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Background and Aim: Escherichia coli pathobionts and particularly the adherent‐invasive E. coli (AIEC) may play a putative role in initiating and maintaining the inflammatory process in the intestinal tissues of inflammatory bowel disease (IBD) patients, by providing stimulatory factors that trigger gut immune system activation. The aim of this study is to conduct a systematic review and meta‐analysis to determine the prevalence of AIEC among patients with Crohn's disease (CD) and ulcerative colitis (UC). Methods: Electronic databases were searched up to February 2020 for relevant publications reporting the prevalence of AIEC in IBD patients. The prevalence rate of AIEC among CD and UC patients, the odds ratio (OR) and 95% confidence interval (CI) were calculated compared to non‐IBD controls. Results: The final dataset included 12 studies, all investigating AIEC isolates from ileal/colonic specimens. The OR for prevalence of AIEC in CD patients was 3.27 (95% CI 1.79–5.9) compared with non‐IBD controls. The overall pooled prevalence of AIEC among CD patients was 29% (95% CI 0.17–0.45), whereas this prevalence was calculated to be 9% (95% CI 0.03–0.19) in controls. Moreover, the prevalence of AIEC in UC subjects was calculated 12% (95% CI 0.01–0.34), while AIEC showed a prevalence of 5% (95% CI 0.0–0.17) among the controls. The OR for prevalence of AIEC in UC patients was 2.82 (95% CI 1.11–7.14) compared with controls. Conclusions: There is a substantial increase in the prevalence of AIEC in IBD patients compared with controls. This review supports the growing evidence that AIEC could be involved in both CD and UC pathogenesis. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) are emerging as the master regulators of tumor initiation, proliferation, and metastasis; however, their diagnostic value as potential biomarkers should be clarified. Vitamin D influences the expression of several genes in various pathways, including the CYP24A1 gene in the vitamin D metabolism pathway. In the present research, we surveyed the expression levels and clinical significance of novel lncRNAs related to CYP24A1 and PFDN4 genes in colorectal cancer (CRC) using real‐time polymerase chain reaction. Furthermore, we assessed the expression of these genes after vitamin D treatment in HCT‐116 and HT‐29 colon cancer cell lines. Our results indicated that the transcription of CYP24A1, PFDN4, and nearby lncRNAs was affected by vitamin D treatment in HCT‐116 and HT‐29 cell lines. Moreover, CYP24A1, PFDN4, lnc‐CYP24A1‐3:1, and lnc‐TSHZ2‐19:1 were upregulated and had the potential to distinguish colorectal cancer tissues from the adjacent tissues by the large area under the receiver operating characteristic curve (0.94, 0.66, 0.70, and 0.60, respectively). lnc‐TSHZ2‐19:1 expression level significantly correlated with gender (p =.03). In conclusion, CYP24A1, PFDN4, lnc‐CYP24A1‐3:1, and lnc‐TSHZ2‐19:1 can be used as potential diagnostic biomarkers in the specific and sensitive assessment of CRC. Besides this, vitamin D treatment may modulate the expression of these genes in a cell‐specific manner. [ABSTRACT FROM AUTHOR]

The human gastrointestinal (GI) tract harbors gut microbiome, which plays a crucial role in preserving homeostasis at the intestinal host‐microbial interface. Conversely, specific gut microbiota may be altered during various pathological conditions and produce a number of toxic compounds and oncoproteins, in turn, to induce both inflammatory response and carcinogenesis. Recently, promising findings have been documented toward the implementation of certain intestinal microbiome in the next era of cancer biology and cancer immunotherapy. Notably, intestinal microbiota can cooperate with immune checkpoint inhibitors (ICIs) of its host, especially in enhancing the efficacy of programmed death 1 (PD‐1) protein and its ligand programmed death ligand 1 (PD‐L1) blockade therapy for cancer. Herein, we review the dual function of gut microbiota in triggering GI cancers, its association with host immunity and its beneficial functions in modulation of cancer immunotherapy responses. Furthermore, we consider the significance of gut microbiota as a potential biomarker for predicting the efficacy of cancer immunotherapy. Finally, we summarize the relevant limitations that affect the effectiveness and clinical applications of gut microbiome in response to immunotherapy. [ABSTRACT FROM AUTHOR]

