Targeting gut microbiota: new therapeutic opportunities in multiple sclerosis

Multiple sclerosis (MS) causes long-lasting, multifocal damage to the central nervous system. The complex background of MS is associated with autoimmune inflammation and neurodegeneration processes, and is potentially affected by many contributing factors, including altered composition and function of the gut microbiota. In this review, current experimental and clinical evidence is presented for the characteristics of gut dysbiosis found in MS, as well as for its relevant links with the course of the disease and the dysregulated immune response and metabolic pathways involved in MS pathology. Furthermore, therapeutic implications of these investigations are discussed, with a range of pharmacological, dietary and other interventions targeted at the gut microbiome and thus intended to have beneficial effects on the course of MS.

Expression of Genes Associated With Epithelial-Mesenchymal Transition in Merkel Cell Polyomavirus-Negative Merkel Cell Carcinoma

Two accepted possible pathways for Merkel cell carcinoma (MCC) pathogenesis include the clonal integration of the Merkel cell polyomavirus (MCPyV) into the neoplastic cells and by UV irradiation. We hypothesize that, in UV etiology, the expression of genes associated with epithelial-mesenchymal transition (EMT) would be higher in MCPyV-negative MCCs. We compared RNA expression in 16 MCPyV-negative with that in 14 MCPyV-positive MCCs in 30 patients using NanoString panel of 760 gene targets as an exploratory method. Subsequently, we confirmed the findings with a publicly available RNA sequencing data set. The NanoString method showed that 29 of 760 genes exhibited significant deregulation. Ten genes (CD44, COL6A3, COL11A1, CXCL8, INHBA, MMP1, NID2, SPP1, THBS1, and THY1) were part of the EMT pathway. The expression of CDH1/E-cadherin, a key EMT gene, and TWIST1, regulator gene of EMT, was higher in MCPyV-negative tumors. To further investigate the expression of EMT genes in MCPyV-negative MCCs, we analyzed publicly available RNA sequencing data of 111 primary MCCs. Differential expression and gene set enrichment analysis of 35 MCPyV-negative versus 76 MCPyV-positive MCCs demonstrated significantly higher expression of EMT-related genes and associated pathways such as Notch signaling, TGF-β signaling, and Hedgehog signaling, and UV response pathway in MCPyV-negative MCCs. The significance of the EMT pathway in MCPyV-negative MCCs was confirmed independently by a coexpression module analysis. One of the modules (M3) was specifically activated in MCPyV-negative MCCs and showed significant enrichment for genes involved in EMT. A network analysis of module M3 revealed that CDH1/E-cadherin was among the most connected genes (hubs). E-cadherin and LEF1 immunostains demonstrated significantly more frequent expression in MCPvV-negative versus MCPyV-positive tumors (P < .0001). In summary, our study showed that the expression of EMT-associated genes is higher in MCPyV-negative MCC. Because EMT-related proteins can be targeted, the identification of EMT pathways in MCPyV-negative MCCs is of potential therapeutic relevance.

Machine-learning-based Analysis Identifies miRNA Expression Profile for Diagnosis and Prediction of Colorectal Cancer: A Preliminary Study

BACKGROUND

The stage of colorectal cancer (CRC) at the day of diagnosis has the greatest influence on survival rate. Thus, for CRC, which is mainly identified as advanced disease, non-invasive, molecular blood or stool tests could boost the diagnosis and lower mortality. Evaluation of miRNA expression levels in serum of patients diagnosed with CRC is a potential tool in early screening. Screening can be supported by machine learning (ML) as a tool for developing a cancer risk predictive model based on genetic data.

MATERIALS AND METHODS

miRNA was isolated from the serum of 8 patients diagnosed with CRC and 10 patients from a control group matched for age and sex. The expression of 179 miRNAs was determined using a serum/plasma panel (Exiqon). Determinations were conducted using real-time PCR technique on an Applied Biosystems QuantStudio3 device in 96-well plates. A predictive model was developed through the Azure Machine Learning platform.

RESULTS

A wide panel of 29 up-regulated miRNAs in CRC were identified and divided into two subgroups: 1) miRNAs with significantly higher serum level in cancer patients vs. controls (24 miRNAs) and 2) miRNAs detected only in cancer patients and not in controls (5 miRNAs). Re-analysis of published miRNA profiles of CRC tumours or CRC exosomes revealed that only 2 out of 29 miRNAs were up-regulated in all datasets including ours (miR-34a and miR-25-3p).

