A genome-wide analysis of the molecular alterations occurring in the adenomatous and carcinomatous components of the same tumor based on the adenoma–carcinoma sequence

Identification of molecular alterations occurring in the adenomatous and carcinomatous components within the same tumor would greatly enhance understanding of the neoplastic progression of colorectal cancer. We examined somatic copy number alterations (SCNAs) and mRNA expression at the corresponding loci involved in the adenoma–carcinoma sequence in the isolated adenomatous and cancer glands of the same tumor in 15 cases of microsatellite-stable “carcinoma in adenoma,” using genome-wide SNP and global gene expression arrays. Multiple copy-neutral loss of heterozygosity events were detected at 4q13.2, 15q15.1, and 14q24.3 in the adenomatous component and at 4q13.2, 15q15.1, and 14q24.3 in the carcinomatous component. There were significant differences in the copy number (CN) gain frequencies at 20q11.21–q13.33, 8q13.3, 8p23.1, and 8q21.2–q22.2 between the adenomatous and carcinomatous components. Finally, we found a high frequency of five genotypes involving CN gain with upregulated expression of the corresponding gene (RPS21, MIR3654, RSP20, SNORD54, or ASPH) in the carcinomatous component, whereas none of these genotypes were detected in the adenomatous component. This finding is interesting in that CN gain with upregulated gene expression may enhance gene function and play a crucial role in the progression of an adenoma into a carcinomatous lesion.     

A portable,integrated analyzer for microfluidic – based molecular analysis

A portable, fully automated analyzer that provides actuation and flow control to a disposable, self-contained, microfluidic cassette (“chip”) for point-of-care, molecular testing is described. The analyzer provides mechanical actuation to compress pouches that pump liquids in the cassette, to open and close diaphragm valves for flow control, and to induce vibrations that enhance stirring. The analyzer also provides thermal actuation for the temperature cycling needed for polymerase chain reaction (PCR) amplification of nucleic acids and for various drying processes. To improve the temperature uniformity of the PCR chamber, the system utilizes a double-sided heating/cooling scheme with a custom feedforward, variable, structural proportional-integral-derivative (FVSPID) controller. The analyzer includes a programmable central processing unit that directs the sequence and timing of the various operations and that is interfaced with a computer. The disposable cassette receives a sample, and it carries out cell lysis, nucleic acid isolation, concentration, and purification, thermal cycling, and either real time or lateral flow (LF) based detection. The system’s operation was demonstrated by processing saliva samples spiked with B. cereus cells. The amplicons were detected with a lateral flow assay using upconverting phosphor reporter particles. This system is particularly suited for use in regions lacking centralized laboratory facilities and skilled personnel.     

Chronic cough – assessment of treatment efficacy based on two questionnaires

Introduction

Efficacy of chronic cough treatment is ambiguous. The aim of the study was to analyze chronic cough alleviation after specific treatment and the relationship between cough etiology and treatment efficacy.

Material and methods

A stepwise diagnostic approach was used to diagnose cough etiology in non-smoking adults with chronic cough. In all patients specific treatment was applied. Two different questionnaires – a visual analog scale and a 5-degree scale – were used to assess cough severity before and after 4-6 months of treatment.

Results

A significant correlation between pre-treatment and post-treatment results of both questionnaires was found (Spearman coefficient 0.43, p = 0.0003 and 0.73, p < 0.0001, respectively). Baseline questionnaire analysis revealed no differences in cough severity between patients with different cough causes or multiple cough causes. Although specific treatment resulted in a significant decrease of cough severity in the entire group, only partial improvement was noted. According to the visual analogue scale, a decrease of cough severity by at least 50% was achieved only in 54.4% of patients (37/68). Similarly, satisfactory improvement was noted in only 54.4% (37/68) of patients when using the 5-point scale. There were three sub-groups of patients, in whom no relevant decrease of cough severity was observed despite treatment: patients with 1. three coexisting cough causes, 2. non-asthmatic eosinophilic bronchitis, and 3. chronic idiopathic cough.

