Emerging circulating MiRNAs and LncRNAs in upper gastrointestinal cancers.

INTRODUCTION: Circulating non-coding RNAs (ncRNAs) possess high stability in circulation, making them capable of being utilized in the diagnosis, prognosis, and treatment of upper gastrointestinal (GI) tract cancers. AREAS COVERED: Herein, the potential clinical application of emerging circulating miRNAs and lncRNAs in upper GI cancers are comprehensively reviewed. EXPERT OPINION: For esophageal cancer (EC), the circulating miRNAs, miR-21, miR-223, and miR-375 have been validated as promising diagnostic biomarkers in a meta-analysis. For gastric cancer (GC), miR-17, miR-18a, miR-21, miR-25, miR-223, miR-451, and lncRNA-H19 have been reported in several studies and are likely to be promising biomarkers. Unlike EC, many circulating lncRNAs have been newly reported for GC and each is often limited to one study. They show excellent or outstanding discrimination performance, such as XIST, LOC100506474, UCA1, LINC00467, ZNFX1-AS1, HULC, AA174084, CEBPA-AS1, MIAT, PCSK2-2:1, HOTTIP, H19 (AUCs 0.8 to 0.9), and particularly CUDR, LSINCT-5, PTENP1, HOTAIR, and LncRNA-GC1 (AUCs > 0.9). Most importantly, using a group of ncRNAs as a diagnostic panel would give a more promising diagnostic or prognostic performance. However, different clinical trials and large, multi-center cohorts as well as comprehensive meta-analyses should also be conducted to validate and use emerging circulating ncRNAs as the indicators of GI cancers.

In silico identification of MAPK14-related lncRNAs and assessment of their expression in breast cancer samples.

Mitogen-activated protein kinase (MAP kinase) pathways participate in regulation of several cellular processes involved in breast carcinogenesis. A number of non-coding RNAs including both microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) regulate or being regulated by MAPKs. We performed an in-silico method for identification of MAPKs with high number of interactions with miRNAs and lncRNAs. Bioinformatics approaches revealed that MAPK14 ranked first among MAPKs. Subsequently, we identified miRNAs and lncRNAs that were predicted to be associated with MAPK14. Finally, we selected four lncRNAs with higher predicted scores (NORAD, HCG11, ZNRD1ASP and TTN-AS1) and assessed their expression in 80 breast cancer tissues and their adjacent non-cancerous tissues (ANCTs). Expressions of HCG11 and ZNRD1ASP were lower in tumoral tissues compared with ANCTs (P values < 0.0001). However, expression levels of MAPK14 and NORAD were not significantly different between breast cancer tissues and ANCTs. A significant association was detected between expression of HCG11 and estrogen receptor (ER) status in a way that tumors with up-regulation of this lncRNA were mostly ER negative (P value = 0.04). Expressions of ZNRD1ASP and HCG11 were associated with menopause age and breast feeding duration respectively (P values = 0.02 and 0.04 respectively). There was a trend towards association between ZNRD1ASP expression and patients' age of cancer diagnosis. Finally, we detected a trend toward association between expression of NORAD and history of hormone replacement therapy (P value = 0.06). Expression of MAPK14 was significantly higher in grade 1 tumors compared with grade 2 tumors (P value = 0.02). Consequently, the current study provides evidences for association between lncRNA expressions and reproductive factors or tumor features.

Assessment of anti-cancer effects of koenimbine on colon cancer cells.

