miR-802 Suppresses Acinar-to-Ductal Reprogramming During Early Pancreatitis and Pancreatic Carcinogenesis

BACKGROUND & AIMS

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive tumor that is almost uniformly lethal in humans. Activating mutations of KRAS are found in >90% of human PDACs and are sufficient to promote acinar-to-ductal metaplasia (ADM) during tumor initiation. The roles of miRNAs in oncogenic Kras-induced ADM are incompletely understood.

METHODS

The Ptf1a^Cre/+LSL-Kras^G12D/+ and Ptf1a^Cre/+LSL-Kras^G12D/+LSL-p53R172H/⁺ and caerulein-induced acute pancreatitis mice models were used. mir-802 was conditionally ablated in acinar cells to study the function of miR-802 in ADM.

RESULTS

We show that miR-802 is a highly abundant and acinar-enriched pancreatic miRNA that is silenced during early stages of injury or oncogenic Kras^G12D-induced transformation. Genetic ablation of mir-802 cooperates with Kras^G12D by promoting ADM formation. miR-802 deficiency results in de-repression of the miR-802 targets Arhgef12, RhoA, and Sdc4, activation of RhoA, and induction of the downstream RhoA effectors ROCK1, LIMK1, COFILIN1, and EZRIN, thereby increasing F-actin rearrangement. mir-802 ablation also activates SOX9, resulting in augmented levels of ductal and attenuated expression of acinar identity genes. Consistently with these findings, we show that this miR-802-RhoA-F-actin network is activated in biopsies of pancreatic cancer patients and correlates with poor survival.

CONCLUSIONS

We show miR-802 suppresses pancreatic cancer initiation by repressing oncogenic Kras-induced ADM. The role of miR-802 in ADM fills the gap in our understanding of oncogenic Kras-induced F-actin reorganization, acinar reprogramming, and PDAC initiation. Modulation of the miR-802-RhoA-F-actin network may be a new strategy to interfere with pancreatic carcinogenesis.

Association of three micro-RNA gene polymorphisms with the risk of cervical cancer: a meta-analysis and systematic review

OBJECTIVE

Regulation of single nucleotide polymorphisms (SNP) in micro-RNA (miRNA) on the host cells may be one of the most important factors influencing the occurrence of cervical cancer based on the prevalence of HPV infection and the development of cervical cancer. In order to explore the contribution of miRNA polymorphism to the occurrence and development of cervical cancer, we conducted an analytical study.

METHODS

We selected the polymorphisms of three widely studied miRNAs (miRNA-146a rs2910164, miRNA-499 rs3746444, and miRNA-196a2 rs11614913). Then, we conducted a meta-analysis (for the first time) to investigate their susceptibility to cervical cancer. Case control studies on the correlation between these three miRNAs and cervical cancer susceptibility were investigated by searching on from Pubmed, The Cochrane Library, Embase, CBM, CNKI, Wanfang database, and VIP database. Basic characteristics were recorded and meta-analysis of the case studies was performed using the STATA 15.1 software.

RESULTS

The miRNA-146a rs2910164 mutation significantly reduced the risk of cervical cancer in both recessive model (OR = 0.804, 95% CI = 0.652-0.992, P = 0.042; CC vs. CG+GG) and allelic model (OR = 0.845, 95% CI = 0.721-0.991, P = 0.038; C vs. G). There was no significant correlation between miRNA-499 rs3746444 and the risk of cervical cancer. The miRNA-196a2 rs11614913 mutation was significantly associated with a reduced risk of cervical cancer in homozygous model (OR = 0.641, 95% CI = 0.447-0.919, P = 0.016; TT vs. CC), dominant model (OR = 0.795, 95% CI = 0.636-0.994, P = 0.045; CT+TT vs. CC), recessive model (OR = 0.698, 95% CI = 0.532-0.917, P = 0.01; TT vs. CC+CT), and allelic models (OR = 0.783, 95% CI = 0.643-0.954, P = 0.015, T vs. C).