Background: Several studies have examined the relationship between diet quality indices and colorectal cancer (CRC). However, data on the association of these indices and colorectal adenomas (CRA) as a precursor of CRC are scarce. Our objective was to investigate the association of Healthy Eating Index (HEI-2010) and Mediterranean-Style Dietary Pattern Score (MSDPS) with CRC and CRA risk. Methods: This is a hospital-based case–control study including 259 cases (129 CRC and 130 CRA patients) and 240 controls with non-neoplastic conditions. Dietary intake of subjects was examined using a valid and reliable food frequency questionnaire. The HEI-2010 and MSDPS were then calculated based on a-priori methods. Multivariate logistic regression analyses were conducted to estimate the relationship between HEI-2010 and MSDPS and the risk of CRC and CRA. Results: After adjustment for confounders, compared with the first tertiles, the highest tertiles of HEI-2010 and MSDPS were significantly associated with lower odds of CRC (OR = 0.04; 95% CI = 0.01–0.12, OR = 0.19; 95% CI = 0.09–0.38, respectively). Similarly, the highest tertiles of HEI-2010 (OR = 0.04; 95% CI = 0.08–0.32) and MSDPS (OR = 0.19; 95% CI = 0.17–0.58) were associated with reduced odds of CRA compared to the lowest tertiles. Conclusion: The findings of this study suggested that a high-quality diet assessed by HEI-2010 and MSDPS is inversely associated with the risk of CRC and CRA. [ABSTRACT FROM AUTHOR]

Aim: In the present study, we evaluated the clinical prognostic value of human leukocyte antigen (HLA (Class I tumor cell expression in a series of colorectal cancer (CRC) patients and also explored the association of this expression profile with molecular features such as mutation status of KRAS and BRAF, microsatellite stability status, and clinicopathological characteristics of the patients.Patients and Methods: Formalin-fixed paraffin-embedded tumor tissue of 258 CRC patient's sections were immunohistochemically stained and subsequently quantified for HLA Class I expression by the tumor cells. Determination of microsatellite instability (MSI) tumor status was ascertained using mononucleotide repeat microsatellite targets. KRAS and BRAF mutations were screened by polymerase chain reaction (PCR)-sequencing and cast-PCR, respectively.Results: HLA Class I expression was normal in 91 cases (35.3%), downregulated in 119 (46.1%), and loss of expression in 48 (18.6%) cases. Forty (15.5%) tumors were MSI-H (MSH), 49 were MSI-L (19%), and 169 were microsatellite stable (MSS) (65.5%). Thirty-six (14%) and 15 (5.8%) of the patients exhibited mutation in the KRAS and BRAF, respectively. It was found that patients with downregulated expression of HLA Class I were associated with Stage II tumors (P < 0.001) and a MSS tumor status (P < 0.001), while patients with loss of expression were associated with MSH status (P < 0.001). Univariate and multivariate analyses revealed that HLA Class I downregulated expression was an independent prognostic parameter for shorter overall patient survival time (hazard ratio: 1.8, P = 0.003).Conclusions: HLA Class I expression is an independent and sensitive clinical prognostic marker that might be used in CRC patients. [ABSTRACT FROM AUTHOR]

Clostridioides difficile infection (CDI) is one of the most common causes of nosocomial diarrhea in developed countries and the main cause in healthcare settings. This case–control study was designed to evaluate the composition of the gut microbiota dominant bacterial groups in patients with CDI compared to the healthy control subjects. A total of 100 adult subjects involving 50 inpatients with CDI and 50 healthy persons were enrolled in the study. C. difficile isolates were characterized according to the anaerobic culture and presence of toxin genes with multiplex PCR. An ecological analysis was performed real-time quantitative PCR for bacterial elements. The abundances of Enterococcus spp., Lactobacillus spp., Escherichia coli, C. difficile, and Akkermansia muciniphila were higher in group CDI compared with group HC (P < 0.05). The abundances of Bacteroides spp., Bifidobacterium spp., and Faecalibacterium prausnitzii were lower in group CDI than in group HC (P < 0.05). No significant difference was observed in the copy number of Prevotella genus between the CDI and HC subjects (P-value = 0.087). We observed that economic status and income levels were reduced at patients with CDI, however, there was no significant difference between CDI and HC group results and other variables, such as age, BMI, and educational level. These findings showed a reduction in butyrate-producing bacteria and increase in lactic acid-producing bacteria was seen in CDI status. Overrepresentation of Akkermansia may be a predictive marker for the development of nosocomial diarrhea can result in a worse CDI prognosis. [ABSTRACT FROM AUTHOR]