BACKGROUND: Recent studies have highlighted the role of natural elements in reduction of cancer cell growth and apoptosis. Koenimbine, a natural product isolated from Murraya koenigii (L) Spreng is a substance with cytotoxic effects on cancer cells. AIM: The effects of koenimbine on HT-29 and SW48 colon cancer cells were evaluated by MTT and Annexin V assays. Expression levels of Wnt/ß-catenin pathway genes were quantified by real time PCR. RESULTS: The IC50 values of koenimbine in HT-29 and SW48 was calculated to be 50 µg/ml based on the results of MTT assay. This value was 75 µg/ml in IEC-18 cells which were used as normal control. Annexin V assays revealed induction of cell apoptosis and necrosis in HT-29 and SW48 cells but not IEG18 cells by koenimbine. Koenimbin treatment resulted in significant down-regulation of CYCLD1 expression in SW48 cell line, but up-regulation of this gene in HT29 cell line. Expression of TBLR1, DKK1, GSK3B and ß-catenin was significantly decreased after koenimbin treatment in HT-19 cell line. Moreover, expression of DKK1 and GSK3B was significantly decreased after koenimbin treatment in SW-40 cell line. TCF4 expression was not detected in any of cell lines either before or after treatment with koenimbin. CONCLUSION: The current in vitro study showed the cytotoxic effects of koenimbin on two colon cancer cell lines and the effects of this substance on expression of selected genes from Wnt-ß catenin pathway. Future in vivo studies are needed before suggestion of this substance as an anti-cancer drug.

Expression analysis of growth arrest specific 8 and its anti-sense in breast cancer tissues.

The Growth arrest specific 8 (GAS8) and its anti-sense transcript (GAS8-AS1) are located in a genomic region that is frequently mutated in breast cancer. These transcripts have established tumor suppressor effects in some human malignancies. In the current investigation, we aimed at identification of the role of GAS8 and GAS8-AS1 in breast cancer. We measured gene expression of GAS8 and GAS8-AS1 in paired tumoral and non-tumoral tissues obtained from 88 breast cancer patients by means of real time PCR. No significant differences were identified in expressions of GAS8 and GAS8-AS1 in tumoral samples compared with non-tumoral tissues (Fold changes = 1.53 and 1.71; P values = .28 and 0.14 respectively). Transcript levels of GAS8-AS1 was significantly correlated with estrogen receptor (ER) status (P = .01). Expression of GAS8 gene was associated with history of oral contraceptive use (P = .04). The similar expressions of GAS8 and GAS8-AS1 genes in tumoral and non-tumoral tissues of breast in spite of previous reports regarding their fundamental tumor suppressor roles in other tissues show that these genes are not involved in the pathogenesis of breast cancer. So, these genes have distinct roles in diverse tissues.

Gene expression of indoleamine and tryptophan dioxygenases and three long non-coding RNAs in breast cancer.

The kynurenine pathway (KP) has a principal role in the metabolism of tryptophan. This pathway is also involved in the pathogenesis of cancer. We evaluated expression of two rate limiting enzymes from this pathway (IDO1 and TDO2) as well as three long non-coding RNAs (lncRNAs) that have been predicted to alter expression of IDO1 (ITGB2-AS1, HCP5 and MIR155HG) in 82 breast cancer tissues and their adjacent non-cancerous tissues (ANCTs). While IDO1 expression levels were not significantly different between malignant tissues and ANCTs (expression ratio = 0.56, P = .21), TDO2 was significantly down-regulated in malignant tissues compared with ANCTs (Expression ratio = 0.001, P < .001). Among lncRNAs, expression of HCP5 was significantly lower in malignant tissues compared with ANCTs (Expression ratio = 0.17, P < .001). However, expression of ITGB2-AS1 was higher in malignant tissues compared with ANCTs (Expression ratio = 3.38, P = .01). Expressions of genes were not associated with any of clinical or demographic data of patients. However, there were trends towards association between IDO1 expression and tumor size as well as estrogen receptor (ER) status (P values 0.09 and 0.08 respectively). Significant pairwise correlations were found between expression levels of genes especially in ANCTs. Notably, TDO2 expression levels were correlated with expression of all other genes in ANCTs but none of them in tumor tissues. Based on the area under curve (AUC) values, HCP5 and TDO2 had "fair" diagnostic power (AUC values of 0.73 and 0.72). Notably, combination of HCP5, ITGB2-AS1 and TDO2 genes increased the diagnostic power to the level of "good". The current investigation underscores the role of KP in breast cancer and potentiates some genes within this pathway as diagnostic markers in breast cancer.