CONCLUSION

In summary, this meta-analysis shows that the mutant genotypes of miRNA-146a rs2910164 and miRNA-196a2 rs11614913 are associated with a reduced risk of cervical cancer. Therefore, they may be two gene regulatory points for the prevention of cervical cancer.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO registration number CRD42021270079.

ESAT-6 impedes IL-18 mediated phagosome lysosome fusion via microRNA-30a upon Calcimycin treatment in mycobacteria infected macrophages

The weaponry possessed by Mycobacterium tuberculosis (M. tb) in the form of immunodominant antigens hijack the host immune system to give a survival advantage to this intracellular fiend, but the mechanism of this control is not entirely known. Since we have previously reported the mechanism of autophagy inhibition by early secreted antigenic target 6 kDa (ESAT-6) through microRNA (miR)-30a-3p in Calcimycin treated differentiated THP-1 (dTHP-1) cells, the present study was undertaken to deduce the effect of miR-30a on the immunomodulatory profile of ESAT-6 treated cells and the mechanism involved thereof, if any. Initially, the effect of recombinant ESAT-6 (rESAT-6) on the immunomodulatory profile in Calcimycin-treated phorbol 12-myristate 13-acetate (PMA) dTHP-1 cells was checked. Later, transfection studies using miR-30a-3p inhibitor or -5p mimic highlighted the contrary roles of different arms of the same miRNA in regulating IL-18 response by ESAT-6 in dTHP-1 cells after Calcimycin treatment. By using either IL-18 neutralizing antibody or inhibitors of phosphoinositide 3-kinase (PI3K)/NF-κB/phagosome-lysosome fusion in the miRNA-30a transfected background, IL-18 mediated signaling and intracellular killing of mycobacteria was reversed in the presence of ESAT-6. Overall, the results of this study conclusively prove the contrary roles of miR-30a-3p and miR-30a-5p in regulating IL-18 signaling by ESAT-6 in dTHP-1 cells upon Calcimycin treatment that affected phagosome-lysosome fusion and intracellular survival of mycobacteria.

Biomarkers in axial spondyloarthritis and low back pain: a comprehensive review

The spectrum of axial spondyloarthritis (AxSpA) (including both non-radiographic and radiographic AxSpA), also known as ankylosing spondylitis AS, has achieved growing recognition. With the development of treatments not only effective in controlling disease activity but also in slowing radiographic progression, and given the cost and risk profiles of these novel treatments and the limitations of current clinical criteria, imaging and peripheral blood biomarkers (C-reactive protein, HLA-B27 testing), the need for better biomarkers has never been greater. The purpose of this review is to present up-to-date information on the biomarkers for the diagnosis for assessing disease diagnosis, activity, treatment response, and radiographic progression of AxSpA, and entails multiple search strings used to identify articles of interest published in PubMed and the Cochrane database up to May 1, 2021. We present the current status of research in serologic biomarkers such as cytokines, adipokines, matrix metalloproteinases, calprotectin, CD74, antibodies, bone turnover markers, and circulating protein fragments of cartilage and connective tissue degradation and other biomarkers. Despite a great deal of work, most serologic results have been disappointing and to date none perform better than CRP. Recent promising preliminary data for some has been published, but require further confirmation. Transcriptomic biomarkers such as micro-RNAs and genetic biomarkers also show promise to assist in diagnosis and possibly for radiographic severity, including a recently developed panel of genetic risk markers used in a polygenic risk score instrument in AS diagnosis. These need further confirmation and application in AS as well as in nr-AxSpA.

