Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease

The cases of inflammatory bowel disease (IBD) are increasing rapidly around the world. Due to the multifactorial causes of IBD, there is an urgent need to understand the pathogenesis of IBD. As such, the usage of high-throughput techniques to profile genetic mutations, microbiome environments, transcriptome and proteome (e.g. lipidome) is increasing to understand the molecular changes associated with IBD, including two major etiologies of IBD: Crohn disease (CD) and ulcerative colitis (UC). In the case of transcriptome data, RNA sequencing (RNA-seq) technique is used frequently. However, only protein-coding genes are analyzed, leaving behind all other RNAs, including non-coding RNAs (ncRNAs) to be unexplored. Among these ncRNAs, long non-coding RNAs (lncRNAs) may hold keys to understand the pathogenesis of IBD as lncRNAs are expressed in a cell/tissue-specific manner and dysregulated in a disease, such as IBD. However, it is rare that RNA-seq data are analyzed for lncRNAs. To fill this gap in knowledge, we re-analyzed RNA-seq data of CD and UC patients compared with the healthy donors to dissect the expression profiles of lncRNA genes. As inflammation plays key roles in the pathogenesis of IBD, we conducted loss-of-function experiments to provide functional data of IBD-specific lncRNA, lung cancer associated transcript 1 (LUCAT1), in an in vitro model of macrophage polarization. To further facilitate the lncRNA research in IBD, we built a web database, IBDB (https://ibd-db.shinyapps.io/IBDB/), to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in IBD patients compared with healthy donors.

Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages

The NLRP3 inflammasome plays a pivotal role in regulating inflammation and immune responses. Its activation can lead to an inflammatory response and pyroptotic cell death. This is beneficial in the case of infections, but excessive activation can lead to chronic inflammation and tissue damage. Moreover, while most of the mammalian genome is transcribed as RNAs, only a small fraction codes for proteins. Among non-protein-coding RNAs, long non-coding RNAs (lncRNAs) have been shown to play key roles in regulating gene expression and cellular processes. They interact with DNA, RNAs, and proteins, and their dysregulation can provide insights into disease mechanisms, including NLRP3 inflammasome activation. Here, we systematically analyzed previously published RNA sequencing (RNA-seq) data of NLRP3 inflammasome activation in monocytes/macrophages to uncover inflammasome-regulated lncRNA genes. To uncover the functional importance of inflammasome-regulated lncRNA genes, one inflammasome-regulated lncRNA, ENSG00000273124, was knocked down in an in vitro model of macrophage polarization. The results indicate that silencing of ENSG00000273124 resulted in the up-regulation tumor necrosis factor (TNF), suggesting that this lncRNA might be involved in pro-inflammatory response in macrophages. To make our analyzed data more accessible, we developed the web database InflammasomeDB.

Methods and Tools in RNA Biology

Breakthroughs in innovative techniques and instruments have driven the exploration of non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) [...].

DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes

Cancer and cardiovascular disease are the leading causes of death worldwide. Recent evidence suggests that these two life-threatening diseases share several features in disease progression, such as angiogenesis, fibrosis, and immune responses. This has led to the emergence of a new field called cardio-oncology. Doxorubicin is a chemotherapy drug widely used to treat cancer, such as bladder and breast cancer. However, this drug causes serious side effects, including acute ventricular dysfunction, cardiomyopathy, and heart failure. Based on this evidence, we hypothesize that comparing the expression profiles of cells and tissues treated with doxorubicin may yield new insights into the adverse effects of the drug on cellular activities. To test this hypothesis, we analyzed published RNA sequencing (RNA-seq) data from doxorubicin-treated cells to identify commonly differentially expressed genes, including long non-coding RNAs (lncRNAs) as they are known to be dysregulated in diseased tissues and cells. From our systematic analysis, we identified several doxorubicin-induced genes. To confirm these findings, we treated human cardiac fibroblasts with doxorubicin to record expression changes in the selected doxorubicin-induced genes and performed a loss-of-function experiment of the lncRNA MAP3K4-AS1. To further disseminate the analyzed data, we built the web database DoxoDB.

T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes

Type II diabetes (T2D) is a growing health problem worldwide due to increased levels of obesity and can lead to other life-threatening diseases, such as cardiovascular and kidney diseases. As the number of individuals diagnosed with T2D rises, there is an urgent need to understand the pathogenesis of the disease in order to prevent further harm to the body caused by elevated blood glucose levels. Recent advances in long non-coding RNA (lncRNA) research may provide insights into the pathogenesis of T2D. Although lncRNAs can be readily detected in RNA sequencing (RNA-seq) data, most published datasets of T2D patients compared to healthy donors focus only on protein-coding genes, leaving lncRNAs to be undiscovered and understudied. To address this knowledge gap, we performed a secondary analysis of published RNA-seq data of T2D patients and of patients with related health complications to systematically analyze the expression changes of lncRNA genes in relation to the protein-coding genes. Since immune cells play important roles in T2D, we conducted loss-of-function experiments to provide functional data on the T2D-related lncRNA USP30-AS1, using an in vitro model of pro-inflammatory macrophage activation. To facilitate lncRNA research in T2D, we developed a web application, T2DB, to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in T2D patients compared to healthy donors or subjects without T2D.

