Int. J. Transl. Med., Volume 1, Issue 3 (December 2021) – 14 articles

Non-coding RNAs (ncRNAs) are functional RNA molecules that comprise about 80% of both mammals and prokaryotes genomes. Recent studies have identified a large number of small regulatory RNAs in Escherichia coli and other bacteria. In prokaryotes, RNA regulators are a diverse group of molecules that modulate a wide range of physiological responses through a variety of mechanisms. Similar to eukaryotes, bacterial microRNAs are an important class of ncRNAs that play an important role in the development and secretion of proteins and in the regulation of gene expression. Similarly, riboswitches are cis-regulatory structured RNA elements capable of directly controlling the expression of downstream genes in response to small molecule ligands. As a result, riboswitches detect and respond to the availability of various metabolic changes within cells. The most extensive and most widely studied set of small RNA regulators act through base pairing with RNAs. These types of RNAs are vital for prokaryotic life, activating or suppressing important physiological processes by modifying transcription or translation. The majority of these small RNAs control responses to changes in environmental conditions. Finally, clustered regularly interspaced short palindromic repeat (CRISPR) RNAs, a newly discovered RNA regulator group, contains short regions of homology to bacteriophage and plasmid sequences that bacteria use to splice phage DNA as a defense mechanism. The detailed mechanism is still unknown but devoted to target homologous foreign DNAs. Here, we review the known mechanisms and roles of non-coding regulatory RNAs, with particular attention to riboswitches and their functions, briefly introducing translational applications of CRISPR RNAs in mammals. Full article

Glycogen is present in all tissues, but it is primarily stored in the liver and in muscle. As a branched chain carbohydrate, it is broken down by phosphorylase and debrancher enzymes, which are cytoplasmic. It is also degraded by a lysosomal α-glucosidase (GAA) also known as acid α-glucosidase and lysosomal acid α-glucosidase. The deficiency of GAA in patients is known as Pompe disease, and the phenotypes as infantile, juvenile and later onset forms. Pompe disease is treated by enzyme replacement therapy (ERT) with a recombinant form of rhGAA. Following ERT in Pompe mice and human patients there is residual carbohydrate material present in the cytoplasm of cells. The goal of this work is to improve ERT and attempt to identify and treat the residual cytoplasmic carbohydrate. Initial experiments were to determine if rhGAA can completely degrade glycogen. The enzyme cannot completely degrade glycogen. There is a residual glycosylated protein as well as a soluble glycosylated protein, which is a terminal degradation product of glycogen and as such serves as a biomarker for lysosomal glycogen degradation. The glycosylated protein has a very unusual carbohydrate composition for a glycosylated protein: m-inositol, s-inositol and sorbitol as the major carbohydrates, as well as mannitol, mannose, glucose and galactose. This work describes the residual material which likely contains the same protein as the soluble glycosylated protein. The biomarker is present in serum of control and Pompe patients on ERT, but it is not present in the serum of Pompe mice not on ERT. Pompe mice not on ERT have another glycosylated protein in their serum which may be a biomarker for Pompe disease. This protein has multiple glycosylation sites, each with different carbohydrate components. These glycosylated proteins as well as the complexity of glycogen structure are discussed, as well as future directions to try to improve the outcome of ERT for Pompe patients by being able to monitor the efficacy of ERT in the short term and possibly to adjust the timing and dose of enzyme infusions. Full article