'Omics' of suicidal behaviour: A path to personalised psychiatry

Psychiatric disorders, including suicide, are complex disorders that are affected by many different risk factors. It has been estimated that genetic factors contribute up to 50% to suicide risk. As the candidate gene approach has not identified a gene or set of genes that can be defined as biomarkers for suicidal behaviour, much is expected from cutting edge technological approaches that can interrogate several hundred, or even millions, of biomarkers at a time. These include the '-omic' approaches, such as genomics, transcriptomics, epigenomics, proteomics and metabolomics. Indeed, these have revealed new candidate biomarkers associated with suicidal behaviour. The most interesting of these have been implicated in inflammation and immune responses, which have been revealed through different study approaches, from genome-wide single nucleotide studies and the micro-RNA transcriptome, to the proteome and metabolome. However, the massive amounts of data that are generated by the '-omic' technologies demand the use of powerful computational analysis, and also specifically trained personnel. In this regard, machine learning approaches are beginning to pave the way towards personalized psychiatry.

The miR-223-3p Regulates Pyroptosis Through NLRP3-Caspase 1-GSDMD Signal Axis in Periodontitis

Salivary exosomes contain various components and may play important roles in oral diseases. The purpose of this study was to verify the possible function of miR-223-3p from salivary exosomes in periodontitis. We isolated the salivary exosomes and found that the miR-223-3p content of salivary exosomes from periodontitis was less than the healthy control. Furthermore, we performed dual-luciferase reporter assay and real-time PCR to verify that (NOD)-like receptor (NLR) pyrin domain-containing 3 (NLRP3) was the target of miR-223-3p. When we knocked down the miR-223-3p expression in THP-1-derived macrophages, the expression of NLRP3 and the downstream inflammatory mediators interleukin-1β (IL-1β) and IL-6 were upregulated. By using integrated bioinformatics analysis, we found that pyroptosis and cytokine secretion participated in inflammatory gingival tissues. In addition, NLRP3, and the pyroptosis executioner, gasdermin D (GSDMD) was highly active in inflammatory gingival tissues compared with healthy controls by western blotting and immunohistochemistry. In summary, we speculated that miR-223-3p in salivary exosomes might regulate GSDMD-mediated pyroptosis by targeting NLRP3 in periodontitis. Detection of miR-223-3p expression in salivary exosomes could be used as an important non-invasive method to diagnose and evaluate the severity of periodontitis.

MicroRNA-7188-5p and miR-7235 regulates Multiple sclerosis in an experimental mouse model

The short non-coding microRNAs (miRNAs) have emerged as reliable modulators of various pathological conditions including autoimmune diseases in mammals. The current study, aims to identify new potential differential expressed miRNAs and their downstream mRNA targets of the autoimmune disease, Multiple sclerosis (MS). The study identifies a new set of miRNA(s) that are probably implicated in MS using computational tools. The study further carried-out different in vivo and in vitro experiments to check these identified miRNAs could be role in as therapeutic and prognostic applications. Preliminary insilico screening revealed that miR-659-3p, miR-659-5p, miR-684, miR-3607-3p, miR-3607-5p, miR-3682-3p, miR-3682-5p miR-4647, miR-7188-3p, miR-7188-5p and miR-7235 are specifically elevated in the secondary lymphoid cells of EAE mice. In addition, expression of the downstream target mRNA of these miRNAs such as FXBO33, SGMS-1, ZDHHC-9, GABRA-3, NRXN-2 were reciprocal to miRNA expression in lymphoid cells. These confirmed by applying the mimic and silencing miRNA models, suggesting new inflammatory target genes of these promising miRNA markers. The in vivo adoptive transfer model revealed that the suppression of miRNA-7188-5p and miR-7235 changed the pattern of astrocytes and CNS pathophysiology. The current study opens a new miRNA and their mRNA targets in MS disease. The absence of miRNA-7188-5p and miR-7235 enhanced the disease alleviation, confirms the regulatory effect of these targets. These optimized results highlights new set of miRNA's with therapeutic potential in experimental MS. Further studies are required to confirm these miRNA as therapeutic biomarker.