The Non-Coding RNA Journal Club: Highlights on Recent Papers-12

We are delighted to share with you our twelfth Journal Club and highlight some of the most interesting papers published recently [...].

Potential Usages of A-to-I RNA Editing Patterns as Diagnostic Biomarkers

Adenosine to inosine (A-to-I) RNA editing is one of the most frequent RNA modifications found in the mammalian transcriptome. Recent studies clearly indicate that RNA editing enzymes, adenosine deaminase acting on RNAs (ADARs), are upregulated in stressed cells and under dis-ease conditions, suggesting that monitoring RNA editing patterns might be useful as diagnostic biomarkers of various diseases. Here, we provide an overview of epitranscriptomics, and focus particularly on the detection and analysis of A-to-I RNA editing using bioinformatic tools in RNA-seq datasets, as well as briefly reviewing the existing evidence about its involvement in disease progressions. Finally, we argue for the detection of RNA editing patterns as part of the routine analysis in RNA-based datasets, with the aim of accelerating the identification of RNA editing targets linked to disease.

Potential Involvement of LncRNAs in Cardiometabolic Diseases

Characterized by cardiovascular disease and diabetes, cardiometabolic diseases are a major cause of mortality around the world. As such, there is an urgent need to understand the pathogenesis of cardiometabolic diseases. Increasing evidence suggests that most of the mammalian genome are transcribed as RNA, but only a few percent of them encode for proteins. All of the RNAs that do not encode for proteins are collectively called non-protein-coding RNAs (ncRNAs). Among these ncRNAs, long ncRNAs (lncRNAs) are considered as missing keys to understand the pathogeneses of various diseases, including cardiometabolic diseases. Given the increased interest in lncRNAs, in this study, we will summarize the latest trend in the lncRNA research from the perspective of cardiometabolism and disease by focusing on the major risk factors of cardiometabolic diseases: obesity, cholesterol, diabetes, and hypertension. Because genetic inheritance is unavoidable in cardiometabolic diseases, we paid special attention to the genetic factors of lncRNAs that may influence cardiometabolic diseases.

Generation and characterization of induced pluripotent stem (iPS) cell line (SDUCTi001-A) using fibroblasts derived from male-healthy donor

Induced pluripotent stem (iPS) cell lines have wide valuable applications in experimental research, including developmental, pathological, and drug screening studies. Using integration-free episomal plasmids, we have generated a new iPS cell line from a 26-year-old healthy male donor. Characterization of the established cell line confirmed the expression of pluripotency markers, differentiation into the three germ layers, and absence of chromosomal abnormalities.

MicroRNAs in Cancer and Cardiovascular Disease

Although cardiac tumor formation is rare, accumulating evidence suggests that the two leading causes of deaths, cancers, and cardiovascular diseases are similar in terms of pathogenesis, including angiogenesis, immune responses, and fibrosis. These similarities have led to the creation of new exciting field of study called cardio-oncology. Here, we review the similarities between cancer and cardiovascular disease from the perspective of microRNAs (miRNAs). As miRNAs are well-known regulators of translation by binding to the 3'-untranslated regions (UTRs) of messenger RNAs (mRNAs), we carefully dissect how a specific set of miRNAs are both oncomiRs (miRNAs in cancer) and myomiRs (muscle-related miRNAs). Furthermore, from the standpoint of similar pathogenesis, miRNAs categories related to the similar pathogenesis are discussed; namely, angiomiRs, Immune-miRs, and fibromiRs.

The current status of gene expression profilings in COVID‐19 patients

Background

The global pandemic of coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has swept through every part of the world. Because of its impact, international efforts have been underway to identify the variants of SARS‐CoV‐2 by genome sequencing and to understand the gene expression changes in COVID‐19 patients compared to healthy donors using RNA sequencing (RNA‐seq) assay. Within the last two and half years since the emergence of SARS‐CoV‐2, a large number of OMICS data of COVID‐19 patients have accumulated. Yet, we are still far from understanding the disease mechanism. Further, many people suffer from long‐term effects of COVID‐19; calling for a more systematic way to data mine the generated OMICS data, especially RNA‐seq data.

Methods

By searching gene expression omnibus (GEO) using the key terms, COVID‐19 and RNA‐seq, 108 GEO entries were identified. Each of these studies was manually examined to categorize the studies into bulk or single‐cell RNA‐seq (scRNA‐seq) followed by an inspection of their original articles.

Results

The currently available RNA‐seq data were generated from various types of patients’ samples, and COVID‐19 related sample materials have been sequenced at the level of RNA, including whole blood, different components of blood [e.g., plasma, peripheral blood mononuclear cells (PBMCs), leukocytes, lymphocytes, monocytes, T cells], nasal swabs, and autopsy samples (e.g., lung, heart, liver, kidney). Of these, RNA‐seq studies using whole blood, PBMCs, nasal swabs and autopsy/biopsy samples were reviewed to highlight the major findings from RNA‐seq data analysis.