CONCLUSION

Our research suggests the potential role of overexpressed miRNAs as diagnostic or prognostic biomarkers among CRC patients. Such clustering of miRNAs may be a potential direction for discovering new diagnostic panels of cancer (including CRC), especially using ML. The low correspondence between deregulation of miRNAs in serum and tumour tissue revealed in our study confirms previously published reports.

Expression Analysis of Tyrosine Phosphatase Genes at Different Stages of Renal Cell Carcinoma

BACKGROUND

Renal cell carcinoma (RCC) is a common urological cancer, and its risk correlates with environmental factors such as obesity, smoking and hypertension. Microarray technology enables analysis of the expression pattern of the whole phosphatome, members of which are involved in many cellular pathways and may act as either tumour suppressors or oncogenes in cancers.

MATERIALS AND METHODS

We analysed data for the expression level of 87 out of 107 known protein phosphatase genes included in the Hugo Gene Nomenclature Committee Website for 72 RCC tissues and paired healthy tissues obtained from the GEO Database.

RESULTS

Our analysis revealed overexpression of DUSP1, DUSP4, PTP4A3, PTPRC and PTPRE genes at all examined stages of RCC. Moreover, we found overexpression of PTPN12 at stage 2, overexpression of CDKN3 at stages 3 and 4, and overexpression of DUSP10 and PTPN22 at stages 2, 3 and 4. Lower expression of DUSP9, PTPR9 and PTPRO was also observed at all stages.

CONCLUSION

Significant changes in expression patterns of protein tyrosine phosphatase genes confirm the involvement of this group in crucial carcinogenesis pathways underlying RCC. Thus, we postulate that protein tyrosine phosphatases play an important role in RCC promotion and progression, and may be considered as potential therapeutic targets.

The Comparison Between Molecular Tumour Profiling in Microdissected and Surgical Tissue Samples

BACKGROUND/AIM

Laser capture microdissection (LCM) is one of the most important tools in molecular and histopathological tissue analysis. We compared the expression level of protein phosphatase genes in LCM and surgical colorectal cancer samples to evaluate whether there is a significant difference in molecular profiling.

MATERIALS AND METHODS

The expression levels of 99 protein phosphatase and 15 control genes were analysed in 104 microdissected, 81 surgical colorectal cancer and 25 control samples. Microarray expression data were obtained from the GEO Database of the National Center for Biotechnology Information.

RESULTS

The analysis revealed that over 60% of expression results were in agreement with LCM and surgically obtained samples while 32% of non-matched results belonged to the group where no effect was observed in LCM samples and down-regulation- or overexpression was reported in surgical samples.

CONCLUSION

Generally, it is more likely to find critical genetic alterations in surgically obtained than in LCM samples.

Association of the vitamin D receptor FokI gene polymorphism with sex- and non-sex-associated cancers: A meta-analysis

Currently higher morbidity and mortality rates are observed in cancer diseases, especially sex-dependent cancers. A positive role of endogenous vitamin D concentration in cancer diseases has been reported in many publications. Furthermore, there has been observed a relationship between serum vitamin D and testosterone concentrations in an elderly Caucasian population carrying the vitamin D receptor FokI gene polymorphism. The aim of this study was to investigate whether the vitamin D receptor FokI polymorphism is associated with cancerogenesis in sex-dependent cancers. The MEDLINE and ResearchGate databases were used to search for articles up to January 2017, and 96 articles concerning the FokI polymorphism were chosen. Odds ratios with 95% confidence intervals were used to assess the strength of associations between polymorphisms of vitamin D receptor and cancer risk in the described populations. The fixed-effects model and the DerSimonian-Laird random-effects model (with weights based on the inverse variance) were used to calculate summary odds ratios, and both within- and between-study variation were considered. Generally, the F variant reduces the risk of cancer by 4% (odds ratio = 0.96, p value = 0.0057). This effect is particularly evident in female sex-associated cancers (odds ratio = 0.96, 95% confidence interval: 0.93-0.99, p value = 0.0259), but it is not observed in non-sex-associated cancers. Polymorphism FokI is associated with breast and ovarian cancers.