Conclusions

Cough severity does not depend on its etiology. Efficacy of chronic cough treatment in non-smoking patients is only moderate.     

Development of two enzyme-linked immunosorbent assay formats for thifluzamide residues’ analysis based on distinct polyclonal antibodies

Haptens 2-Methyl-4-(trifluoromethyl)thiazole-5-carboxylic acid and 2,6-Dibromo-4-(trifluoromethoxy)aniline, the two moieties of thifluzamide, were conjugated with carrier proteins for the synthesis of artificial antigens. Two distinct anti-thifluzamide polyclonal antibodies (PAb-1 and PAb-2) were produced from the immunized female Balb/c mice. The indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) in two formats based on the PAbs was developed for thifluzamide analysis. The concentration of 50% inhibition (IC₅₀) of ELISA-1 was 1.39?mg?L^?1 and its limit of detection (LOD) was 0.082?mg?L^?1. Meanwhile, ELISA-2 had a similar IC₅₀ of 1.96?mg?L^?1 and a LOD of 0.074?mg?L^?1 as ELISA-1. Both the raised PAbs exhibited high specificity to thifluzamide. The recoveries for spiked samples including water and wheat ranged from 72.0% to 128.4%, and the accuracy of ELISA was confirmed by high-performance liquid chromatography. In summary, the ic-ELISA might be a promising tool for simple, sensitive and rapid detection of thifluzamide residues in real samples.     

Repeat endocarditis: analysis of risk factors based on the International Collaboration on Endocarditis – Prospective Cohort Study

Repeat episodes of infective endocarditis (IE) can occur in patients who survive an initial episode. We analysed risk factors and 1-year mortality of patients with repeat IE. We considered 1874 patients enrolled in the International Collaboration on Endocarditis – Prospective Cohort Study between January 2000 and December 2006 (ICE-PCS) who had definite native or prosthetic valve IE and 1-year follow-up. Multivariable analysis was used to determine risk factors for repeat IE and 1-year mortality. Of 1874 patients, 1783 (95.2%) had single-episode IE and 91 (4.8%) had repeat IE: 74/91 (81%) with new infection and 17/91 (19%) with presumed relapse. On bivariate analysis, repeat IE was associated with haemodialysis (p 0.002), HIV (p 0.009), injection drug use (IDU) (p < 0.001), Staphylococcus aureus IE (p 0.003), healthcare acquisition (p 0.006) and previous IE before ICE enrolment (p 0.001). On adjusted analysis, independent risk factors were haemodialysis (OR, 2.5; 95% CI, 1.2–5.3), IDU (OR, 2.9; 95% CI, 1.6–5.4), previous IE (OR, 2.8; 95% CI, 1.5–5.1) and living in the North American region (OR, 1.9; 95% CI, 1.1–3.4). Patients with repeat IE had higher 1-year mortality than those with single-episode IE (p 0.003). Repeat IE is associated with IDU, previous IE and haemodialysis. Clinicians should be aware of these risk factors in order to recognize patients who are at risk of repeat IE.     

The growing role of precision medicine for the treatment of autoimmune diseases; results of a systematic review of literature and Experts’ Consensus

Autoimmune diseases (AIDs) share similar serological, clinical, and radiological findings, but, behind these common features, there are different pathogenic mechanisms, immune cells dysfunctions, and targeted organs. In this context, multiple lines of evidence suggest the application of precision medicine principles to AIDs to reduce the treatment failure.Precision medicine refers to the tailoring of therapeutic strategies to the individual characteristics of each patient, thus it could be a new approach for management of AIDS which considers individual variability in genes, environmental exposure, and lifestyle. Precision medicine would also assist physicians in choosing the right treatment, the best timing of administration, consequently trying to maximize drug efficacy, and, possibly, reducing adverse events.In this work, the growing body of evidence is summarized regarding the predictive factors for drug response in patients with AIDs, applying the precision medicine principles to provide high-quality evidence for therapeutic opportunities in improving the management of these patients.     