Conclusions

Based on the bulk and scRNA‐seq data analysis, severe COVID‐19 patients display shifts in cell populations, especially those of leukocytes and monocytes, possibly leading to cytokine storms and immune silence. These RNA‐seq data form the foundation for further gene expression analysis using samples from individuals suffering from long COVID.

Proteomic phenotype of cerebral organoids derived from autism spectrum disorder patients reveal disrupted energy metabolism, cellular components, and biological processes

The way in which brain morphology and proteome are remodeled during embryonal development, and how they are linked to the cellular metabolism, could be a key for elucidating the pathological mechanisms of certain neurodevelopmental disorders. Cerebral organoids derived from autism spectrum disorder (ASD) patients were generated to capture critical time-points in the neuronal development, and metabolism and protein expression were investigated. The early stages of development, when neurogenesis commences (day in vitro 39), appeared to be a critical timepoint in pathogenesis. In the first month of development, increased size in ASD-derived organoids were detected in comparison to the controls. The size of the organoids correlates with the number of proliferating cells (Ki-67 positive cells). A significant difference in energy metabolism and proteome phenotype was also observed in ASD organoids at this time point, specifically, prevalence of glycolysis over oxidative phosphorylation, decreased ATP production and mitochondrial respiratory chain activity, differently expressed cell adhesion proteins, cell cycle (spindle formation), cytoskeleton, and several transcription factors. Finally, ASD patients and controls derived organoids were clustered based on a differential expression of ten proteins-heat shock protein 27 (hsp27) phospho Ser 15, Pyk (FAK2), Elk-1, Rac1/cdc42, S6 ribosomal protein phospho Ser 240/Ser 244, Ha-ras, mTOR (FRAP) phospho Ser 2448, PKCα, FoxO3a, Src family phospho Tyr 416-at day 39 which could be defined as potential biomarkers and further investigated for potential drug development.

Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease

The largest solid organ in humans, the liver, performs a variety of functions to sustain life. When damaged, cells in the liver can regenerate themselves to maintain normal liver physiology. However, some damage is beyond repair, which necessitates liver transplantation. Increasing rates of obesity, Western diets (i.e., rich in processed carbohydrates and saturated fats), and cardiometabolic diseases are interlinked to liver diseases, including non-alcoholic fatty liver disease (NAFLD), which is a collective term to describe the excess accumulation of fat in the liver of people who drink little to no alcohol. Alarmingly, the prevalence of NAFLD extends to 25% of the world population, which calls for the urgent need to understand the disease mechanism of NAFLD. Here, we performed secondary analyses of published RNA sequencing (RNA-seq) data of NAFLD patients compared to healthy and obese individuals to identify long non-coding RNAs (lncRNAs) that may underly the disease mechanism of NAFLD. Similar to protein-coding genes, many lncRNAs are dysregulated in NAFLD patients compared to healthy and obese individuals, suggesting that understanding the functions of dysregulated lncRNAs may shed light on the pathology of NAFLD. To demonstrate the functional importance of lncRNAs in the liver, loss-of-function experiments were performed for one NAFLD-related lncRNA, LINC01639, which showed that it is involved in the regulation of genes related to apoptosis, TNF/TGF, cytokine signaling, and growth factors as well as genes upregulated in NAFLD. Since there is no lncRNA database focused on the liver, especially NAFLD, we built a web database, LiverDB, to further facilitate functional and mechanistic studies of hepatic lncRNAs.

Long Non-Coding RNAs in Cardiac and Pulmonary Fibroblasts and Fibrosis

The cardiopulmonary system delivers oxygen throughout the body via blood circulation. It is an essential part of the body to sustain the lives of organisms. The integral parts of the cardiopulmonary system—the heart and lungs—are constantly exposed to damaging agents (e.g., dust, viruses), and can be greatly affected by injuries caused by dysfunction in tissues (e.g., myocardial infarction). When damaged, mesenchymal cells, such as fibroblasts, are activated to become myofibroblasts to initiate fibrosis as part of a regenerative mechanism. In diseased states, the excess accumulation of extracellular matrices secreted by myofibroblasts results in further dysfunction in the damaged organs. These fibrotic tissues cannot easily be removed. Thus, there is a growing interest in understanding the fibrotic process, as well as finding biomolecules that can be targets for slowing down or potentially stopping fibrosis. Among these biomolecules, the interest in studying long non-coding RNAs (lncRNAs; any non-protein-coding RNAs longer than 200 nucleotides) has intensified in recent years. In this commentary, we summarize the current status of lncRNA research in the cardiopulmonary system by focusing on cardiac and pulmonary fibrosis.