Cellular immune responses against cancer-germline genes in cancers.

BACKGROUND: Cancer-germline genes are a class of genes that are normally expressed in testis, trophoblast and few somatic tissues but abnormally expressed in tumor tissues. Their expression signature indicates that they can induce cellular immune responses, thus being applied as targets in cancer immunotherapy. OBJECTIVES: To obtain the data of cellular immune responses against cancer-germline genes in cancer. METHODS: We searched PubMed/Medline with the key words cancer-germline antigen, cancer-testis antigen, CD4+ T cell, CD8+ T cell and cancer. RESULTS: About 40 cancer-germline genes have been shown to induce T cell specific responses in cancer patients. Melanoma, lung and breast cancer are among the mostly assessed cancer types. Several epitopes have been identified which can be used in immunotherapy of cancer. CONCLUSION: Cellular immune responses against cancer-germline genes are indicative of appropriateness of these genes as therapeutic targets.

Associations between XRCC3 Thr241Met polymorphisms and breast cancer risk: systematic-review and meta-analysis of 55 case-control studies.

BACKGROUND: The X-ray repair cross-complementing group 3 (XRCC3) is an efficient component of homologous recombination and is required for the preservation of chromosomal integrity in mammalian cells. The association between Thr241Met single-nucleotide polymorphism (SNP) in this gene and susceptibility to breast cancer has been assessed in several studies. Yet, reports are controversial. The present meta-analysis has been designed to identify whether this SNP is associated with susceptibility to breast cancer. METHODS: We performed a systematic review and meta-analysis for retrieving the case-control studies on the associations between T241 M SNP and the risk of breast cancer. Crude odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to verify the association in dominant, recessive, and homozygote inheritance models. RESULTS: We included 55 studies containing 30,966 sporadic breast cancer cases, 1174 familial breast cancer cases and 32,890 controls in the meta-analysis. In crude analyses, no association was detected between the mentioned SNP and breast cancer risk in recessive, homozygote or dominant models. However, ethnic based analysis showed that in sporadic breast cancer, the SNP was associated with breast cancer risk in Arab populations in homozygous (OR (95% CI) = 3.649 (2.029-6.563), p = 0.0001) and recessive models (OR (95% CI) = 4.092 (1.806-9.271), p = 0.001). The association was significant in Asian population in dominant model (OR (95% CI) = 1.296, p = 0.029). However, the associations was significant in familial breast cancer in mixed ethnic-based subgroup in homozygote and recessive models (OR (95% CI) = 0.451 (0.309-0.659), p = 0.0001, OR (95% CI) = 0.462 (0.298-0.716), p = 0.001 respectively). CONCLUSIONS: Taken together, our results in a large sample of both sporadic and familial cases of breast cancer showed insignificant role of Thr241Met in the pathogenesis of this type of malignancy. Such results were more conclusive in sporadic cases. In familial cases, future studies are needed to verify our results.

Assessment of the expression pattern of mTOR-associated lncRNAs and their genomic variants in the patients with breast cancer.