“How I treat” autoimmune diseases: State of the art on the management of rare rheumatic diseases and ANCA-associated systemic idiopathic vasculitis

This Special Issue of Autoimmunity Reviews constitutes summaries of presentations at the 20th International Meeting on Immunopathology and Orphan Diseases, held in Torino, Italy, 25–28th January 2017. As such, these presentations represent the state of the art on the pathophysiology of autoimmune diseases as well as the most recent insights into the management of these pathologic conditions. The latter includes both the optimal use of established drugs and approaches as well as novel knowledge on the means and consequences of targeted blocking of molecules or cellular mechanisms.The 2nd Turin Congress on systemic idiopathic vasculitis concluded the works of the International Meeting on Immune Pathology and Orphan Diseases.This Satellite Congress was mainly addressed to the management of antineutrophil cytoplasm antibody (ANCA)-associated vasculitis: advances on induction therapy and maintenance treatment. Guidelines and recommendations were critically discussed, reviewing available evidence and providing experts' insights. New intensive therapeutic approaches had been also reported.     

The laboratory approach to the diagnosis of autoimmune diseases: is it time to change?

Array technology and proteomics are about to launch the era of multiplexed analysis, which allows simultaneous detection of numerous autoantibody specificities and the possibility of defining broad autoantibody profiles. This will probably improve disease staging, risk stratification, prognosis and treatment. However, although these technologies are very promising, they are still in their infancy, and therefore need to undergo strict analytical and clinical validation processes. The latter should involve clinicians and pathologists in prospective, multicentric studies conducted on large numbers of patients to define the specific significance of the various autoantibody profiles. Establishing common standards for the publication and sharing of microarray-generated data will be important for this purpose. Only when these studies have been completed will these new technologies find a place in clinical laboratories. Although we are entering a decade which will probably see a radical change in the diagnostic approach to autoimmune diseases, we do not yet have sufficient knowledge to apply proteomic technologies on a large scale. For the time being, therefore, it is advisable to continue using well-established approaches and diagnostic algorithms such as those reported in the international guidelines, which have been prepared in accordance with the principles of appropriateness and evidence-based medicine.     

Regulation and dysregulation of Epstein–Barr virus latency: Implications for the development of autoimmune diseases

Epstein–Barr virus (EBV) is a human herpesvirus hiding in a latent form in memory B cells in the majority of the world population. Although, primary EBV infection is asymptomatic or causes a self-limiting disease, infectious mononucleosis, the virus is associated with a wide variety of neoplasms developing in immunosuppressed or immunodeficient individuals, but also in patients with an apparently intact immune system. In memory B cells, tumor cells, and lymphoblastoid cell lines (LCLs, transformed by EBV in vitro) the expression of the viral genes is highly restricted. There is no virus production (lytic viral replication associated with the expression of all viral genes) in tight latency. The expression of latent viral oncogenes and RNAs is under a strict epigenetic control via DNA methylation and histone modifications that results either in a complete silencing of the EBV genome in memory B cells, or in a cell-type dependent usage of latent promoters in tumor cells, germinal center B cells, and LCLs. Both the latent and lytic EBV proteins are potent immunogens and elicit vigorous B- and T-cell responses. In immunosuppressed and immunodeficient patients, or in individuals with a functional defect of EBV-specific T cells, lytic EBV replication is regularly activated and an increased viral load can be detected in the blood. Enhanced lytic replication results in new infection events and EBV-associated transformation events, and seems to be a risk factor both for malignant transformation and the development of autoimmune diseases. One may speculate that an increased load or altered presentation of a limited set of lytic or latent EBV proteins that cross-react with cellular antigens triggers and perpetuates the pathogenic processes that result in multiple sclerosis, systemic lupus erythematosus (SLE), and rheumatoid arthritis. In addition, in SLE patients EBV may cause defects of B-cell tolerance checkpoints because latent membrane protein 1, an EBV-encoded viral oncoprotein can induce BAFF, a B-cell activating factor that rescues self-reactive B cells and induces a lupus-like autoimmune disease in transgenic mice.     