The PTPN13 Y2081D (T>G) (rs989902) polymorphism is associated with an increased risk of sporadic colorectal cancer

AIM

Colorectal cancer (CRC) is one of the most common cancers worldwide and, although the majority of cases are sporadic, its development and progression depends on a range of factors: environmental, genetic and epigenetic. A variety of genetic pathways have been described as being crucial in CRC, including protein tyrosine phosphatases (PTPs). PTPN13 (also called FAP-1) is a non-receptor PTP and interacts with a number of important components of growth and apoptosis pathways. It is also involved in the inhibition of Fas-induced apoptosis.

METHOD

The single nucleotide polymorphism genotype at Y2081D (T>G) (rs989902) of PTPN13 exon 39 was determined in DNA extracted from blood samples from 174 sporadic CRC patients and 176 healthy individuals. Also, a meta-analysis was performed based on three articles accessed via the PubMed and ResearchGate databases.

RESULTS

The risk of CRC was 2.087 times greater for patients with the GG genotype than for those with the TT genotype (P = 0.0475). In the meta-analysis, a significantly increased risk of cancer associated with the G allele was observed in the squamous cell carcinoma of the head and neck subgroup (TT vs GG+GT, OR 1.23, 95% CI [1.02, 1.47], P = 0.0258), and a significantly decreased risk in the breast cancer subgroup (TT vs GG+GT, OR 0.63, 95% CI [0.41, 0.96], P = 0.0334) and in the CRC subgroup (GT+TT vs GG, OR 0.51, 95% CI [0.41, 0.95], P = 0.0333).

CONCLUSION

PTPN13 rs989902 is significantly associated with the risk of CRC in the Polish population. Given that this report provides the first evidence of an association of PTPN13 rs989902 with the risk of CRC in a Caucasian population, further large scale studies are necessary to confirm this finding.

High PTPRQ Expression and Its Relationship to Expression of PTPRZ1 and the Presence of KRAS Mutations in Colorectal Cancer Tissues

BACKGROUND

The risk of sporadic colorectal cancer (CRC) is strongly influenced by Iifestyle, environmental and genetic factors. Protein tyrosine phosphatases belong to a group of enzymes whose role in CRC has not yet been intensively studied. They play an important role in activation/de-activation of many enzymes, influencing cell biology by catalyzing reactions opposing those catalyzed by kinases. Protein tyrosine phosphatase receptor-like type Q (PTPRQ) and protein tyrosine phosphatase receptor-like type Z polypeptide 1 (PTPRZ1) have both been shown to be important in development of many cancer types including CRC.

MATERIALS AND METHODS

The expression level of PTPRQ and PTPRZ1 was determined by real-time polymerase chain reaction in 16 CRC tissues obtained from patients diagnosed with adenocarcinoma coli.

RESULTS

We revealed a high level of PTPRQ expression (p=0.0080), as well as an association between expression levels of PTPRQ and PTPRZ1 (p<0.0001). Moreover PTPRQ expression was higher in tissues presenting with Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation (p=0.0293).

CONCLUSION

We confirmed the contribution of PTPRZ1 and especially PTPRQ in CRC development, supporting the hypothesis that PTPRQ is a candidate oncogene, playing a crucial role in phosphorylation/dephosphorylation signaling pathways.

Vitamin D receptor gene polymorphisms in relation to the risk of colorectal cancer in the Polish population

The protective effect of vitamin D against several cancers including colorectal cancer is modulated by the vitamin D receptor (VDR) and its ligand, the active form of vitamin D. VDR response has been found to play a role in various genes encoding proteins involved in crucial cellular pathways. Single nucleotide polymorphisms (SNPs) of the VDR gene that modulate its activity are located in the promoter region, exons 2–9, and their vicinity and also in the 3′UTR region. Some of them have been previously studied in relation to cancer susceptibility and prognosis. The aim of our study was to investigate four polymorphisms, BsmI, ApaI, TaqI, and FokI, of the VDR gene in Polish patients with sporadic colorectal cancer and to evaluate their association with susceptibility to cancer. We found a significant association between the BsmI genotype and cancer (individuals with the bb genotype are more susceptible to cancer compared to those with other genotypes, p = 0.025, Fisher’s exact test for 2 × 2 table). Also, the TT genotype at TaqI and the AA genotype at ApaI are correlated with a higher risk of cancer (p = 0.00071 and p = 1.0 × 10⁻⁵, respectively). We found relatively strong linkage disequilibrium between the TaqI and ApaI loci (T with A and t with a, respectively). Both of these loci are associated with cancer. We do not observe any such association for the FokI polymorphism. In conclusion, a small modification in VDR expression may play a role in such a multipathway process as tumorigenesis.