Immune checkpoint (ICP) molecules modulate the immune response by either inducing or preventing T cell activation. Over-expression of some ICPs on malignant cells has been shown to regulate anti-tumor immune responses. We aimed to investigate the expression levels of two immune checkpoint molecules which have not been studied extensively in patients with colorectal cancer (CRC). Programmed Death Ligand 2 (co-inhibitory) and 4-1BB ligand (co-stimulatory) were assessed in tumor tissues of CRC patients compared to the adjacent normal tissues. Following tissue excision during surgical operation from 21 CRC patients, RNA extraction, cDNA synthesis and semi-quantitative real-time PCR were done for measuring the expressions of PD-L2 and 4-1BBL genes. In protein level, indirect immunohistochemistery (IHC) was performed on tissue sections. We revealed that PD-L2 was expressed in about 81% CRCs and insignificantly correlated with the tumor differentiation grade. Although a 3.25-fold change in the gene expression of PD-L2 was found in tumor tissues compared to the adjacent normal tissues (P = 0.005), but decreased level of 4-1BBL in counterpart tissues was not significant. Our results were confirmed by IHC for PDL-2 (P = 0.02) and 4-1BBL, however it was not statistically significant for the latter one. Although not significant, we could find an association between the elevated expression of PD-L2 and the tumor differentiation grade. Increased expression of negative regulator of the anti-tumor immune responses like PD-L2, as a prominent way of tumor escape, can be considered for cancer immunotherapy approaches in CRC patients using blocking monoclonal antibodies. [ABSTRACT FROM AUTHOR]

Background: Blastocystis is a protozoan parasite living in the intestine of humans and a wide range of animals. Although Blastocystis grows in several cultivation media, axenification and serial cultivations for long time are the main challenges of the researchers. Therefore, the long-term storage of subtypes/strains of Blastocystis using cryopreservation provides a suitable source of this parasite for the physiological, biochemical, and biological studies. Methods: In the current study, seven xenic isolates including two separated isolates from ST1-3 and one isolate from ST6 were cryopreserved using a standard method with minor modifications. After 3 months, all isolates were recovered and cultivated in DMEM medium. Results: The findings of the method showed all seven isolates were successfully recovered in DMEM medium. In addition, all isolates remained viable after several sub-cultures. Conclusions: It seems that cryopreservation is a simple method that can provide a suitable condition for the long-term storage of Blastocystis. [ABSTRACT FROM AUTHOR]

Purpose: To evaluate the prognostic role of BRAF and KRAS mutations after adjustment for microsatellite instability (MSI) in Iranian colorectal cancer (CRC) patients. Methods: BRAF and KRAS mutations and MSI status were assessed in 258 Iranian subjects with CRC. Two hundred fifty-eight consecutive stages I-IV CRC patients, who underwent surgical resection of adenocarcinoma from 2012 to 2016, were enrolled in the research. Pyrosequencing and Cast-PCR methods were used to the detection of KRAS and BRAF mutations. Kaplan-Meier and Cox regression were employed to estimate hazard ratios (HR) for the association between BRAF and KRAS mutation and overall survival (OS). Results: KRAS and BRAF mutations were detected in 36 (14%) and 15 (5.8%) cases of 258 patients with CRC, respectively. BRAF mutations that all comprised V600E and KRAS mutations was found in codon 12 and 13 (80.6% and 19.4%), respectively. KRAS mutations were detected in 19 (15.4%) patients of 123 microsatellite stable (MSS) CRC and it is significantly associated with tumor location and metastasis. BRAF and KRAS mutant vs. wild type of BRAF and KRAS, 5-year OS was 73.3% vs. 82.3% and 83.3% vs. 81.5% (long-rank P > 0.05), respectively. KRAS mutant vs. KRAS-wild-type tumors in MSS/MSI-L status CRC patients, 5-year OS was 78.9% vs. 90.4% (long-rank p = 0.046). Conclusion: The present study revealed that BRAF and KRAS mutations were not related to the worse overall survival, while KRAS mutation can be a prognostic factor for overall survival in sporadic microsatellite-stable (MSS) status in Iranian CRC patients. [ABSTRACT FROM AUTHOR]

