis Rev ; 41(4): 853-869, 2022 12.
Article in English | MEDLINE | ID: mdl-35948758

ABSTRACT

Cancer largely adheres to Darwinian selection. Evolutionary forces are prominent during metastasis, the final and incurable disease stage, where cells acquire combinations of advantageous phenotypic features and interact with a dynamically changing microenvironment, in order to overcome the metastatic bottlenecks, while therapy exerts additional selective pressures. As a strategy to increase their fitness, tumors often co-opt developmental and tissue-homeostasis programs. Herein, 25 years after its discovery, we review TP73, a sibling of the cardinal tumor-suppressor TP53, through the lens of cancer evolution. The TP73 gene regulates a wide range of processes in embryonic development, tissue homeostasis and cancer via an overwhelming number of functionally divergent isoforms. We suggest that TP73 neither merely mimics TP53 via its p53-like tumor-suppressive functions, nor has black-or-white-type effects, as inferred by the antagonism between several of its isoforms in processes like apoptosis and DNA damage response. Rather, under dynamic conditions of selective pressure, the various p73 isoforms which are often co-expressed within the same cancer cells may work towards a common goal by simultaneously activating isoform-specific transcriptional and non-transcriptional programs. Combinatorial co-option of these programs offers selective advantages that overall increase the likelihood for successfully surpassing the barriers of the metastatic cascade. The p73 functional pleiotropy-based capabilities might be present in subclonal populations and expressed dynamically under changing microenvironmental conditions, thereby supporting clonal expansion and propelling evolution of metastasis. Deciphering the critical p73 isoform patterns along the spatiotemporal axes of tumor evolution could identify strategies to target TP73 for prevention and therapy of cancer metastasis.


Subject(s)
Neoplasms , Tumor Suppressor Proteins , Humans , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Tumor Protein p73/genetics , Tumor Suppressor Protein p53/genetics , Protein Isoforms/genetics , Protein Isoforms/metabolism , Genes, Tumor Suppressor , Neoplasms/genetics , Neoplasms/pathology , Tumor Microenvironment
11.
Oxid Med Cell Longev ; 2022: 4748447, 2022.
Article in English | MEDLINE | ID: mdl-35585878

ABSTRACT

The world's population is ageing at an accelerated pace. Ageing is a natural, physiological but highly complex and multifactorial process that all species in the Tree of Life experience over time. Physical and mental disabilities, and age-related diseases, would increase along with the increasing life expectancy. Ginger (Zingiber officinale) is a plant that belongs to the Zingiberaceae family, native to Southeast Asia. For hundreds of years, ginger has been consumed in various ways by the natives of Asian countries, both as culinary and medicinal herb for the treatment of many diseases. Mounting evidence suggests that ginger can promote healthy ageing, reduce morbidity, and prolong healthy lifespan. Ginger, a well-known natural product, has been demonstrated to possess antioxidant, anti-inflammatory, anticancer, and antimicrobial properties, as well as an outstanding antiviral activity due to a high concentration of antiviral compounds. In this review, the current evidence on the potential role of ginger and its active compounds in the prevention of ageing is discussed.


Subject(s)
Healthy Aging , Zingiber officinale , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/therapeutic use , Antioxidants/pharmacology , Antioxidants/therapeutic use , Antiviral Agents , Plant Extracts/pharmacology , Plant Extracts/therapeutic use
12.
Cell Mol Life Sci ; 79(5): 229, 2022 Apr 09.
Article in English | MEDLINE | ID: mdl-35396689

ABSTRACT

Skeletal muscle tissue engineering aims at generating biological substitutes that restore, maintain or improve normal muscle function; however, the quality of cells produced by current protocols remains insufficient. Here, we developed a multifactor-based protocol that combines adenovector (AdV)-mediated MYOD expression, small molecule inhibitor and growth factor treatment, and electrical pulse stimulation (EPS) to efficiently reprogram different types of human-derived multipotent stem cells into physiologically functional skeletal muscle cells (SMCs). The protocol was complemented through a novel in silico workflow that allows for in-depth estimation and potentially optimization of the quality of generated muscle tissue, based on the transcriptomes of transdifferentiated cells. We additionally patch-clamped phenotypic SMCs to associate their bioelectrical characteristics with their transcriptome reprogramming. Overall, we set up a comprehensive and dynamic approach at the nexus of viral vector-based technology, bioinformatics, and electrophysiology that facilitates production of high-quality skeletal muscle cells and can guide iterative cycles to improve myo-differentiation protocols.