MicroRNA-199-3p targets Sp1 transcription factor to regulate proliferation and epithelial to mesenchymal transition of human lung cancer cells

The present study was undertaken to study the function of miRNA-199-3p in the regulation of human lung cancer growth and metastasis. The results showed significant (P < 0.05) downregulation of miRNA-199-3p in lung cancer tissues and cell lines. Overexpression of miR-197 caused considerable inhibition of the viability and colony formation of the lung cancer cells. The inhibition of proliferation was found to be due to the arrest of the SK-LU-1 lung cancer cells. At the G2/M phase of the cell cycle. In silico analysis and subsequent the dual-luciferase assays showed that miR-199-3p targets Sp1 at molecular. The expression of Sp1 was significantly (P < 0.05) upregulated in lung cancer cells and tissues. Nonetheless, miR-199-3p overexpression could cause post-transcriptional suppression of Sp1. Silencing of Sp1suppress the proliferation of SK-LU-1 lung cancer cells. However, overexpression Sp1 transcription factor prevents the tumor-suppressive effects of miR-199-3p on lung cancer cells. Additionally, miR-199-3p was found to suppresses the migration, invasion and epithelial-to-mesenchymal transition of human lung cancer cells. Summing up, miRNA-199-3p/SP1 axis controls the growth and metastasis of SK-LU-1 lung cancer cells.

Perspectives and challenges in validating new diagnostic technologies

This paper focuses on several new diagnostic technologies, which are set to dominate the testing landscape in the near future and have applications in animal health diagnostics, namely: next-generation sequencing, assays to detect biomarkers, and point-of-care tests. An example of real-time loop-mediated isothermal amplification validation is also provided. Validating these new technologies presents several challenges, which are addressed in this paper.

Highly sensitive wide-range target fluorescence biosensors of high-emittance metasurfaces

We demonstrate highly sensitive fluorescence (FL) biosensors made of plasmon-photon-hybrid high-emittance metasurfaces, which are hybrid structures composed of perforated silicon waveguides and stacked complementary (SC) gold nanostructures. The SC metasurfaces are applicable to a wide range of targets from antibodies to nucleic acids. As a test bed, a representative antibody of immunoglobulin G is immobilized on the metasurfaces through microfluidic paths and then is directly detected in a scaled manner even at a very low concentration of 5 pg mL^-1, i.e., 34 fM. Moreover, a cancer marker of p53 antibody is indirectly detected on the SC metasurfaces at a low concentration of 50 pg mL^-1, which is significantly lower than the medical diagnosis criterion of a few ng mL^-1. Furthermore, single-strand DNAs that are oligonucleotides and complementary to SARS-CoV-2 RNA are detected with 1 h immobilization time in the range of fmol mL^-1 in a scaled manner. These experimental results indicate that the present FL metasurface sensors function efficiently as biosensors for a wide range of biomarkers.

Time-Series Transcriptome Analysis Reveals the miR-27a-5p-Ppm1l Axis as a New Pathway Regulating Macrophage Alternative Polarization After Myocardial Infarction

BACKGROUND

Timely differentiation of monocytes into M2-like macrophages is important in the cardiac healing process after myocardial infarction (MI), but molecular mechanisms governing M2-like macrophage differentiation at the transcriptional level after MI have not been fully understood.Methods and Results:A time-series microarray analysis of mRNAs and microRNAs in macrophages isolated from the infarcted myocardium was performed to identify the microRNAs involved in regulating the process of differentiation to M2-like macrophages. Correlation analysis revealed 7 microRNAs showing negative correlations with the progression of polarity changes towards M2-like subsets. Next, correlation coefficients for the changes in expression of mRNAs and miRNAs over time were calculated for all combinations. As a result, miR-27a-5p was extracted as a possible regulator of the largest number of genes in the pathway for the M2-like polarization. By selecting mouse mRNAs and human mRNAs possessing target sequences of miR-27a-5p and showing expression patterns inversely correlated with that of miR-27a-5p, 8 potential targets of miR-27a-5p were identified, includingPpm1l. Using the mouse bone marrow-derived macrophages undergoing differentiation into M2-like subsets by interleukin 4 stimulation, we confirmed that miR-27a-5p suppressed M2-related genes by negatively regulatingPpm1lexpression.