Nitric oxide (NO) is a proangiogenic factor acting through the soluble guanylate cyclase (sGC) pathway. However, angiogenic growth increases energy demand, which may be hampered by NO inhibition of cytochrome c oxidase (CcO). Then, NO activity would be the balanced result of sGC activation (pro-angiogenic) and CcO inhibition (anti-angiogenic). NO activity in a rat and eNOS^−/− mice aortic ring angiogenic model and in a tube formation assay (human aortic endothelial cells) were analyzed in parallel with mitochondrial O₂ consumption. Studies were performed with NO donor (DETA-NO), sGC inhibitor (ODQ), and NOS or nNOS inhibitors (L-NAME or SMTC, respectively). Experiments were performed under different O₂ concentrations (0–21%). Key findings were: (i) eNOS-derived NO inhibits angiogenic growth by a mechanism independent on sGC pathway and related to inhibition of mitochondrial O₂ consumption; (ii) NO inhibition of the angiogenic growth is more evident in hypoxic vessels; (iii) in the absence of eNOS-derived NO, the modulation of angiogenic growth, related to hypoxia, disappears. Therefore, NO, but not lower O₂ levels, decreases the angiogenic response in hypoxia through competitive inhibition of CcO. This anti-angiogenic activity could be a promising target to impair pathological angiogenesis in hypoxic conditions, as it occurs in tumors or ischemic diseases. Full article

Angiogenesis is essential during development or when tissue restoration and oxygenation is required. Limited or excessive formation of blood vessels is a hallmark of several pathologies, and many angiogenesis-related pathways are being studied to highlight potential targets for effective angiogenesis-stimulating or inhibiting therapeutic approaches. A few studies point to the adrenergic system as a significant regulator of angiogenesis, directly or indirectly. Functional adrenergic receptors are expressed on endothelial cells and affect their response to the adrenergic system. The latter can also upregulate the release of growth factors by mural cells of the vessel wall, blood cells or cancer cells, thus subsequently affecting endothelial cell functions and angiogenesis. In the present study we summarize up-to-date literature on the known effects of the adrenergic receptors on physiological and pathological angiogenesis. Full article

Diagnosis and management of proliferative diabetic retinopathy are reliant upon retinal imaging. A systematic literature review of non-invasive imaging to guide diagnosis and treatment of proliferative diabetic retinopathy was performed. There is a trend of moving away from invasive (e.g., fundus fluorescein angiography) to non-invasive (e.g., wide-field optical coherence tomography (OCT), OCT angiography and colour fundus photography) imaging modalities to allow for more objective assessments that can be readily repeated in a time-efficient manner without compromising patient safety. Such quantitative assessments generating large amounts of data could benefit from artificial intelligence approaches to aid clinical decision making. These non-invasive imaging modalities continue to improve both in terms of the quality of image acquisition and progress in image interpretation. It is important that newer non-invasive imaging modalities are appropriately validated in large-scale prospective observational studies or randomised clinical trials. Full article

This is the world’s first tutorial article on Python Packaging for beginners and practitioners for translational medicine or medicine in general. This tutorial will allow researchers to demonstrate and showcase their tools on PyPI packages around the world. Nowadays, for translational medicine, researchers need to deal with big data. This paper describes how to build an executable Python Package Index (PyPI) code and package. PyPI is a repository of software for the Python programming language with 5,019,737 files and 544,359 users (programmers) as of 19 October 2021. First, programmers must understand how to scrape a dataset over the Internet; second, they must read the dataset file in csv format; third, build a program to compute the target values; fourth, convert the Python program to the PyPI package.; and fifth, upload the PyPI package. This paper depicts a covidlag executable package as an example for calculating the accurate case fatality rate (CFR) and the lag time from infection to death. You can install the covidlag by pip terminal command and test it. This paper also introduces deathdaily and scorecovid packages on PyPI Stats, which can inform how many users have downloaded the specified PyPI package. The usefulness and applicability of a developed tool can be verified by PyPI Stats with the number of downloaded users. Full article

The incidence of diabetes and the pathological conditions associated with chronic hyperglycemia is increasing worldwide. Among them, diabetic retinopathy represents a leading cause of vision loss, causing a significant structural and functional impairment of the retinal and choroidal capillary network. Current therapies include anti-angiogenic and anti-inflammatory drugs administered through repetitive and invasive intraocular injections, and associated with significant adverse effects. The presence of ocular barriers affects the efficiency of topically administered therapeutics for treating the posterior segment of the eye. In this scenario, nanomedicine could improve current therapies for diabetic retinopathy by providing tools that can decrease the number of injections thanks to their controlled release properties, while some materials showed a natural ability to mitigate pathological neo-angiogenesis. Moreover, specific surface modifications could open new scenarios for the development of topical treatments. This review describes current advances in generating nanomedicine for diabetic retinopathy, focusing on the properties of the different materials tested explicitly for this purpose. Full article