Epitranscriptomics in fibroblasts and fibrosis

Fibroblasts play an important role in the pathogenic mechanisms of several socially significant diseases, including pulmonary and cardiovascular fibrosis, liver cirrhosis, systemic sclerosis, progressive kidney disease. The alterations of the epitranscriptome, including more than 170 distinct post-transcriptional RNA modifications or editing events, justified their investigation as an important modulator of fibrosis. Recent development of high-throughput methods allows the identification of RNA modification sites and their mechanistic aspect in the fibrosis development. The most common RNA modification is methylation of N⁶-adenosine deposited by the m⁶A methyltransferase complex (METTL3/14/16, WTAP, KIAA1429, and RBM15/15B), erased by demethylases (FTO and ALKBH5), and recognized by binding proteins (e.g., YTHDF1/2/3, YTHDC1/2, IGF2BP1/2/3, etc.). Adenosine to inosine (A-to-I) RNA editing is another abundant editing event converting adenosine to inosine in double-stranded RNA regions through the action of the adenosine deaminase (ADAR) proteins. Last, but not least, 5-methylcytosine (m⁵C) regulates the stability and translation of mRNAs. All those RNA modifications have been observed in mRNA as well as the non-coding regions of pre-mRNA and ncRNAs, and demonstrate to be involved in fibrosis in different cellular and animal models. This Mini-Review focuses on the latest research on epitranscriptomic marks related to fibroblast biology and fibrosis as well as elucidates the future research directions in this context.

Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions

Long non-coding RNAs (lncRNAs) belong to a class of non-protein-coding RNAs with their lengths longer than 200 nucleotides. Most of the mammalian genome is transcribed as RNA, yet only a small percent of the transcribed RNA corresponds to exons of protein-coding genes. Thus, the number of lncRNAs is predicted to be several times higher than that of protein-coding genes. Because of sheer number of lncRNAs, it is often difficult to elucidate the functions of all lncRNAs, especially those arising from their relationship to their binding partners, such as DNA, RNA, and proteins. Due to their binding to other macromolecules, it has become evident that the structures of lncRNAs influence their functions. In this regard, the recent development of epitranscriptomics (the field of study to investigate RNA modifications) has become important to further elucidate the structures and functions of lncRNAs. In this review, the current status of lncRNA structures and functions influenced by epitranscriptomic marks is discussed.

Superoxide dismutase isozymes in cerebral organoids from autism spectrum disorder patients

Autism spectrum disorder is a pervasive neurodevelopmental disorder with a substantial contribution to the global disease burden. Despite intensive research efforts, the aetiopathogenesis remains unclear. The Janus-faced antioxidant enzymes superoxide dismutase 1-3 have been implicated in initiating oxidative stress and as such may constitute a potential therapeutic target. However, no measurement has been taken in human autistic brain samples. The aim of this study is to measure superoxide dismutase 1-3 in autistic cerebral organoids as an in vitro model of human foetal neurodevelopment. Whole brain organoids were created from induced pluripotent stem cells from healthy individuals (n = 5) and individuals suffering from autism (n = 4). Using Pierce bicinchoninic acid and enzyme-linked immunosorbent assays, the protein and superoxide dismutase 1, 2, and 3 concentrations were quantified in the cerebral organoids at days 22, 32, and 42. Measurements were normalized to the protein concentration. Results represented using medians and interquartile ranges. Using Wilcoxon matched-pairs signed-rank test, an abrupt rise in the superoxide dismutase concentration was observed at day 32 and onwards. Using Wilcoxon rank-sum test, no differences were observed between healthy (SOD1: 35.56 ng/mL ± 3.46; SOD2: 2435.80 ng/mL ± 1327.00; SOD3: 1854.88 ng/mL ± 867.94) and autistic (SOD1: 32.85 ng/mL ± 5.26; SOD2: 2717.80 ng/mL ± 1889.10; SOD3: 1690.18 ng/mL ± 615.49) organoids. Cerebral organoids recapitulate many aspects of human neurodevelopment, but the diffusion restriction may render efforts in modelling differences in oxidative stress futile due to the intrinsic hypoxia and central necrosis.

Long Non-Coding RNAs in Induced Pluripotent Stem Cells and Their Differentiation

The breakthrough technology for reprogramming somatic cells into induced pluripotent stem cells (iPSC) has created a new path for science and medicine. The iPSC technology provides a powerful tool for elucidating the mechanisms of cellular differentiation and cell fate decision as well as to study targets and pathways relevant to pathological processes. Since they can be generated from any person, iPSC are a promising resource for regenerative medicine potentiating the possibility to discover new drugs in a high-throughput screening format and treat diseases through personalized cell therapy-based strategies. However, the reprogramming process is complex, and its regulation needs fine tuning. The regulatory mechanisms of cell reprogramming and differentiation are still not elucidated, but significant results show that multiple long non-coding RNAs (lncRNAs) play essential roles. In this mini review, we discuss the latest research on lncRNAs in iPSC stemness, neuronal and cardiac differentiation.

FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis

Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and various stress and disease conditions, respectively. To revisit this long-held concept, we focused on fibroblasts, a common cell type in various organs and tissues. Using fibroblasts and changes in their expression profiles during fibrosis as a model system, we show that the overall expression level of lncRNA genes is significantly lower than that of protein-coding genes. Furthermore, we identified lncRNA genes whose expression is upregulated during fibrosis. Using dermal fibroblasts as a model, we performed loss-of-function experiments and show that the knockdown of the lncRNAs LINC00622 and LINC01711 result in gene expression changes associated with cellular and inflammatory responses, respectively. Since there are no lncRNA databases focused on fibroblasts and fibrosis, we built a web application, FibroDB, to further promote functional and mechanistic studies of fibrotic lncRNAs.