CONCLUSIONS

Ppm1land miR-27a-5p may be the key molecules regulating M2-like polarization, with miR-27a-5p inhibiting the M2-like polarization through downregulation ofPpm1lexpression.

Mutations in cis that affect mRNA synthesis, processing and translation

Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.

Micro-RNA Quantification, Target Gene Identification, and Pathway Analysis

RNA sequencing has become a powerful tool for profiling the expression level of small RNAs from both solid tissues and liquid biopsies. In conjunction with pathway analysis, it offers exciting possibilities for the identification of disease specific biomarkers. In this chapter, we describe a workflow for processing this type of sequencing data. We start by removing technical sequences (adapters) and by performing quality control, a critical task that is necessary to identify possible issues caused by sample preparation and library sequencing. We then describe read alignment and gene-level abundance estimation. Building on these results, we normalize expression profiles and compute differentially expressed microRNAs between sample groups of interest. We conclude by showing how to employ pathway analysis to identify molecular signatures corresponding to biological processes that are significantly altered by the action for microRNAs.

Various aspects of inflammation in heart failure

Despite significant advances in the prevention and treatment of heart failure (HF), the prognosis in patients who have been hospitalised on at least one occasion due to exacerbation of HF is still poor. Therefore, a better understanding of the underlying pathophysiological mechanisms of HF is crucial in order to achieve better results in the treatment of this clinical syndrome. One of the areas that, for years, has aroused the interest of researchers is the activation of the immune system and the elevated levels of biomarkers of inflammation in patients with both ischaemic and non-ischaemic HF. Additionally, it is intriguing that the level of circulating pro-inflammatory biomarkers correlates with the severity of the disease and prognosis in this group of patients. Unfortunately, clinical trials aimed at assessing interventions to modulate the inflammatory response in HF have been disappointing, and the modulation of the inflammatory response has had either no effect or even a negative effect on the HF prognosis. The article presents a summary of current knowledge on the role of immune system activation and inflammation in the pathogenesis of HF. Understanding the immunological mechanisms pathogenetically associated with left ventricular remodelling and progression of HF may open up new therapeutic possibilities for HF.

Post-transcriptional suppression of G protein-coupled receptor 15 (GPR15) by microRNA-1225 inhibits proliferation, migration, and invasion of human colorectal cancer cells

The G protein-coupled receptors (GPRs) have been shown to regulate several cancer related processes. The aberrant expression of GPRs has been linked to the development of several cancers. The present study was designed to examine the expression and decipher the role of GPR15 in the development of human colorectal cancer. The results revealed GPR15 to be significantly (P < 0.05) upregulated in colorectal cancer cells. The silencing of GPR15 inhibited the growth of the colorectal cancer cells via induction of apoptosis. Induction of apoptosis in colorectal cancer cells was associated increase in Bax and decrease in Bcl-2 expression. The silencing of GPR-15 also caused a significant (P < 0.05) decline in the migration and invasion of the colorectal cancer cells. Bioinformatic analysis and luciferase assay revealed that the expression of GPR15 to be post-transcriptionally regulated by microRNA-1225 (miR-1225). The expression of miR-1225 was found to significantly (P < 0.05) downregulated in colorectal cancer cells and its overexpression caused suppression of GPR15 and inhibited the proliferation of the colorectal cancer cells. Nonetheless, overexpression of GPR15 could avoid the growth inhibitory effects of miR-1225. The results suggest that the GPR15/miR-1225 axis play an important role in the development of colon rectal cancer and exhibit therapeutic implications for its treatment.