Subject(s)
Muscle Development , Muscle Fibers, Skeletal , Cell Differentiation/physiology , Humans , Muscle Development/genetics , Muscle Fibers, Skeletal/metabolism , Muscle, Skeletal/metabolism , MyoD Protein/metabolism , Stem Cells , Workflow
13.
Br J Anaesth ; 128(4): 734-741, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35219449

ABSTRACT

BACKGROUND: Pain after resolution of peripheral nerve block, known as 'rebound pain' (RP), is a major problem in outpatient surgery. The primary objective was to evaluate the benefit of intraoperative ketamine at an anti-hyperalgesic dose on the incidence of rebound pain after upper limb surgery under axillary plexus block in ambulatory patients. The secondary objective was to better understand the rebound pain phenomenon (individual risk factors). METHODS: In this prospective, double-blind study, patients were randomised to receive either a single dose of i.v. ketamine (0.3 mg kg-1) or a placebo. Preoperative mechanical temporal summation and central sensitization inventory were applied to question underlying central sensitisation. Pain catastrophising and Douleur Neuropathique 4 questionnaires were used. Rebound pain was defined as pain intensity score >7 (numeric rating scale, 0-10) after block resolution. Postoperative pain was recorded at Days 1, 4, and 30 after discharge. RESULTS: A total of 109 subjects completed the study, and 40.4% presented with rebound pain. Ketamine administration did not reduce rebound pain incidence or intensity. Temporal summation and central sensitisation inventory scores did not differ between subjects with and without rebound pain. The predictive risk factors were bone surgery (odds ratio [OR]=5.2; confidence interval [CI], 1.9-14.6), severe preoperative pain (OR=4.2; CI, 1.5-11.7), and high pain catastrophising (OR=4.8; CI, 1.0-22.3). At Day 30, the average daily pain was higher in the rebound pain group involving neuropathic characteristics. CONCLUSION: Ketamine at an anti-hyperalgesic dose showed no benefit on rebound pain development. Although central sensitisation might not be involved, preoperative pain intensity, and catastrophising stand as risk factors. Because rebound pain remains frequent despite adequate procedure-specific postoperative analgesia, future studies should focus on patient-specific pain management.


Subject(s)
Ketamine , Double-Blind Method , Humans , Ketamine/therapeutic use , Pain, Postoperative/drug therapy , Peripheral Nerves , Prospective Studies
14.
Int J Mol Med ; 49(3)2022 03.
Article in English | MEDLINE | ID: mdl-35059730

ABSTRACT

The highly heterogeneous symptomatology and unpredictable progress of COVID­19 triggered unprecedented intensive biomedical research and a number of clinical research projects. Although the pathophysiology of the disease is being progressively clarified, its complexity remains vast. Moreover, some extremely infrequent cases of thrombotic thrombocytopenia following vaccination against SARS­CoV­2 infection have been observed. The present study aimed to map the signaling pathways of thrombocytopenia implicated in COVID­19, as well as in vaccine­induced thrombotic thrombocytopenia (VITT). The biomedical literature database, MEDLINE/PubMed, was thoroughly searched using artificial intelligence techniques for the semantic relations among the top 50 similar words (>0.9) implicated in COVID­19­mediated human infection or VITT. Additionally, STRING, a database of primary and predicted associations among genes and proteins (collected from diverse resources, such as documented pathway knowledge, high­throughput experimental studies, cross­species extrapolated information, automated text mining results, computationally predicted interactions, etc.), was employed, with the confidence threshold set at 0.7. In addition, two interactomes were constructed: i) A network including 119 and 56 nodes relevant to COVID­19 and thrombocytopenia, respectively; and ii) a second network containing 60 nodes relevant to VITT. Although thrombocytopenia is a dominant morbidity in both entities, three nodes were observed that corresponded to genes (AURKA, CD46 and CD19) expressed only in VITT, whilst ADAM10, CDC20, SHC1 and STXBP2 are silenced in VITT, but are commonly expressed in both COVID­19 and thrombocytopenia. The calculated average node degree was immense (11.9 in COVID­19 and 6.43 in VITT), illustrating the complexity of COVID­19 and VITT pathologies and confirming the importance of cytokines, as well as of pathways activated following hypoxic events. In addition, PYCARD, NLP3 and P2RX7 are key potential therapeutic targets for all three morbid entities, meriting further research. This interactome was based on wild­type genes, revealing the predisposition of the body to hypoxia­induced thrombosis, leading to the acute COVID­19 phenotype, the 'long­COVID syndrome', and/or VITT. Thus, common nodes appear to be key players in illness prevention, progression and treatment.