Establishment of an induced pluripotent stem (iPS) cell line (SDUKIi006-A) from a 21-year old male patient diagnosed with atypical autism disorder

Autism is a complex neuropsychiatric disorder defined by significant challenges in communication skills and social behavior as well as repetitive conduct and interests. Recent advances in stem cell technologies allow in vitro modeling of the underlying molecular disease mechanisms. Using integration-free episomal plasmids, we have generated a novel iPS cell line (SDUKIi006-A) from a patient diagnosed with atypical autism ("FYNEN cohort" of Southern Denmark). Characterization of the established cell line validated its expression of pluripotency markers, differentiation into the three germ layers, and the absence of chromosomal abnormalities.

Generation of autism spectrum disorder patient-derived iPSC line SDUKIi004-A

Autism is a heterogeneous neurodevelopmental disorder defined by deficits in socialization, communication, and patterns of behavior. Using stem cells to model brain disordersmay yield new understanding about the underlying neuropathological processes and could prove essential for drug development. We present here a newhuman inducedpluripotentstem cell (iPSC) line (SDUKIi004-A) generated from skin fibroblasts derived from a 21-year old male patient diagnosed with Pervasive DevelopmentalDisorder-Not Otherwise Specified (PDD-NOS)("FYNEN-cohort"). Reprogramming of the fibroblasts was accomplished using integration-free episomal plasmids. Characterization validated the expression of pluripotency markers, differentiation into the three germ layers, and absence of chromosomal abnormalities.

Derivation of induced pluripotent stem cells (SDUKIi003-A) from a 20-year-old male patient diagnosed with Asperger syndrome

Autism spectrum disorder is a heterogenous neurodevelopmental disorder. The patients experience challenges in social interaction and communication skills as well as restricted and/or repetitive behaviors. To understand the molecular mechanisms underlying developmental brain disorders, patient-derived cellular models represent a useful tool. We have generated a human induced pluripotent stem cell line (SDUKIi003-A) from skin fibroblasts derived from a 20-year old male patient diagnosed with Asperger syndrome ("FYNEN-cohort" of Southern Denmark). The reprogramming of the fibroblasts was accomplished using integration-free episomal plasmids. Characterization validated the expression of pluripotency markers, differentiation into the three germ layers, and absence of chromosomal abnormalities.

In vitro models for ASD-patient-derived iPSCs and cerebral organoids

Autism spectrum disorder (ASD) is a set of pervasive neurodevelopmental disorders. The causation is multigenic in most cases, which makes it difficult to model the condition in vitro. Advances in pluripotent stem cell technology has made it possible to generate in vitro models of human brain development. Induced pluripotent stem cells (iPSCs) can be generated from somatic cells and have the ability to differentiate to all of the body's cells. This chapter aims to give an overview of the iPSC technology for generating neural cells and cerebral organoids as models for neurodevelopment and how these models are utilized in the study of ASD. The combination of iPSC technology and the genetic modification tool CRISPR/Cas9 is described, and current limitations and future perspectives of iPSC technology is discussed.

Artemin and an Artemin-Derived Peptide, Artefin, Induce Neuronal Survival, and Differentiation Through Ret and NCAM

Artemin (ARTN) is a neurotrophic factor from the GDNF family ligands (GFLs) that is involved in development of the nervous system and neuronal differentiation and survival. ARTN signals through a complex receptor system consisting of the RET receptor tyrosine kinase and a glycosylphosphatidylinositol-anchored co-receptor GFL receptor α, GFRα3. We found that ARTN binds directly to neural cell adhesion molecule (NCAM) and that ARTN-induced neuritogenesis requires NCAM expression and activation of NCAM-associated signaling partners, thus corroborating that NCAM is an alternative receptor for ARTN. We designed a small peptide, artefin, that could interact with GFRα3 and demonstrated that this peptide agonist induces RET phosphorylation and mimics the biological functions of ARTN – neuroprotection and neurite outgrowth. Moreover, artefin mimicked the binding of ARTN to NCAM and required NCAM expression and activation for its neurite elongation effect, thereby suggesting that artefin represents a binding site for NCAM within ARTN. We showed that biological effects of ARTN and artefin can be inhibited by abrogation of both NCAM and RET, suggesting a more complex signaling mechanism that previously thought. As NCAM plays a significant role in neurodevelopment, regeneration, and synaptic plasticity we suggest that ARTN and its mimetics are promising candidates for treatment of neurological disorders and warrant further investigations.

Epigenetics and cerebral organoids: promising directions in autism spectrum disorders

Autism spectrum disorders (ASD) affect 1 in 68 children in the US according to the Centers for Disease Control and Prevention (CDC). It is characterized by impairments in social interactions and communication, restrictive and repetitive patterns of behaviors, and interests. Owing to disease complexity, only a limited number of treatment options are available mainly for children that alleviate but do not cure the debilitating symptoms. Studies confirm a genetic link, but environmental factors, such as medications, toxins, and maternal infection during pregnancy, as well as birth complications also play a role. Some studies indicate a set of candidate genes with different DNA methylation profiles in ASD compared to healthy individuals. Thus epigenetic alterations could help bridging the gene-environment gap in deciphering the underlying neurobiology of autism. However, epigenome-wide association studies (EWAS) have mainly included a very limited number of postmortem brain samples. Hence, cellular models mimicking brain development in vitro will be of great importance to study the critical epigenetic alterations and when they might happen. This review will give an overview of the state of the art concerning knowledge on epigenetic changes in autism and how new, cutting edge expertise based on three-dimensional (3D) stem cell technology models (brain organoids) can contribute in elucidating the multiple aspects of disease mechanisms.