Impact of the PPARGC1A Gly482Ser polymorphism on left ventricular structural and functional abnormalities in patients with hypertension

The Gly482Ser polymorphism in the peroxisome proliferator-activated receptor gamma coactivator-1α (PPARGC1A) has been reported to contribute to the development of left ventricular (LV) hypertrophy. Little is known, however, about its possible impact on cardiac dysfunction. Enhanced myocardial fibrosis accompanying increased LV mass might represent a link with coexisting functional abnormalities. We investigated the association between the PPARGC1A Gly482Ser polymorphism and LV morphology and performance in essential hypertension, with special consideration of fibrosis intensity. A total of 205 hypertensive patients (60±8 years) underwent echocardiography with assessment of cardiac morphology, LV systolic (strain and strain rate) and diastolic function (peak early diastolic mitral flow velocity/peak late diastolic mitral flow velocity (E/A) ratio, peak early diastolic myocardial velocity (Em), and E/e' ratio (where e' is the peak early diastolic mitral annular velocity)), evaluation of serum procollagen type III amino-terminal propeptide (PIIINP) and procollagen type I carboxy-terminal propeptide (PICP)-markers of fibrosis and the PPARGC1A Gly482Ser genotyping. Subjects with the Ser-Ser genotype demonstrated more profound LV hypertrophy and diastolic function impairment, and higher PICP/PIIINP than the Ser-Gly and Gly-Gly groups. In multivariable analysis, the presence of the Ser-Ser allele was an independent correlate of E/e' (β=0.17, P<0.02), Em (β=-0.18, P<0.01) and LV mass index (β=0.28, P<0.001). In conclusion, in hypertensive patients, the PPARGC1A Gly482Ser polymorphism is associated with LV hypertrophy and diastolic dysfunction, with the presence of the Ser-Ser allele promoting these abnormalities. One of the possible mechanisms mediating the adverse effect on diastolic performance might be a relative increase in the anabolism of rigid collagen type I over that of the more elastic collagen type III, as indicated by an increased ratio of PICP to PIIINP.

Cannabinoid receptor 1 gene polymorphisms and nonalcoholic Fatty liver disease in women with polycystic ovary syndrome and in healthy controls

Context. Polycystic ovary syndrome (PCOS) is frequently associated with nonalcoholic fatty liver disease (NAFLD). The endocannabinoid system may play a crucial role in the pathogenesis of NAFLD. Polymorphism of the cannabinoid receptor 1 gene (CNR1) may be responsible for individual susceptibility to obesity and related conditions. Objective. To determine the role of genetic variants of CNR1 in the etiopathology of NAFLD in women with PCOS. Design and Setting. Our department (a tertiary referral center) conducted a cross-sectional, case-controlled study. Subjects. 173 women with PCOS (aged 20-35) and 125 healthy, age- and weight-matched controls were studied. Methods. Hepatic steatosis was assessed by ultrasound evaluation. Single nucleotide polymorphisms of CNR1 (rs806368, rs12720071, rs1049353, rs806381, rs10485170, rs6454674) were genotyped. Results. Frequency of the G allele of rs806381 (P < 0.025) and the GG genotype of rs10485170 (P < 0.03) was significantly higher in women with PCOS and NAFLD than in PCOS women without NAFLD. Frequency of the TT genotype of rs6454674 was higher in PCOS women with NAFLD (not significantly, P = 0.059). In multivariate stepwise regression, allele G of rs806381 was associated with PCOS + NAFLD phenotype. Conclusion. Our preliminary results suggest the potential role of CNR1 polymorphisms in the etiology of NAFLD, especially in PCOS women.