Mesenchymal Stem Cells (MSCs) have therapeutic potential in a variety of diseases; however, the safety and efficacy of their use remain ambiguous. Clinical applications of MSCs are under intensive investigation due to their immunomodulatory features and lack of immune reactivity. Therefore, having a clear perspective on the exact mechanisms underlying the regulation of cytokine secretion in different microenvironments seems crucially important. In the current study, samples from human bone marrow and adipose were collected, and peripheral blood mononuclear cells (PBMCs) were isolated and cultured in conventional medium. After MSC expansion, the cells from passage 3 (P3) and passage 9 (P9) were utilized to identify MSC cell surface markers and their differentiation capacity. The P3, P5, P7, and P9 cells were used for RNA extraction to qualify the expression of the main immunomodulatory cytokines IDO, VCAM-1, TGF-β, IL-6, IL-10, and PGE2 at mRNA levels. The results indicate that VCAM-1 expression in the subcultures was reduced in bone marrow-derived MSCs. After an increase in P5, P7, and P9, IL-6 expression was reduced. In adipose-derived MSCs, the mRNA levels of IL-10 in higher passages were decreased compared with P3; other studied cytokines had no significant changes in their expression levels in either bone marrow or adipose-derived MSCs. Based on these results, it can be concluded that a suitable source for MSCs in cell therapy with stable expression of main cytokines, even in higher subcultures, appears to be adipose-derived MSCs with the exception of IL-10 secretion. [ABSTRACT FROM AUTHOR]

Blastocystis is a prevalent parasite that has a wide distribution. In order to design HRM real-time PCR, primers were selected from SSU rRNA gene to amplify specific fragment with different melting temperatures for each subtype of Blastocystis. Subsequently, HRM real-time PCR was performed and melting curve analysis was done by Rotor-Gene Q software. The results of HRM real-time PCR was then compared with sequence results of "barcoding region" of SSU rRNA gene of Blastocystis. To evaluate sensitivity of test, 10-fold serial dilutions of the parasite were prepared from ~ 106 to 1 parasite per mL of stool sample and were investigated by HRM real-time PCR. In order to determine specificity of method, HRM real-time PCR was done for some microorganisms and Blastocystis-negative stool samples. In silico analysis showed that all seventeen subtypes of Blastocystis were distinguish. In vitro analysis revealed that the test discriminated subtypes with specific melting temperatures. [ABSTRACT FROM AUTHOR]

Context: Patients with inflammatory bowel disease (IBD) were found to have the higher intestinal expression of Angiotensin-Converting Enzyme2 (ACE2) that could consequently increase susceptibility to COVID-19 infection. Objective: This study reports the outcomes of COVID-19 infection in a large cohort of IBD patients. We compare levels of serum ACE and IFN-α between COVID19 patients with and without IBD. We performed a cross-sectional retrospective multicenter study. Methods: We enrolled patients with IBD screened for SARS-COV-2 in six medical centres in Iran from June to November 2020. The blood samples were drawn to measure COVID-19 IgM and IgG, and serum levels of sACE2, sACE1, and interferon-α, regardless of suspicious symptoms have done the molecular test. Results: A total of 534 IBD patients were included in the study. Of these, 109 (20.0%) cases had detectable IgG and IgM against SARS-CoV-2. sACE2 levels were higher in IBD patients than controls, whereas ACE1and IFN-α levels were similar among groups. [ABSTRACT FROM AUTHOR]