Subject(s)
COVID-19 , Thrombocytopenia , Thrombosis , Vaccines , Artificial Intelligence , COVID-19/complications , COVID-19 Vaccines/adverse effects , Humans , SARS-CoV-2 , Thrombocytopenia/chemically induced , Thrombocytopenia/genetics , Thrombosis/genetics , Post-Acute COVID-19 Syndrome
15.
Front Biosci (Landmark Ed) ; 27(1): 13, 2022 Jan 11.
Article in English | MEDLINE | ID: mdl-35090318

ABSTRACT

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first occurred in Wuhan (China) in December of 2019. Since the outbreak, it has accumulated mutations on its coding sequences to optimize its adaptation to the human host. The identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe. METHODS: In this study, we compared 320,338 SARS-CoV-2 genomes isolated from all over the world to the first sequenced genome in Wuhan, China. To this end, we analysed over time the codon usage patterns of SARS-CoV-2 genes encoding for the membrane protein (M), envelope (E), spike surface glycoprotein (S), nucleoprotein (N), RNA-dependent RNA polymerase (RdRp) and ORF1ab. RESULTS: We found that genes coding for the proteins N and S diverged more rapidly since the outbreak by accumulating mutations. Interestingly, all genes show a deoptimization of their codon usage with respect to the human host. Our findings suggest a general evolutionary trend of SARS-CoV-2, which evolves towards a sub-optimal codon usage bias to favour the host survival and its spread. Furthermore, we found that S protein and RdRp are more subject to an increasing purifying pressure over time, which implies that these proteins will reach a lower tendency to accept mutations. In contrast, proteins N and M tend to evolve more under the action of mutational bias, thus exploring a large region of their sequence space. CONCLUSIONS: Overall, our study shed more light on the evolution of SARS-CoV-2 genes and their adaptation to humans, helping to foresee their mutation patterns and the emergence of new variants.


Subject(s)
COVID-19 , Codon Usage , Genome, Viral/genetics , Humans , Phylogeny , SARS-CoV-2
16.
Viruses ; 15(1)2022 12 30.
Article in English | MEDLINE | ID: mdl-36680144

ABSTRACT

The COVID-19 pandemic has persisted for almost three years. However, the mechanisms linked to the SARS-CoV-2 effect on tissues and disease severity have not been fully elucidated. Since the onset of the pandemic, a plethora of high-throughput data related to the host transcriptional response to SARS-CoV-2 infections has been generated. To this end, the aim of this study was to assess the effect of SARS-CoV-2 infections on circulating and organ tissue immune responses. We profited from the publicly accessible gene expression data of the blood and soft tissues by employing an integrated computational methodology, including bioinformatics, machine learning, and natural language processing in the relevant transcriptomics data. COVID-19 pathophysiology and severity have mainly been associated with macrophage-elicited responses and a characteristic "cytokine storm". Our counterintuitive findings suggested that the COVID-19 pathogenesis could also be mediated through neutrophil abundance and an exacerbated suppression of the immune system, leading eventually to uncontrolled viral dissemination and host cytotoxicity. The findings of this study elucidated new physiological functions of neutrophils, as well as tentative pathways to be explored in asymptomatic-, ethnicity- and locality-, or staging-associated studies.


Subject(s)
COVID-19 , Humans , SARS-CoV-2/genetics , Neutrophils , Transcriptome , Pandemics
17.
Molecules ; 26(24)2021 Dec 15.
Article in English | MEDLINE | ID: mdl-34946681

ABSTRACT

Different types of DNA lesions forming in close vicinity, create clusters of damaged sites termed as "clustered/complex DNA damage" and they are considered to be a major challenge for DNA repair mechanisms resulting in significant repair delays and induction of genomic instability. Upon detection of DNA damage, the corresponding DNA damage response and repair (DDR/R) mechanisms are activated. The inability of cells to process clustered DNA lesions efficiently has a great impact on the normal function and survival of cells. If complex lesions are left unrepaired or misrepaired, they can lead to mutations and if persistent, they may lead to apoptotic cell death. In this in silico study, and through rigorous data mining, we have identified human genes that are activated upon complex DNA damage induction like in the case of ionizing radiation (IR) and beyond the standard DNA repair pathways, and are also involved in cancer pathways, by employing stringent bioinformatics and systems biology methodologies. Given that IR can cause repair resistant lesions within a short DNA segment (a few nm), thereby augmenting the hazardous and toxic effects of radiation, we also investigated the possible implication of the most biologically important of those genes in comorbid non-neoplastic diseases through network integration, as well as their potential for predicting survival in cancer patients.