Vitamin D receptor gene polymorphism and cardiovascular risk variables in elderly Polish subjects

The aim of this work was to evaluate whether the FokI and BsmI polymorphisms of the VDR gene are associated with anthropometric and biochemical features of cardiovascular disease (CVD) in a Caucasian population aged over 65, participants of the Polish PolSenior study. We performed the study on randomly selected subjects: 427 women and 454 men aged over 65. Measurements of anthropometric parameters were carried out and biochemical parameters were estimated using commercial kits. VDR polymorphisms (rs10735810, rs1544410) were genotyped by PCR and FRLP. The prevalence of BsmI genotypes was 50% Bb, 23% bb, 27% BB in women and 48% Bb, 20% bb, 32% BB in men. The prevalence of FokI was 48% Ff, 22% ff, 30% FF in women and 50% Ff, 18% ff, 32% FF in men. The women bearing the rare allele b differ in homeostatic model assessment (HOMA) (p < 0.049) from women bearing common allele B, and the men differ in insulin level (p < 0.047) and HOMA (p < 0.017). There were no significant differences in anthropometric or biochemical parameters between genotypes in FokI in female and male groups. The common allele B is connected with biochemical risk factors of CVD in older Caucasian men and women.

Normal exon copy number of the GLI2 and GLI3 genes in patients with esophageal atresia

Esophageal atresia (EA) is a congenital developmental defect of the alimentary tract concerning the interruption of the esophagus with or without connection to the trachea. The incidence of EA is 1 in 3000-3500 of live-born infants, and occurs in both isolated and syndromic (in combination with abnormalities in other organ systems) forms. The molecular mechanisms underlying the development of EA are poorly understood. Knockout studies in mice indicate that genes like Sonic hedgehog, Gli2, and Gli3 play a role in the etiology of EA. These facts led us to hypothesize that Sonic hedgehog-GLI gene rearrangements are associated with EA in humans. To test this hypothesis, we screened patients with isolated and syndromic EA for GLI2 and/or GLI3 microrearrangements using methods to estimate the copy number (Multiplex Ligation-dependent Probe Amplification, real-time polymerase chain reaction). To our best knowledge this is the first study assessing copy number of GLI2 and GLI3 genes in patients with EA.

DRD2 C313T and DRD4 48-bp VNTR polymorphisms and physical activity of healthy men in Lower Silesia, Poland (HALS study)

BACKGROUND

Both animal and human studies have proved that the dopaminergic system of the brain controls many aspects of behavior, e.g. motivation, addiction, motor movement, locomotion. It has been hypothesized that dopamine signalling may regulate spontaneous physical activity as well.

AIM

Literature data suggests that an intact function of dopamine receptors (DRD2-DRD4) inhibits physical activity. This study searched for associations between a propensity to be active (or sedentary) and genetic variants of DRD2 and DRD4.

SUBJECTS AND METHODS

Invitations to participate in the study were sent to 900 randomly selected, adult men living in Lower Silesia, Poland. Genotyping of DRD2 C313T and DRD4 48-bp VNTR polymorphisms of enrolled subjects (371 (DRD2 C313T) and 397 (DRD4 48-bp VNTR)) was performed. Level of physical activity was evaluated using the International Physical Activity Questionnaire (IPAQ).

RESULTS

No associations were found between level of physical activity (low, moderate, high) and the two polymorphisms: DRD2 C313T (p = 0.49) and DRD4 48-bp VNTR (p = 0.31). Studied subjects did not differ as to the number of hours spent sitting either.

CONCLUSION

The results exclude the presence of significant relationships between polymorphic variants of the dopamine receptors genes and the level of physical activity in men.

Intermediate- and low-methylation epigenotypes do not correspond to CpG island methylator phenotype (low and -zero) in colorectal cancer

BACKGROUND

Most recent genome-wide studies on the CpG island methylation in colorectal cancer (CRC) have led to the discovery of at least 3 distinct methylation clusters. However, there remains an uncertainty whether the CRC clusters identified in these studies represent compatible phenotypes.

METHODS

We carried out comprehensive genome-scale DNA methylation profiling by Illumina Infinium HumanMethylation27 of 21 DNA pools that represent 84 CRC samples divided according to their high-, intermediate-, and low-methylation epigenotypes (HME, IME, and LME, respectively) and 70 normal-adjacent colonic tissues. We have also examined the relationship among 3 epigenotypes and chromosomal gains and deletions (assessed by Comparative Genomic Hybridization) in a group of 100 CRC samples.