Brain-derived neurotrophic factor (BDNF) and neurotrophin 3 (NT3) levels in post-mortem brain tissue from patients with depression compared to healthy individuals - a proof of concept study

The neurotrophic factors (NTF) hypothesis of depression was postulated nearly a decade ago and is nowadays widely acknowledged. Previous reports suggest that cerebral concentrations of NTF may be reduced in suicide victims who received minimal or no antidepressant pharmacotherapy. Recent evidence suggests that antidepressant treatment may improve or normalise cerebral concentrations of neurotrophic factors. Therefore, we examined the concentration of brain-derived neurotrophic factor (BDNF) and neurotrophin 3 (NT3) in different brain regions (cortex, cingulate gyrus, thalamus, hippocampus, putamen and nucleus caudatus) of 21 individuals - 7 patients of which 4 patients with major depressive disorder (MDD) and overall age 86.8±5 years who received antidepressant pharmacotherapy (selective serotonin re-uptake inhibitors [SSRI]; tricyclic antidepressants [TCA]), 3 patients with MDD without antidepressant treatment and overall age 84.3±5 years versus 14 unaffected subjects at age 70.3±13.8. We detected significant elevation of BDNF (parietal cortex) and NT3 (parietal, temporal and occipital cortex, cingulate gyrus, thalamus, putamen and nucleus caudatus regions) in MDD patients who received antidepressant medication compared to MDD untreated patients and controls. Moreover, we detected a significant decrease of NT3 levels in the parietal cortex of patients suffering from MDD non-treated patients without treatment compared to healthy individuals. Although the limited statistical power due to the small sample size in this proof of concept study corroborates data from previous studies, which show that treatment with antidepressants mediates alterations in neuroplasticity via the action of NTF. However, more research using post-mortem brain tissue with larger samples needs to be carried out as well as longitudinal studies to further verify these results.

Mixed haemosporidian infections are associated with higher fearfulness in Yellow Wagtail (Motacilla flava)

Blood parasite infections have been shown to influence behavioural traits of their avian hosts, in particular activity level and boldness. Following the hypothesis that a mixed infection by different parasite species should have higher effects than single-species infections, we analysed activity and boldness in wild-caught Yellow Wagtails (Motacilla flava L., 1758), a trans-Saharan migrant, during the energetically demanding spring migration. Eighty-five percent of the birds were naturally infected with Haemoproteus Kruse, 1890 or Plasmodium Marchiafava and Celli, 1885 (Sporozoa, Haemosporida) and 27% of individuals had parasites from both genera. No differences in activity were found among uninfected, single infection, and mixed infection groups. Birds with infections from both genera appeared to be more fearful when first introduced to a cage. These birds also tended to be less likely to approach a novel object compared with uninfected birds and birds infected by a single genus only.

“Neurodevelopment in a dish” Elucidates the Mechanisms of Autism Spectrum Disorder

Introduction

Autism spectrum disorders (ASD) is a group of neurodevelopmental disorders characterized by deficits in social cognition, communication, and behavioral flexibility. Most of the cases appear to be caused by the combination of autism risk genes and environmental factors affecting early embryonal brain development. The current animal and 2D cellular models are not able to recapitulate the complex integrity of the developing brain. Therefore a model of the brain that can cast a light on the pathological processes during brain development is of a high need.

Aim and objectives

The aim of our research is to develop a three-dimensional brain organotypic system (brain organoids) for culturing patient's derived induced pluripotent stem cells (iPSC).

Methodology

We propose a multidisciplinary approach, involving the generation of patient specific iPSC from somatic cells (fibroblasts) and 3D culturing techniques to build a complex “humanized” in vitro platform for ASD research. Further we will investigate differences in gene expression of potential disease related markers and cellular phenotype between autistic patients and controls.

Results

Brain organoids have the ability to recreate the right complexity of the brain. On the cellular and gene expression level, organoids demonstrate a high similarity to the neurodevelopment in vivo and can therefore recapitulate early stages of the neurogenesis.