The mechanistic target of rapamycin (mTOR) is a fundamental component of a signaling pathway that is involved in the pathogenesis of breast cancer via different mechanisms. This pathway is functionally linked with a number of small nucleolar RNA host genes (SNHGs). In the present project, we have searched for the expression quantitative trait loci (eQTLs) within SNHGs that are possibly involved in the pathogenesis of breast cancer. Following this in silico step, we have assessed expression levels of mTOR and four SNHGs in malignant and nonmalignant samples obtained from 80 patients with breast cancer. We also genotyped rs4615861 of SNHG3 and rs3087978 of SNHG5 in the peripheral blood of patients. SNHG12 expression was not detected in any of the assessed malignant or nonmalignant tissues. So this gene was excluded from further steps. Expression of mTOR and other three long noncoding RNAs (lncRNAs) were significantly increased in the malignant tissues compared with the nonmalignant tissues. When classifying patients into down-/upregulation categorized based on the transcript levels of each gene in malignant tissue versus nonmalignant tissues, we noticed associations between expression of SNHG1 and stage (p = 0.03), expression of SNHG5 and grade (p = 0.05), as well as between expression of SNHG3 and history of oral contraceptive use (p = 0.04). We also detected higher levels of SNHG3 expression in estrogen receptor/progesterone receptor (ER/PR) negative tumors compared with the ER/PR positive tumors (p = 0.003 and p = 0.01, respectively). Moreover, there was a trend toward higher expression of this lncRNA in HER2-positive tumors compared with the HER2-negative ones (p = 0.07). Combination of transcript levels of all genes could differentiate malignant tissues from nonmalignant tissues with the diagnostic power of 69% (p = 0.0001). The rs3087978 was associated with the expression of mTOR in malignant tissues in a way that TT and TG genotypes were associated with the higher and lower levels of expressions, respectively (p = 0.01). The current study underscores the significance of SNHGs in the pathogenesis of breast cancer.

Cancer-testis antigens: An update on their roles in cancer immunotherapy.

BACKGROUND: Several recent studies have assessed suitability of tumor antigens for immunotherapy. Based on the restricted expression pattern in somatic tissues, cancer-testis antigens (CTAs) are possible candidates for cancer immunotherapy. These antigens are expressed in various tumors including gastrointestinal, breast, skin and hematologic malignancies. OBJECTIVES: To find clinical trials utilizing CTAs in cancer patients. METHODS: We searched PubMed, google scholar and specific websites that registers clinical trials. RESULTS: A number of clinical trials have been designed to evaluate safety and efficacy of CTA-based treatments. The results of some of them have been promising. In the current literature search, we summarized the clinical trials of CTA-based therapies in cancer patients. CONCLUSIONS: Based on the availability of different formulations of CTA-based vaccines, future researches should compare efficiency of these modalities.

A Clinical and Molecular Genetic Study of 50 Families with Autosomal Recessive Parkinsonism Revealed Known and Novel Gene Mutations.

In this study, the role of known Parkinson's disease (PD) genes was examined in families with autosomal recessive (AR) parkinsonism to assist with the differential diagnosis of PD. Some families without mutations in known genes were also subject to whole genome sequencing with the objective to identify novel parkinsonism-related genes. Families were selected from 4000 clinical files of patients with PD or parkinsonism. AR inheritance pattern, consanguinity, and a minimum of two affected individuals per family were used as inclusion criteria. For disease gene/mutation identification, multiplex ligation-dependent probe amplification, quantitative PCR, linkage, and Sanger and whole genome sequencing assays were carried out. A total of 116 patients (50 families) were examined. Fifty-four patients (46.55%; 22 families) were found to carry pathogenic mutations in known genes while a novel gene, not previously associated with parkinsonism, was found mutated in a single family (2 patients). Pathogenic mutations, including missense, nonsense, frameshift, and exon rearrangements, were found in Parkin, PINK1, DJ-1, SYNJ1, and VAC14 genes. In conclusion, variable phenotypic expressivity was seen across all families.

Lactobacilli Differentially Modulate mTOR and Wnt/ ß-Catenin Pathways in Different Cancer Cell Lines.