Aim: This study aimed to evaluate high fat medium (HFM) effect on the gene expression profile of human Sk-hep1 cells and to determine critical differential proteins. Background: There is a correlation between high fat diet (HFD), obesity, and non-alcoholic fatty liver disease. Despite wide range of investigations, understanding molecular mechanism of HFD effect on onset and progression of NAFLD warrants further examination. In this study, network analysis is applied to obtain a clear perspective about HFD effects and NAFLD. Methods: Gene expression profiles of human Sk-hep1 cells treated with HFM versus controls were extracted from GEO. Data were analyzed by GEO2R where the significant and characterized DEGs were included in the PPI network. The top 10 nodes of query DEGs based on four centrality parameters were selected to determine central nodes. The common hub nodes with at least other one central group were identified as central nodes. Action map was provided for the introduced central nodes. Results: Heterogeneous nuclear ribonucleoprotein family including A1, A2/B1, D, R, and D-like, and five proteins (PRPF40A, SRSF1, PCF11, LSM8, and HSP90AA1) were introduced as differential proteins. Conclusion: mRNA processing and several biological terms including hypoxia and oxidative stress, apoptosis, regulation of cell morphology and cytoskeletal organization, and differentiation of micro tubes were introduced as dysregulated terms under HFM condition. [ABSTRACT FROM AUTHOR]

Non-invasive biomarkers of inflammatory bowel diseases (IBD) are of critical importance. Here, we evaluated the S100A8 and S100A9 mRNA expression, as the heterodimers of calprotectin, in the blood leucocytes of IBD patients to find how their expression associates with the disease characteristics. In this cross-sectional study, 59 IBD patients and 30 healthy subjects were included. The flare and remission phases of disease were identified in 46 and 13 patients, respectively. Blood leucocytes were isolated, and the S100A8 and S100A9 mRNA expression were evaluated in the isolated leucocytes using relative quantification real-time PCR. The mean S100A8 and S100A9 mRNA expression were significantly higher in IBD patients than in the controls (p = 0.03 and p = 0.02, respectively). The mean S100A8 and S100A9 mRNA expression were significantly higher in the flare phase of the disease compared with the remission phase (p = 0.01 and p = 0.007, respectively). S100A8 distinguished IBD patients from controls with the sensitivity and specificity of 73% and 64%, and flare phase of disease from remission with the sensitivity and specificity of 67% and 62%. On the other hand, S100A9 distinguished IBD patients from controls with the sensitivity and specificity of 81% and 70%, and flare phase of disease from remission with the sensitivity and specificity of 68% and 64%. The S100A8 and S100A9 mRNA are differentially expressed in blood leucocytes of IBD patients compared to healthy controls as well as active versus quiescent disease. Thus, they can be potentially used as a blood-based biomarker in the monitoring of IBD. [ABSTRACT FROM AUTHOR]

Background: Microsatellite instability (MSI) is a prognostic marker in colorectal cancer (CRC). The biological significance of MSI‐low (MSI‐L) phenotype and its differences with microsatellite stable (MSS) phenotype remains unclear. The aim of this study is indicating the role of mononucleotide repeat in identifying MSI‐L and revealing the association of MSI‐L with elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) and oncologic outcome in CRC patients. Methods: MSI and EMAST status were analyzed using three quasimonomorphic panel (BAT‐25, BAT‐26, and NR‐27) and five tetranucleotide repeats (D20S82, D20S85, D9S242, D8S321, and MYCL1), respectively, by capillary electrophoresis method without the need to fluorescent primers. The associations of MSI status with clinicopathological features, EMAST status, metastasis, and overall survival (OS) were investigated. Results: Among 159 CRC patient 22.0% were MSI‐H, 40.3% were MSS, 37.7% were MSI‐L, and 41.5% showed EMAST + phenotype. MSI‐L were associated with advanced stages, EMAST+ tumors and worse OS (p ≤ 0.001). Metastasis was relatively common in MSI‐L/EMAST + CRCs and BAT‐25 were the most unstable marker in these tumors. Conclusions: MSI‐L tumors have different clinicopathological features from MSS and MSI‐H tumors. The MSI‐L phenotype is a worse prognostic biomarker in CRC and when accompanied by EMAST could be a predictor for metastasis. [ABSTRACT FROM AUTHOR]