Conclusion

To date organoids are the most relevant cellular in vitro platform for the understanding the mechanisms behind ADS pathology. Organoids are a good modeling system for elucidating the role of epigenetic and environmental factors for development of ASD.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Effect of severe plastic deformation by ECAP on corrosion behaviour of aluminium alloy AA 7075

Purpose: The present study compares the corrosion behaviour of overaged AA 7075 before and after equal channel angular pressing ECAP in two media, containing chlorides, in order to answer the question how grain refinement of aluminium alloys influences their corrosion properties.Design/methodology/approach: The effect of equal channel angular pressing ECAP on corrosion behaviour of aluminium alloy AA 7075 was studied in two water solutions, containing chloride ions: 1) 0.01 M Na2SO4 with addition of 0.01%Cl-, and 2) 3g/l H2O2 and 57g/l NaCl. The changes in electrochemical characteristics, provoked by grain size refinement after equal channel angular pressing ECAP, were found using potentiodynamic polarisation. Steady state potential, corrosion potential, corrosion current density; breakdown (pitting) potential of overaged and deformed by equal channel angular pressing ECAP aluminium alloy AA 7075 were measured.Findings: In the environment with lower chloride concentration equal channel angular pressing ECAP process led to increase in pitting corrosion resistance and in the medium with higher chloride concentration - to decrease in pitting corrosion resistance. That way grain refinement does not demonstrate a uni-directional influence on corrosion resistance of AA 70775.Research limitations/implications: The results suggest the possibility for development of materials having the same chemical composition but with different corrosion resistance to different environments.Originality/value: The paper presents the corrosion behaviour of ultrafine-grained aluminium alloy AA 7075 and the influence of the chloride ions concentration in the corrosion medium on this behaviour.

Host preferences of ornithophilic biting midges of the genus Culicoides in the Eastern Balkans

Many biting midges of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) are competent vectors of a diverse number of pathogens. The identification of their feeding behaviour and of vector-host associations is essential for understanding their transmission capacity. By applying two different nested polymerase chain reaction (PCR) assays, of which one targeted the avian cyt b gene and the other targeted the COI gene of a wide range of vertebrates, we identified the blood hosts of six biting midge species including Culicoides circumscriptus, Culicoides festivipennis, Culicoides punctatus, Culicoides pictipennis, Culicoides alazanicus and Culicoides cf. griseidorsum, the latter two of which are reported in Bulgaria for the first time. Bird DNA was found in 50.6% of 95 investigated bloodmeals, whereas mammalian DNA was identified in 13.7%. Two Culicoides species were found to feed on both birds and mammals. There was remarkable diversity in the range of avian hosts: 23 species from four orders were identified in the abdomens of four Culicoides species. The most common bird species identified was the magpie, Pica pica (n = 7), which was registered in all four ornithophilic biting midge species. Six bloodmeals from the great tit, Parus major, were recorded only in C. alazanicus. None of the studied species of Culicoides appeared to be restricted to a single avian host.

Gold nanoparticle-based sensors activated by external radio frequency fields

A novel molecular beacon (a nanomachine) is constructed that can be actuated by a radio frequency (RF) field. The nanomachine consists of the following elements arranged in molecular beacon configuration: a gold nanoparticle that acts both as quencher for fluorescence and a localized heat source; one reporter fluorochrome, and; a piece of DNA as a hinge and recognition sequence. When the nanomachines are irradiated with a 3 GHz RF field the fluorescence signal increases due to melting of the stem of the molecular beacon. A control experiment, performed using molecular beacons synthesized by substituting the gold nanoparticle by an organic quencher, shows no increase in fluorescence signal when exposed to the RF field. It may therefore be concluded that the increased fluorescence for the gold nanoparticle-conjugated nanomachines is not due to bulk heating of the solution, but is caused by the presence of the gold nanoparticles and their interaction with the RF field; however, existing models for heating of gold nanoparticles in a RF field are unable to explain the experimental results. Due to the biocompatibility of the construct and RF treatment, the nanomachines may possibly be used inside living cells. In a separate experiment a substantial increase in the dielectric losses can be detected in a RF waveguide setup coupled to a microfluidic channel when gold nanoparticles are added to a low RF loss liquid. This work sheds some light on RF heating of gold nanoparticles, which is a subject of significant controversy in the literature.

Tracking neuronal marker expression inside living differentiating cells using molecular beacons

Monitoring gene expression is an important tool for elucidating mechanisms of cellular function. In order to monitor gene expression during nerve cell development, molecular beacon (MB) probes targeting markers representing different stages of neuronal differentiation were designed and synthesized as 2'-O-methyl RNA backbone oligonucleotides. MBs were transfected into human mesencephalic cells (LUHMES) using streptolysin-O-based membrane permeabilization. Mathematical modeling, simulations and experiments indicated that MB concentration was equal to the MB in the transfection medium after 10 min transfection. The cells will then each contain about 60,000 MBs. Gene expression was detected at different time points using fluorescence microscopy. Nestin and NeuN mRNA were expressed in approximately 35% of the LUHMES cells grown in growth medium, and in 80–90% of cells after differentiation. MAP2 and tyrosine hydroxylase mRNAs were expressed 2 and 3 days post induction of differentiation, respectively. Oct 4 was not detected with MB in these cells and signal was not increased over time suggesting that MB are generally stable inside the cells. The gene expression changes measured using MBs were confirmed using qRT-PCR. These results suggest that MBs are simple to use sensors inside living cell, and particularly useful for studying dynamic gene expression in heterogeneous cell populations.

