Corrigendum: Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer.

[This corrects the article DOI: 10.3389/fcimb.2021.599734.].

Identification of cluster of differentiation molecule-associated microRNAs as potential therapeutic targets for gastrointestinal cancer immunotherapy.

BACKGROUND: Cluster of differentiation molecules are markers of immune cells that have been identified as a potential immunotherapeutic target for cancer treatment. MicroRNAs are small non-coding RNAs that act as tumor suppressors or oncogenes whose importance in diagnosis, prognosis, and treatment of gastric and colorectal cancers has been widely reported. However, their association with cluster of differentiation molecules in gastrointestinal cancers has not been well studied. Therefore, our study aimed to analyze the relationship between microRNAs and cluster of differentiation molecules in gastrointestinal cancers, and to identify cluster of differentiation molecule-associated microRNAs as prognostic biomarkers for gastrointestinal cancer patients. METHODS: Targetscan, Starbase, DIANA microT, and miRDB were used to investigate microRNA profiles that might be correlated with cluster of differentiation molecules in gastrointestinal cancers. Moreover, The Cancer Genome Atlas data analysis was used to investigate the association between cluster of differentiation molecules and microRNA expression in patients with gastric, colon, rectal, pancreatic, and esophageal cancers. The Kaplan-Meier plotter was used to identify the association between overall survival and cluster of differentiation molecule-associated microRNA expression in gastrointestinal cancer patients. RESULTS: miR-200a, miR-559, and miR-1236 were negatively associated with CD86, CD81, and CD160, respectively, in almost all types of gastrointestinal cancers, which were further verified in the in vitro studies by transfecting microRNA mimics in gastric cancer, colon cancer, pancreatic, and esophageal cell lines. CONCLUSION: Our study showed that miR-200a, miR-1236, and miR-559 are identified as cluster of differentiation-associated microRNAs in gastrointestinal cancers, providing a novel perspective to identify new therapeutic targets for cancer immunotherapy in gastrointestinal cancer patients.

Metagenome Analysis of Intestinal Bacteria in Healthy People, Patients With Inflammatory Bowel Disease and Colorectal Cancer.

Objectives: Several reports suggesting that the intestinal microbiome plays a key role in the development of inflammatory bowel disease (IBD) or colorectal cancer (CRC), but the changes of intestinal bacteria in healthy people, patients with IBD and CRC are not fully explained. The study aimed to investigate changes of intestinal bacteria in healthy subjects, patients with IBD, and patients with CRC. Materials: We collected data from the European Nucleotide Archive on healthy people and patients with colorectal cancer with the study accession number PRJEB6070, PRJEB7774, PRJEB27928, PRJEB12449, and PRJEB10878, collected IBD patient data from the Integrated Human Microbiome Project from the Human Microbiome Project Data Portal. We performed metagenome-wide association studies on the fecal samples from 290 healthy subjects, 512 IBD patients, and 285 CRC patients. We used the metagenomics dataset to study bacterial community structure, relative abundance, functional prediction, differentially abundant bacteria, and co-occurrence networks. Results: The bacterial community structure in both IBD and CRC was significantly different from healthy subjects. Our results showed that IBD patients had low intestinal bacterial diversity and CRC patients had high intestinal bacterial diversity compared to healthy subjects. At the phylum level, the relative abundance of Firmicutes in IBD decreased significantly, while the relative abundance of Bacteroidetes increased significantly. At the genus level, the relative abundance of Bacteroides in IBD was higher than in healthy people and CRC. Compared with healthy people and CRC, the main difference of intestinal bacteria in IBD patients was Bacteroidetes, and compared with healthy people and IBD, the main difference of intestinal bacteria in CRC patients was in Fusobacteria, Verrucomicrobia, and Proteobacteria. The main differences in the functional composition of intestinal bacteria in healthy people, IBD and CRC patients were L-homoserine and L-methionine biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis II, L-methionine biosynthesis I, and superpathway of L-lysine, L-threonine, and L-methionine biosynthesis I. The results of stratified showed that the abundance of Firmicutes, Bacteroidetes, and Actinobacteria involved in metabolic pathways has significantly changed. Besides, the association network of intestinal bacteria in healthy people, IBD, and CRC patients has also changed. Conclusions: In conclusion, compared with healthy people, the taxonomic and functional composition of intestinal bacteria in IBD and CRC patients was significantly changed.

Long Non-Coding RNAs: Potential Biomarkers and Targets for Hepatocellular Carcinoma Therapy and Diagnosis.