RESULTS

The HME subgroup showed features associated with CpG island methylator phenotype - high (CIMP-high) including methylation of specific CpG sites (CpGs) as well as significantly lower mean number of chromosomal imbalances when compared with other epigenotypes. The IME subgroup displayed the lowest number of methylated CpGs (717 vs. 2,399 and 2,679 in HME and LME, respectively) and highest mean number of chromosomal imbalances when compared with HME (P, 0.001) and LME (P, 0.004). A comparison between the methylation profiles of 3 epigenotypes revealed more similarities between the HME and LME (1,669 methylated CpGs overlapped) than HME and IME (673 methylated CpGs overlapped).

CONCLUSION

Our results provide evidence that IME and LME CRCs show opposite features to those that have been previously attributed to CIMP-low and CIMP-0 CRCs.

IMPACT

These discrepancies should be considered when interpreting the data from a particular epigenotyping method.

CAG repeat polymorphism in the androgen receptor gene and the level of physical activity (HALS Study)

AIM

Androgens influence human behavior. They affect sport performance, physical activity and emotional responses. CAG repeat polymorphism of androgen receptor (AR) gene is associated with transcriptional activity of AR. Decreased number of CAG repeats leads to increased androgen sensitivity. The purpose of this study was to investigate associations between AR CAG polymorphism and physical activity phenotype.

METHODS

Within the framework of the HALS Study we randomly selected 900 adult Caucasian males from one administrative region of Poland (Lower Silesia). Eventually, AR CAG repeat was genotyped by a PCR based assay in 360 male subjects. International Physical Activity Questionnaire (IPAQ) was used to determine the level of physical activity of studied subjects. It was expressed as multiples of resting metabolic rate by minutes of performance during a week (METs-minute/week).

RESULTS

No association between AR CAG repeat polymorphism and physical activity (P=0.2, ANOVA) was observed. Men with short CAG presented the lowest level of physical activity reaching 3.44 log (METs-minute/week) (SE 0.053; 95% CI, 3.34-3.54), while in men with medium and long CAG it was respectively 3.58 (SE 0.063; 95% CI, 3.46-3.71) and 3.52 (SE 0.039; 95% CI, 3.44-3.60) log (METs-minute/week).

CONCLUSIONS

There is no association between AR CAG repeat polymorphism and the level of physical activity in healthy men.

beta(3)-adrenergic receptor polymorphism and metabolic syndrome in postmenopausal women

OBJECTIVES

Some studies indicate that the Trp64Arg polymorphism in the gene encoding the beta(3)-adrenergic receptor (ADRB3) is associated with obesity, insulin resistance and earlier onset of type 2 diabetes mellitus. The aim of the present study was to evaluate the frequency of ADRB3 polymorphism and its association with metabolic syndrome in postmenopausal women.

METHODS

We performed the study on 284 randomly chosen postmenopausal women, aged 50-60 years, who were then selected to the study. Measurements of anthropometric parameters and biochemical estimations such as lipid profile, glucose and insulin level in serum were carried out using commercial kits. ADRB3 genotyping was performed by polymerase chain reaction and mini-sequencing.

RESULTS

The frequency of the Trp64/Arg64 genotype in the investigated population was 13%, and of the Trp64/Trp64 genotype, 85%. The Arg64/Arg64 genotype was present in only 2% of women. Metabolic syndrome was recognized in 22% of women bearing Trp64/Arg64 genotype and in 14% of women bearing Trp64/Trp64 genotype, without a statistically significant difference between the two groups (p > 0.05 in the chi(2) test). Women bearing the Trp64/Arg64 genotype had lower serum levels of high-density lipoprotein cholesterol (HDL-C) than Trp64/Trp64 genotype women (63.2 +/- 13.0 vs. 71.4 +/- 17.4 mg/dl). Both groups did not differ in any other investigated parameter.

CONCLUSION

Trp64Arg polymorphism of the beta(3)-adrenergic receptor gene is not related to metabolic syndrome in postmenopausal Polish women; however, it seems to be associated with decreased HDL-C levels.