BACKGROUND: Lactobacilli are a group of beneficial bacteria whose anti cancer effects have been evaluated in different cancer cell lines as well as animal models and human subjects. Such anti cancer effects can be exerted via different mechanisms such as modulation of immune response as well as inhibition of pathogens colonization. In addition, lactobacilli have direct cytotoxic effects against cancer cells which may be exerted through modulation of expression cancer related pathways. OBJECTIVES: The aim of this study is to find the mechanism of anti cancer effects of two lactobacilli strains, Lactobacillus. crispatus (LC) and Lactobacillus. rhamnosus (LR). MATERIALS AND METHODS: We analyzed expression of some mTOR and Wnt/ ß-catenin pathways genes in three cancer cell lines (HeLa, MDA-MB-231 and HT-29) following treatment with LC and LR culture supernatants. RESULTS: Of note, the expression of CCND1 as a marker of cell proliferation, survival, and angiogenesis, has been decreased following LR treatment in all cell lines. In addition, the expression of SFRP2, an antagonist of Wnt pathway, has been increased in HT-29 following LR treatment and in HeLa cells following LR and LC treatments. Furthermore, we have demonstrated the downregulation of S6K1 expression, a marker of poor prognosis, following LR treatment in HT-29 and following LR and LC treatments in MDA-MB-231 cell line. CONCLUSIONS: Consequently, lactobacilli can modulate expression of mTOR and Wnt/ ß-catenin pathways genes in cancer cell lines in a strain specific as well as cell type specific manner.

Lactobacilli Modulate Hypoxia-Inducible Factor (HIF)-1 Regulatory Pathway in Triple Negative Breast Cancer Cell Line.

OBJECTIVE: Hypoxia-Inducible Factor (HIF)-1 plays an essential role in the body's response to low oxygen concentrations and regulates expression of several genes implicated in homeostasis, vascularization, anaerobic metabolism as well as immunological responses. Increased levels of HIF-1α are associated with increased proliferation and more aggressive breast tumor development. Lactobacilli have been shown to exert anti-cancer effects on several malignancies including breast cancer. However, the exact mechanism of such effect is not clear yet. The aim of this study was to analyze the expression of selected genes from HIF pathway in a triple negative breast cancer cell line (expressing no estrogen and progesterone receptors as well as HER-2/Neu), MDA-MB-231, following treatment with two lactobacilli culture supernatants. MATERIALS AND METHODS: In this experimental study, we analyzed the expression of HIF-1α, SLC2A1, VHL, HSP90, XBP1 and SHARP1 genes from HIF pathway in MDA-MB-231 cells, before and after treatment with Lactobacillus crispatus and Lactobacillus rhamnosus culture supernatants (LCS and LRS, respectively) by means of quantitative reverse-transcription polymerase chain reaction (qRT-PCR). RESULTS: Both LRS and LCS had cytotoxic effects on MDA-MB-231 cells, while the former type was more cytotoxic. LRS dramatically down-regulated expression levels of the HIF-1α, HSP90 and SLC2A1 in the MDA-MB-231 cells. LCS had similar effect on the expression of HSP90, to what was observed in the LRS treatment. The expression level of tumor suppressor genes VHL and SHARP1 were also decreased in LCS treated cells. CONCLUSION: Although both LCS and LRS had cytotoxic effects on the MDA-MB-231 cells, it is proposed that LRS could be more appropriate for pathway directed treatment modalities, as it did not decrease expression of tumor suppressor genes involved in HIF pathway. Down-regulation of HIF pathway mediated oncogenes by LRS suggests that the cytotoxic effects of this Lactobacillus may at least be partly caused by this mechanism. As previous studies have shown that inhibition of HIF-1α and HSP90 expressions have therapeutic impact on cancer treatment, the inhibitory effect of LRS on expression of these genes implies that this Lactobacillus can be used in treatment strategies.

Immunomodulatory effects of Lactobacillus strains: emphasis on their effects on cancer cells.

Lactobacilli are a group of normal microbiota whose immunomodulatory effects have been known for a long time. Recently, they have gained more attention for their direct and indirect effects on cancer cells. Several cell line experiments, animal model studies as well as clinical trials have indicated their inhibitory effects on cancer initiation and progression. Different lactobacilli strains could modulate innate and adoptive immune system. Such effects have been documented in modulation of function of T cells, dendritic cells and macrophages as well as cytokine production. In this review, the various immunomodulatory effects of lactobacilli on tumor cells as well as their direct cytotoxic effects on cancer cells are discussed.