The role of CAF derived exosomal microRNAs in the tumour microenvironment of melanoma

Exosomes play a crucial role in the crosstalk between cancer associated fibroblasts (CAFs) and cancer cells, contributing to carcinogenesis and the tumour microenvironment. Recent studies have revealed that CAFs, normal fibroblasts and cancer cells all secrete exosomes that contain miRNA, establishing a cell-cell communication network within the tumour microenvironment. For example, miRNA dysregulation in melanoma has been shown to promote CAF activation via induction of epithelial-mesenchymal transition (EMT), which in turn alters the secretory phenotype of CAFs in the stroma. This review assesses the roles of melanoma exosomal miRNAs in CAF formation and how CAF exosome-mediated feedback signalling to melanoma lead to tumour progression and metastasis. Moreover, efforts to exploit exosomal miRNA-mediated network communication between tumour cells and their microenvironment, and their potential as prognostic biomarkers or novel therapeutic targets in melanoma will also be considered.

Targeting cellular senescence as a new approach to chronic obstructive pulmonary disease therapy

Increasing evidence suggests that there is acceleration of normal lung ageing in chronic obstructive pulmonary disease (COPD), with the accumulation of senescent cells in the lung, which release an array of inflammatory proteins, which drive further senescence and disease progression. This suggests that drugs that target cellular senescence (senotherapies) may treat the underlying disease process in COPD and reduce disease progression and mortality. Several existing or future drugs may inhibit the development of cellular senescence, which is driven by chronic oxidative stress (senostatics), whereas other drugs selectively remove senescent cells (senolytics). Clinical studies of senotherapies have commenced in several age-related diseases, and these approaches appear to be safe and feasible, although no clinical studies in COPD patients have yet been reported.

Biomarkers for hepatocellular cancer

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. If diagnosed early, curative treatment options such as surgical resection, loco-regional therapies, and liver transplantation are available to patients, increasing their chances of survival and improving their quality of life. Unfortunately, most patients are diagnosed with late stage HCC where only palliative treatment is available. Therefore, biomarkers which could detect HCC early with a high degree of sensitivity and specificity, may play a crucial role in the diagnosis and management of the disease. This review will aim to provide an overview of the different biomarkers of HCC comprising those used in the diagnosis of HCC in at risk populations, as well as others with potential for prognosis, risk predisposition and prediction of response to therapeutic intervention.

Nociceptive related microRNAs and their role in rheumatoid arthritis

Rheumatoid Arthritis (RA) is an autoimmune disease with unknown etiology and a global incidence around 1%, a positive family history increases the risk of RA roughly three to five times. Pain is one of the first symptoms to appear in this disease. MicroRNAs (miRNAs) belong to the class of small non-coding RNAs; they regulate multiple cellular processes including embryonic development, cellular proliferation, differentiation and apoptosis among others. A great deal of evidence points to the employment of miRNAs as therapeutic targets and biomarkers for several pathologies. The main objective of this Review is to assess how miRNAs participate in the pathogenesis of RA. Two advanced searches were conducted in databases, one using "micro-RNA" and "rheumatoid arthritis" as key words, and another one with "micro-RNA", "pain" and "nociception". In this Review, we describe how six miRNAs: miR-16-5p, miR-23b-3b, miR-124-3p, miR-146a-5p, miR-155-5p and miR-223-3p, involved in the modulation and transmission of the nociceptive input are unregulated in RA patients. Key molecular pathways involved in nociception, inflammation and autoimmune responses, are regulated by these miRNAs; the NF-κB, TNF-α, interleukins and TLR4. By means of gene repression, the miRNAs here described modulate the nociceptive process as well as the autoimmune response that characterize this disease.