SOX2 and OCT4 mRNA-expressing cells, detected by molecular beacons, localize to the center of neurospheres during differentiation

Neurospheres are used as in vitro assay to measure the properties of neural stem cells. To investigate the molecular and phenotypic heterogeneity of neurospheres, molecular beacons (MBs) targeted against the stem cell markers OCT4 and SOX2 were designed, and synthesized with a 2'-O-methyl RNA backbone. OCT4 and SOX2 MBs were transfected into human embryonic mesencephalon derived cells, which spontaneously form neurospheres when grown on poly-L-ornitine/fibronectin matrix and medium complemented with bFGF. OCT4 and SOX2 gene expression were tracked in individual cell using the MBs. Quantitative image analysis every day for seven days showed that the OCT4 and SOX2 mRNA-expressing cells clustered in the centre of the neurospheres cultured in differentiation medium. By contrast, cells at the periphery of the differentiating spheres developed neurite outgrowths and expressed the tyrosine hydroxylase protein, indicating terminal differentiation. Neurospheres cultured in growth medium contained OCT4 and SOX2-positive cells distributed throughout the entire sphere, and no differentiating neurones. Gene expression of SOX2 and OCT4 mRNA detected by MBs correlated well with gene and protein expression measured by qRT-PCR and immunostaining, respectively. These experimental data support the theoretical model that stem cells cluster in the centre of neurospheres, and demonstrate the use of MBs for the spatial localization of specific gene-expressing cells within heterogeneous cell populations.

In vivo transfection and/or cross-priming of dendritic cells following DNA and adenoviral immunizations for immunotherapy of cancer--changes in peripheral mononuclear subsets and intracellular IL-4 and IFN-gamma lymphokine profile

In order to provoke an immune response, a tumor vaccine should not only maximize antigen-specific signals, but should also provide the necessary "co-stimulatory" environment. One approach is to genetically manipulate tumor cells to either secrete lymphokines (GM-CSF, IL-12, IL-15) or express membrane bound molecules (CD80, CD86). Furthermore, patient dendritic cells can be loaded with tumor-associated antigens or peptides derived from them and used for immunotherapy. Genetic modification of dendritic cells can also lead to presentation of tumor-associated antigens. Transfection of dendritic cells with DNA encoding for such antigens can be done in vitro, but transfection efficiency has been uniformly low. Alternatively, dendritic cells can also be modulated directly in vivo either by "naked" DNA immunization or by injecting replication-deficient viral vectors that carry the tumor specific DNA. Naked DNA immunization offers several potential advantages over viral mediated transduction. Among these are the inexpensive production and the inherent safety of plasmid vectors, as well as the lack of immune responses against the carrier. The use of viral vectors enhances the immunogenicity of the vaccine due to the adjuvant properties of some of the viral products. Recent studies have suggested that the best strategy for achieving an intense immune response may be priming with naked DNA followed by boosting with a viral vector. We have successfully completed a phase I and phase II clinical trials on immunotherapy of prostate cancer using naked DNA and adenoviral immunizations against the prostate-specific membrane antigen (PSMA) and phase I clinical trial on colorectal cancer using naked DNA immunization against the carcinoembryonic antigen (CEA). The vaccination was tolerated well and no side effects have been observed so far. The therapy has proven to be effective in a number of patients treated solely by immunizations. The success of the treatment clearly depends on the stage of the disease proving to be most efficient in patients with minimal disease or no metastases. A panel of changes in the phenotype of peripheral blood lymphocytes and the expression of intra-T-cell lymphokines seems to correlate with clinical improvement.

Phosphodiesterase production in an aqueous two-phase system by Nicotiana tabacum 1507

Studies were conducted on the production of phosphodiesterases by Nicotiana tabacum 1507 cell suspension in an aqueous two-phase system formed by adding 4% polyethylene glycol (mol wt 20,000) and 7.5% dextran (mol wt 70,000) to the medium. The time course of growth, biosynthesis, secretion, and partitioning of phosphodiesterases was followed in comparison with N. tabacum 1507 cultivation as a free suspension. Partitioning of phosphodiesterases took place mainly in the bottom dextran phase, and a possibility was revealed for obtaining an enzyme preparation with high phosphodiesterase activity.

Characterization of novel methyl-branched chain fatty acids from a halophilic Bacillus species

The 4-methylated fatty acids 4,9-dimethyldecanoic, 4,11-dimethyldodecanoic, 4,10-dimethyldodecanoic, and 4,13-dimethyltetradecanoic acid as well as the 2-methylated fatty acids 2,13-dimethyltetradecanoic and 2,12-dimethyltetradecanoic acid were identified for the first time in nature in the halophilic bacterium Bacillus sp. isolated from the salt pans of Burgas in Bulgaria. The principal fatty acids in this bacterium were a series of iso-anteiso fatty acids with chain lengths between C11 and C19, but an interesting series of linear alkylbenzene fatty acids with chain lengths between C10 and C14, such as 12-phenyldodecanoic acid, were also identified. The novel 4-methylated fatty acids were characterized using a combination of GC-MS and chemical transformations such as N-acylpyrrolidide derivatization. The 2-methylated fatty acids were also identified by GC-MS and gas chromatographic coelution with synthetic samples. The novel methyl-branched fatty acids probably originated from the selective incorporation of methylmalonyl-CoA by one of the fatty acid-synthesizing enzymes of the bacterium.