Diabetes mellitus (DM), a disorder rapidly growing in prevalence, is linked to the retinal microvasculature complication diabetic retinopathy (DR). As one of the leading global causes of vision impairment and loss, imaging techniques to detect and monitor DR must continue to improve in order to address this growing burden. Optical coherence tomography angiography (OCTA) is a nascent imaging modality that generates three-dimensional visualizations of the retinal and choroidal microvasculature. Compared to fluorescein angiography, the gold-standard imaging modality for retinal vessels, OCTA offers the advantages of being non-invasive, quick, and able to resolve the multiple plexuses within the retina. Quantitative OCTA studies have explored parameters such as vessel density (VD), foveal avascular zone (FAZ), acircularity index, vessel tortuosity (VT), and fractal dimension (FD) amongst DR patients. This review synthesizes the main trends emerging from quantitative OCTA-based studies of DR and interrogates them within the context of DR pathophysiology. We offer a glimpse into how analysis techniques have shifted in the years since OCTA came into existence, while speculating on its future role in clinical practice. Full article

The huge advancement in Internet web facilities as well as the progress in computing and algorithm development, along with current innovations regarding high-throughput techniques, enable the scientific community to gain access to biological datasets, clinical data and several databases containing billions of pieces of information concerning scientific knowledge. Consequently, during the last decade the system for managing, analyzing, processing and extrapolating information from scientific data has been considerably modified in several fields, including the medical one. As a consequence of the mentioned scenario, scientific vocabulary was enriched by novel lexicons such as machine learning (ML)/deep learning (DL) and overall artificial intelligence (AI). Beyond the terminology, these computational techniques are revolutionizing the scientific research in drug discovery pitch, from the preclinical studies to clinical investigation. Interestingly, between preclinical and clinical research, translational research is benefitting from computer-based approaches, transforming the design and execution of translational research, resulting in breakthroughs for advancing human health. Accordingly, in this review article, we analyze the most advanced applications of AI in translational medicine, providing an up-to-date outlook regarding this emerging field. Full article

Food insecurity (FI) has negative implications across the life course that include poor health outcomes among both children and adults. However, the behavioral mechanisms by which FI impacts health behaviors are not clear. By understanding how FI is related to cognitive function/brain structure across the life course, we can design more targeted interventions. A systematic literature review was performed by conducting comprehensive database searches in Google Scholar and PubMed. Inclusion criteria required studies to include measures of FI and cognitive function/brain structure in humans. Study sample, design, outcomes, and biases were extracted. In total, 17 studies met the inclusion criteria. Cognitive domains included general cognition (n = 13), executive function (n = 10), visuospatial abilities (n = 4), and verbal memory (n = 8). No studies examined brain structure. Most studies (88%) indicated significant inverse associations between FI and cognitive function across all stages of the life course, particularly for general cognition and executive function. Significant inverse associations were observed between FI and either general cognition or executive function among children (n = 3) and adults (n = 12). All studies considered confounding variables; however, given that all were observational, no causality can be inferred from the findings. These findings indicate that FI is related to lower cognitive function across the life course. Research should explore how changes in food security status impacts cognitive function and brain structure to develop optimal FI interventions and improve cognitive health. Full article

Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders that affects many individuals throughout their lives. Ulcerative colitis (UC) and Crohn’s disease (CD) are two major forms of IBD. Until the early 1990s, a murine model of spontaneous chronic colitis was unavailable. As a major breakthrough in the basic research field of IBD, three genetically manipulated murine chronic colitis models, including interleukin (IL)-2 knockout (KO), IL-10 KO, and T cell receptor alpha chain (TCRα) KO models, were established in 1993. Since then, complicated immunobiological mechanisms during the development of UC have been gradually discovered by utilizing a wide variety of murine models of IBD, including the TCRα KO mouse model. In particular, it has been recognized that four major factors, including enteric, environmental, and immunological factors as well as enteric microbiota are highly and mutually involved in the pathogenesis of UC. As a pioneer of the TCRα KO murine model of UC, our group has identified that the interactions between the unique TCRα-β+ T cell population and antigen-presenting cells, including dendritic cells and B cells, play a key role for the development and regulation of UC-like chronic colitis, respectively. Here we have summarized clinically proven pathogenic and regulatory factors which have been identified by this novel TCRα KO murine model of UC in the past nearly three decades. Full article

The progression of diabetes leads to macro and microvascular complications, including diabetic neuropathy, which is the most prevalent microvascular complication with diabetes. Clinical manifestations of diabetic neuropathy begin with the loss of distal sensory function, pain, and substantial morbidity. It has been evident that ~50% of diabetic patients develop neuropathy at a certain stage in their lifetime. Interestingly, two major subtypes (type I and II) of diabetes do not share the same epidemiology and pathophysiology of diabetic neuropathy; thus, their management or treatment strategies may vary from each other. The past few decades of research suggest that many etiological features, diagnosis, and management complexities depend on the type of diabetes. However, the underlying mechanism of neuropathy in type I and type II diabetes remains unclear. This review provides the current knowledge on successful assessment, management, and pharmacological biomarkers to explore the treatment and surpass current challenges in diabetic neuropathy. Full article

For many years the growth of solid tumors has been associated with their vascularization. The new vessels are needed to deliver oxygen and nutrients within the tumor mass. At the same time, these poorly stabilized vessels act as “Trojan horses” and open a way out for cancer cells. More recently, tumors have been identified whose growth appears to be independent of endothelial cell activity. Here we describe the ability of cancer cells to differentiate and reorganize themself in channels similar to blood vessels containing blood flow, overcoming the need for the angiogenic process of tumor vascularization. Together with the new vessels arising both from angiogenic and vasculogenic processes, these vessel-like structures can be exploited by tumor cells as a guide for migration and metastatic dissemination. In addition to classical intravascular dissemination, cancer cells can acquire pericytic features, interact with the endothelial basal lamina and migrate toward vessels or outside of the vessels. As expected, these alternative tumor behaviors assume greater importance if we consider that drugs with anti-angiogenic action directed against endothelial cells or their ligands are currently used in cancer therapy. Full article

The study aim is to investigate characteristics, barriers and enablers for attendance at the Diabetic Eye Screening Programme Northern Ireland (DESPNI) among people with diabetes aged 12–26 years. A mixed-methods approach with retrospective analysis and prospective, questionnaire-based data collection was completed. Data were analysed using ordinal logistic regression. A questionnaire collected information on barriers and enablers to attending DESPNI. Age, diabetes duration, attendance at diabetes clinic and lower HbA1c values were significantly associated with better attendance. Those aged 12–15 were more likely to attend screening than 16–26 years, odds ratio (OR) 4.01. Subjects diagnosed less than 5 years were more likely to attend than those with longer diabetes duration (OR = 2.52, p =< 0.001). Subjects who attended diabetes clinics were more likely to attend screening (OR = 1.89, p =< 0.001) and have a lower HbA1c (OR = 1.46, p =< 0.001). Questionnaires revealed major barriers to attendance which included inconvenient appointment times, lack of access and poor communication. While many subjects were aware of the impact of diabetes on the eye, many had little understanding of screening. This study provides pivotal information on potential barriers and enablers for young people attending eye screening. We suggest modest changes such as convenient appointment times, clearer communication and one-stop clinics could improve attendance. Full article