The histological appearance of oesophageal adenocarcinoma—an analysis based on 215 resection specimens

The current study was performed to determine whether the histopathological appearance of oesophageal adenocarcinoma (AC) differs significantly from that of cardiac or gastric AC. Therefore, HE-stained slides of 215 primarily resected oesophageal AC, 108 cardiac and 184 gastric AC were classified according to a variety of clinico-pathologic parameters. According to Lauren’s classification, oesophageal AC (1.4%) less frequently belonged to the diffuse type than cardiac (2.8%) and gastric AC (23.9%; p<0.0001). Tubular and papillary AC, as defined by the WHO classification, were more frequent among oesophageal (94.4%) than among cardiac (87.0%) and gastric AC (59.2%; p<0.0001). Solid carcinomas, according to Carneiro’s classification, were less frequent among oesophageal (2.8%) than among cardiac (10.2%) and gastric AC (9.2%; p<0.0001). Oesophageal AC were graded more frequently G1/G2 (53.9%) than cardiac (30.6%) and gastric AC (27.7%; p<0.0001). Among oesophageal AC, Lauren’s classification (p=0.0067), Carneiro’s classification (p=0.0170), tumour grade (p=0.0005), lymphatic vessel invasion (p<0.0001) but not WHO classification were histological predictors of postoperative survival. In conclusion, oesophageal AC displays the same histological spectrum as cardiac and gastric AC. However, the relative proportion of differentiated, gland-forming carcinomas is significantly more frequent in the oesophagus than in the cardia and in the stomach.     

The genetic and molecular basis of muscular dystrophy: roles of cell–matrix linkage in the pathogenesis

Muscular dystrophies are a heterogeneous group of genetic disorders. In addition to genetic information, a combination of various approaches such as the use of genetic animal models, muscle cell biology, and biochemistry has contributed to improving the understanding of the molecular basis of muscular dystrophy's etiology. Several lines of evidence confirm that the structural linkage between the muscle extracellular matrix and the cytoskeleton is crucial to prevent the progression of muscular dystrophy. The dystrophin–glycoprotein complex links the extracellular matrix to the cytoskeleton, and mutations in the component of this complex cause Duchenne-type or limb-girdle-type muscular dystrophy. Mutations in laminin or collagen VI, muscle matrix proteins, are known to cause a congenital type of muscular dystrophy. Moreover, it is not only the primary genetic defects in the structural or matrix proteins, but also the primary mutations of enzymes involved in the protein glycosylation pathway that are now recognized to disrupt the matrix–cell interaction in a certain group of muscular dystrophies. This group of diseases is caused by the secondary functional defects of dystroglycan, a transmembrane matrix receptor. This review considers recent advances in understanding the molecular pathogenesis of muscular dystrophies that can be caused by the disruption of the cell–matrix linkage.     

Electrospinning of gelatin for tissue engineering – molecular conformation as one of the overlooked problems

Gelatin is one of the most promising materials in tissue engineering as a scaffold component. This biopolymer indicates biocompatibility and bioactivity caused by the existence of specific amino acid sequences, being preferred sites for interactions with cells, with high similarity to natural extracellular matrix. The present paper does not aspire to be a full review of electrospinning of gelatin and gelatin containing nanofibers as scaffolds in tissue engineering. It is focused on the still open question of the role of the higher order structures of gelatin in scaffold’s bioactivity/functionality. Gelatin molecules can adopt various conformations depending on temperature, solvent, pH, etc. Our review indicates the potential ways for formation of α-helix conformation during electrospinning and the methods of further structure stabilization. It is intuitively expected that the native α-helix conformation appearing as a result of partial renaturation of gelatin can be beneficial from the viewpoint of bioactivity of scaffolds, providing thus a much cheaper alternative approach as opposed to expensive electrospinning of native collagen.     

Anti-inflammatory and immunomodulating properties of statins. An additional tool for the therapeutic approach of systemic autoimmune diseases?