Potential roles of microRNA-1 and microRNA-133 in cardiovascular disease

Cardiovascular disease is still the main cause of morbidity and mortality worldwide. Currently, the frontier of research into cardiovascular disease is the field of non-coding RNA. In this review, information was collected on the use of micro-RNAs as non-invasive biomarkers and their role in pathophysiological processes and therapeutic applications. In the case of microRNA-1 and microRNA-133, the roles and regulatory mechanisms of them are reviewed for arrhythmia, myocardial infarction, diabetic cardiomyopathy, myocardial hypertrophy, cardiomyocyte differentiation, and cell reprogramming. It was observed that microRNA-1 and microRNA-133 do not exist independently, but are two co-transcriptional and cooperative regulatory factors. They have diagnostic value as biomarkers, but also have the potential as therapeutic targets such as for antiarrhythmia and cardiac reprogramming.

Molecular Cardioprotection and the Role of Exosomes: The Future Is Not Far Away

Heart disease is the leading cause of death in men and women in the United States. During the past several decades, research into the role of specific intracellular mediators, called exosomes, has advanced the understanding of molecular cardioprotection. Exosomes and the micro-RNAs within them may be potential targets for the development of genetically engineered or biosimilar medications for patients in heart failure or with ischemic cardiac disease. This review discusses anesthetic implications of exosome production and the future micro-RNA applications for cardioprotection.

Quantitation of Molecular Pathway Activation Using RNA Sequencing Data

Intracellular molecular pathways (IMPs) control all major events in the living cell. IMPs are considered hotspots in biomedical sciences and thousands of IMPs have been discovered for humans and model organisms. Knowledge of IMPs activation is essential for understanding biological functions and differences between the biological objects at the molecular level. Here we describe the Oncobox system for accurate quantitative scoring activities of up to several thousand molecular pathways based on high throughput molecular data. Although initially designed for gene expression and mainly RNA sequencing data, Oncobox is now also applicable for quantitative proteomics, microRNA and transcription factor binding sites mapping data. The Oncobox system includes modules of gene expression data harmonization, aggregation and comparison and a recursive algorithm for automatic annotation of molecular pathways. The universal rationale of Oncobox enables scoring of signaling, metabolic, cytoskeleton, immunity, DNA repair, and other pathways in a multitude of biological objects. The Oncobox system can be helpful to all those working in the fields of genetics, biochemistry, interactomics, and big data analytics in molecular biomedicine.

Evaluation of Micro-RNA Levels, Apoptosis and Oxidative Stress Markers in Patients Recieving Chemotherapy

OBJECTIVE

The primary objective of this study was to compare oxidative DNA damage markers, apoptosis markers and changes in miRNA levels in patients diagnosed with cancer and treated through chemotherapy. Our secondary objective was also to evaluate tumor responses that can be determined after post-chemotherapy clinical evaluations by physical examinations, laboratory results and radiological imagings, and to compare the clinical results to oxidative stress and apoptosis markers and micro RNA levels.

MATERIALS AND METHODS

To do that we designed a prospective observational cross-sectional study. A total of 34 cancer patients and 27 healthy controls were included in the study from the Harran University School of Medicine Department of Oncology. Newly diagnosed chemotherapy or radiotherapy naive patients without any chronic diseases were included into the study. Patients with a poor performance status (ECOG 2 and 3) and patients who did not meet the inclusion criteria were excluded. The cancer patients received chemotherapy according to their scheduled periods. Blood samples were taken from the patients before the first chemotherapy course and before the second chemotherapy round. Patients were called for toxicity control on the 10th day after the chemotherapy. Pre-chemotherapy, post-chemotherapy and control group miR-29a expression levels, change in apoptosis markers and oxidative DNA damage markers were obtained and compared. We studied 8-hydroxy 2-deoxyguanosine, total oxidant status, total anti-oxidant status, and oxidative status index for oxidative stress markers. We studied M30 and M65 as apoptosis markers. Clinical results of efficiency of the chemotherapy was acquired and compared to biochemical markers based on chemotherapy results. Chemotherapy toxicities were recorded.