Subject(s)
DNA Damage , DNA Repair , DNA, Neoplasm , Neoplasms , Systems Biology , DNA, Neoplasm/genetics , DNA, Neoplasm/metabolism , Humans , Neoplasms/genetics , Neoplasms/metabolism , Neoplasms/radiotherapy , Radiation, Ionizing
18.
Appl Bionics Biomech ; 2021: 7099510, 2021.
Article in English | MEDLINE | ID: mdl-34840604

ABSTRACT

Due to the increasing number of COVID-19 cases, there is a remarkable demand for robots, especially in the clinical sector. SARS-CoV-2 mainly propagates due to close human interactions and contaminated surfaces, and hence, maintaining social distancing has become a mandatory preventive measure. This generates the need to treat patients with minimal doctor-patient interaction. Introducing robots in the healthcare sector protects the frontline healthcare workers from getting exposed to the coronavirus as well as decreases the need for medical personnel as robots can partially take over some medical roles. The aim of this paper is to highlight the emerging role of robotic applications in the healthcare sector and allied areas. To this end, a systematic review was conducted regarding the various robots that have been implemented worldwide during the COVID-19 pandemic to attenuate and contain the virus. The results obtained from this study reveal that the implementation of robotics into the healthcare field has a substantial effect in controlling the spread of SARS-CoV-2, as it blocks coronavirus propagation between patients and healthcare workers, along with other advantages such as disinfection or cleaning.

19.
Int J Clin Pract ; 75(12): e15008, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34811860

ABSTRACT

AIMS: Preoperative anxiety, which can affect postoperative recovery, is often present in patients undergoing surgery under loco-regional anaesthesia (LRA). Minimising preoperative anxiety with premedication can be effective but results in drug-related side effects. Therefore, the use of non-pharmacological techniques should be encouraged. METHODS: We evaluated whether a virtual reality (VR) incorporating music and a hypnosis session, provided during the performance of LRA, can reduce preoperative anxiety. Fifty patients scheduled for elective hand surgery under an axillary plexus block were enrolled (March-June 2019). The primary outcome measure was the change in the Amsterdam Anxiety and Preoperative Information Scale (APAIS) questionnaire 5 min after the VR session as compared to before the VR session. The secondary outcome measures were the visual analog scale (VAS) for anxiety before and 2 h after the surgery and the Evaluation du Vécu de l'ANesthésie-LocoRégionale (EVAN-LR) satisfaction score. RESULTS: Data from 48 patients were analysed. The APAIS score as well as VAS for anxiety were significantly reduced after a VR session (p < .001 for both scores). Patients were very satisfied (EVAN-LR: 92 (88, 94)). CONCLUSIONS: The use of VR incorporating music and a hypnosis session could be an effective tool in the management of a patient's preoperative anxiety during the performance of an axillary plexus block.


Subject(s)
Anesthesia, Conduction , Hypnosis , Music , Virtual Reality , Anxiety/prevention & control , Hand/surgery , Humans , Patient Satisfaction , Prospective Studies
20.
Int J Mol Sci ; 22(17)2021 Sep 05.
Article in English | MEDLINE | ID: mdl-34502522

ABSTRACT

Acute myeloid leukemia (AML), the most common type of acute leukemia in adults, is mainly asymptomatic at early stages and progresses/recurs rapidly and frequently. These attributes necessitate the identification of biomarkers for timely diagnosis and accurate prognosis. In this study, differential gene expression analysis was performed on large-scale transcriptomics data of AML patients versus corresponding normal tissue. Weighted gene co-expression network analysis was conducted to construct networks of co-expressed genes, and detect gene modules. Finally, hub genes were identified from selected modules by applying network-based methods. This robust and integrative bioinformatics approach revealed a set of twenty-four genes, mainly related to cell cycle and immune response, the diagnostic significance of which was subsequently compared against two independent gene expression datasets. Furthermore, based on a recent notion suggesting that molecular characteristics of a few, unusual patients with exceptionally favorable survival can provide insights for improving the outcome of individuals with more typical disease trajectories, we defined groups of long-term survivors in AML patient cohorts and compared their transcriptomes versus the general population to infer favorable prognostic signatures. These findings could have potential applications in the clinical setting, in particular, in diagnosis and prognosis of AML.


Subject(s)
Computer Simulation , Databases, Nucleic Acid , Gene Expression Profiling , Leukemia, Myeloid, Acute , Adult , Disease-Free Survival , Female , Humans , Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/metabolism , Leukemia, Myeloid, Acute/mortality , Male , Survival Rate
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