Cardiovascular diseases secondary to accelerated atherosclerosis are now accepted as a cause of mortality and morbidity in patients suffering from systemic lupus erythematosus and rheumatoid arthritis. More recently, atherosclerosis is emerging as one of the most serious complications in the anti-phospholipid syndrome, although large epidemiological studies, such as those performed in lupus and rheumatoid arthritis patients, have not been performed up to now. Classical risk factors (dislipidemia, hypertension, diabetes, smoking, etc.) and steroid therapy cannot completely explain the high prevalence of cardiovascular complications in systemic autoimmune diseases. Since the modern view defines atherosclerosis as a chronic inflammatory disorder, it has been suggested that systemic inflammation and soluble immune mediators (circulating autoantibodies, immune-complexes, complement activation products) might play a role in accelerating vessel pathology. The main target appears to be the endothelium because of its ability to switch to a pro-adhesive, pro-inflammatory and pro-coagulant surface in response to these mediators. Recent advances in the knowledge of the pharmacology of statins have indicated that these drugs rather than to be simple cholesterol lowering molecules display a pleiotropic effects on several mechanisms involved in the atherosclerotic plaque formation. Their anti-inflammatory activity and particularly their ability to downregulate endothelial cell activation induced by different stimuli strongly suggest their possible use in conditions in which the systemic inflammation and the endothelial activation/damage are through to represent key pathogenic mechanisms.     

The potential role for infections in the pathogenesis of autoimmune Addison’s disease

Autoimmune Addison’s disease (AAD), or primary adrenocortical insufficiency, is a classical organ-specific autoimmune disease with 160 years of history. AAD is remarkably homogeneous with one major dominant self-antigen, the cytochrome P450 21-hydroxylase enzyme, which is targeted by both autoantibodies and autoreactive T cells. Like most autoimmune diseases, AAD is thought to be caused by an unfortunate combination of genetic and environmental factors. While the number of genetic associations with AAD is increasing, almost nothing is known about environmental factors. A major environmental factor commonly proposed for autoimmune diseases, based partly on experimental and clinical data and partly on shared pathways between anti-viral immunity and autoimmunity, is viral infections. However, there are few reports associating viral infections to AAD, and it has proved difficult to establish which immunological processes that could link any viral infection with the initiation or progression of AAD. In this review, we will summarize the current knowledge on the underlying mechanisms of AAD and take a closer look on the potential involvement of viruses.     

Fowl adenovirus-induced diseases and strategies for their control – a review on the current global situation

The stand-alone pathogenicity of fowl adenoviruses (FAdVs) had long been disputed, given the ubiquity of the viruses versus sporadic outbreaks, and variation between experimental studies. However, a globally emerging trend of FAdV-associated diseases has marked the past two decades, with hepatitis-hydropericardium syndrome mainly in Asia besides Arabian and Latin American countries, and geographically more disseminated outbreaks of inclusion body hepatitis. Finally, the appearance of FAdV-induced gizzard erosion (AGE) in Asia and Europe completed the range of diseases. Epidemiological studies confirmed serotype FAdV-4 as agent of hepatitis-hydropericardium syndrome, whereas inclusion body hepatitis is related to FAdV-2, -8a, -8b and -11. Members of the biologically more distant serotype FAdV-1 induce AGE. Urged by increasing problems in the field, numerous pathogenicity studies with FAdVs from outbreaks substantiated the primary aetiologic role of particular strains for distinct clinical conditions.

Developments in the poultry industry towards highly specialized genetic breeds and rigorous biosecurity additionally contribute to the growing incidence of FAdV-related diseases. Confirming field observations, recent studies connected a higher susceptibility of broilers with their distinct physiology, implying the choice of bird type as a factor to be considered in infection studies. Furthermore, elevated biosecurity standards have generated immunologically naïve breeding stocks, putting broilers at risk in face of vertical FAdV transmission. Therefore, future prevention strategies should include adequate antibodies in breeders prior to production and – if necessary – vaccination, in order to protect progenies. This review aims to deliver a detailed overview on the current global situation about FAdV-induced diseases, their reproduction in vivo and vaccination strategies.