RESULTS

As a result, we found oxidative DNA damage markers and apoptosis markers were high in the cancer group, demonstrating that oxidative DNA damage and apoptosis might play a direct or indirect role in cancer etiology. However, there were subtle differences between pre-chemotherapy and post-chemotherapy levels. Mir-29a expressions were lower in cancer patients as compared to controls. However, the expression levels were not significantly change in pre- and postchemotherapy status. Moreover, we found no relationship between clinical status of patients (progression and regression) and studied biochemical markers.

CONCLUSION

Thus, checking for DNA damage markers and taking precautions to lower the levels of these markers in individuals with cancer risk may be helpful in preventing cancer.

Profiling the microRNA signature of the peripheral sensory ganglia in experimental autoimmune encephalomyelitis (EAE)

BACKGROUND

Multiple sclerosis is an autoimmune disease with a distinct female bias, as well as a high prevalence of neuropathic pain in both sexes. The dorsal root ganglia (DRG) contain the primary sensory neurons that give rise to pain, and damage to these neurons may lead to neuropathic pain. Here, we investigate the sex differences of the DRG transcriptome in a mouse model of MS.

METHODS

Next-generation sequencing was used to establish RNA and microRNA profiles from the DRG of mice with MOG_35-55-induced EAE, a model of CNS inflammation that mimics aspects of MS. Differential expression and multiple meta-analytic approaches were used to compare expression profiles in immunized female and male mice. Differential expression of relevant genes and microRNAs were confirmed by qPCR.

RESULTS

Three thousand five hundred twenty genes and 29 microRNAs were differentially expressed in the DRG of female mice with MOG_35-55-EAE, while only 189 genes and 3 microRNAs were differentially expressed in males with MOG_35-55-EAE. Genes related to the immune system were uniquely regulated in immunized female mice. Direct comparison of sex within disease indicates significant differences in interferon and phagosomal pathways between the sexes. miR-21a-5p is the primary dysregulated microRNA in both sexes, with females having additional dysregulated microRNAs, including miR-122-5p.

CONCLUSIONS

This study provides evidence that females are uniquely affected by MOG_35-55-EAE and that this difference may result from additional signaling not present in the male. The altered transcriptome of females correlates with other studies finding hyperactivity of pain-sensing neurons and suggests underlying sex-specific pathways for neuropathic pain.

MicroRNA-374 targets JAM-2 regulates the growth and metastasis of human pancreatic cancer cells

Pancreatic cancer is one of the devastating human cancers responsible for tremendous human mortality. Current study was undertaken to explore the therapeutic potential of microRNA-374 in human pancreatic cancer. The results showed that microRNA-374 exhibited lower expression in pancreatic cancer cells and tissues. Overexpression of microRNA-374 in cancer cells resulted in significant decrease in the cell viability. The inhibition of the cell viability was mainly due to the induction of apoptosis as evident from the DAPI and AO/EB staining. Annexin V/PI staining also showed that the overexpression of microRNA-374 enhanced the percentage of apoptotic cells. The western blot analysis showed that microRNA-374 overexpression increases Bax and decreased the Bcl-2 expression. The cleaved PARP and Cleaved caspase-3 expression was also considerably increased upon miR-374 overexpression. The TargetScan analysis together with the dual luciferase assay showed that microRNA-374 targets JAM-2 by binding to mRNA at 3'-UTR. The qRT-PCR analysis showed that JAM-2 was significantly upregulated in the pancreatic cancer cell lines and tissues. Moreover, Overexpression of miR-374 suppressed the expression of JAM-2. Additionally, suppression of JAM-2 also inhibited the viability of the pancreatic cancer cells. In vivo studies in xenografted mice models showed that microRNA-374 expression is effective in suppressing the growth and volume of pancreatic tumors. In conclusion, microRNA-374 is downregulated in pancreatic cancers and may exhibit therapeutic implications in the pancreatic cancer treatment.