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide. Increasing studies showed that long non-coding RNAs (lncRNAs), a novel class of RNAs that are greater than 200 nucleotides in length but lack the ability to encode proteins, exert crucial roles in the occurrence and progression of HCC. LncRNAs promote the proliferation, migration, invasion, autophagy, and apoptosis of tumor cells by regulating downstream target gene expression and cancer-related signaling pathways. Meanwhile, lncRNA can be used as biomarkers to predict the efficacy of HCC treatment strategies, such as surgery, radiotherapy, chemotherapy, and immunotherapy, and as a potential individualized tool for HCC diagnosis and treatment. In this review, we overview up-to-date findings on lncRNAs as potential biomarkers for HCC surgery, radiotherapy, chemotherapy resistance, target therapy, and immunotherapy, and discuss the potential clinical application of lncRNA as tools for HCC diagnosis and treatment.

m5C RNA Methylation Primarily Affects the ErbB and PI3K-Akt Signaling Pathways in Gastrointestinal Cancer.

5-Methylcytosine (m5C) is a kind of methylation modification that occurs in both DNA and RNA and is present in the highly abundant tRNA and rRNA. It has an important impact on various human diseases including cancer. The function of m5C is modulated by regulatory proteins, including methyltransferases (writers) and special binding proteins (readers). This study aims at comprehensive study of the m5C RNA methylation-related genes and the main pathways under m5C RNA methylation in gastrointestinal (GI) cancer. Our result showed that the expression of m5C writers and reader was mostly up-regulated in GI cancer. The NSUN2 gene has the highest proportion of mutations found in GI cancer. Importantly, in liver cancer, higher expression of almost all m5C regulators was significantly associated with lower patient survival rate. In addition, the expression level of m5C-related genes is significantly different at various pathological stages. Finally, we have found through bioinformatics analysis that m5C regulatory proteins are closely related to the ErbB/PI3K-Akt signaling pathway and GSK3B was an important target for m5C regulators. Besides, the compound termed streptozotocin may be a key candidate drug targeting on GSK3B for molecular targeted therapy in GI cancer.

m6A RNA modification modulates PI3K/Akt/mTOR signal pathway in Gastrointestinal Cancer.

Rationale: Methylation at the N6 position of adenosine (m6A) is the most prevalent RNA modification within protein-coding mRNAs in mammals, and it is a reversible modification with various important biological functions. The formation and function of m6A are regulated by methyltransferases (writers), demethylases (erasers), and special binding proteins (readers) as key factors. However, the underlying modification mechanisms of m6A in gastrointestinal (GI) cancer remain unclear. Here, we performed comprehensive molecular profiling of the nine known m6A writer, eraser, and reader proteins in GI cancer. Methods: Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were used. Gene alteration and pathway analysis were done in cBioportal. The protein network of m6A regulators and its related pathway members was analyzed in STRING online platform. Phylogenetic tree was constructed in MEGA7. m6A modification sites were predicted by SRAMP. m6A related SNPs were analyzed by m6ASNP. The modulation of m6A on its related pathway members was validated by m6A-seq, real-time PCR and phosphor-MAPK array. Results: We found that m6A regulators were mostly upregulated in GI cancer and their differential expression significantly influenced the overall survival of patients with GI cancer. The phosphatidylinositol-3-kinase (PI3K)/Akt and mammalian target of rapamycin (mTOR) signaling pathways were found to be potentially affected by m6A modification in most human cancers, including GI cancer, which was further verified by m6A-Seq and phospho-MAPK array. Conclusions: Our findings suggest that m6A RNA modification has a fundamental role in the regulation of PI3K/Akt and mTOR signaling pathway function in cancer.

Analysis of Key Genes Regulating the Warburg Effect in Patients with Gastrointestinal Cancers and Selective Inhibition of This Metabolic Pathway in Liver Cancer Cells.

OBJECTIVE: The Warburg effect, also known as aerobic glycolysis, plays a dominant role in the development of gastrointestinal (GI) cancers. In this study, we analyzed the expression of key genes involved in the Warburg effect in GI cancers and investigated the effect of suppressing the Warburg effect in vitro in liver cancer cell lines. METHODS: The Cancer Genome Atlas (TCGA) RNA-Seq data were used to determine gene expression levels, which were analyzed with GraphPad Prism 7.00. Genetic alterations were queried with cBioPortal. The influence of the Warburg effect on liver cancer cell viability, migration and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity was determined by means of MTT, transwell and GAPDH activity assays. RESULTS: The levels of expression of genes associated with the Warburg effect were increased in tumors. To our knowledge, this is the first report of upregulated expression of CUEDC2, HMGB2, PFKFB4, PFKP and SIX1 in liver cancer. Clinically, overexpression of these genes was associated with significantly worse overall survival of liver cancer patients. In vitro, selective inhibition of GADPH suppressed the growth and metastasis of Huh-7, Bel7404 and Hep3B hepatocellular carcinoma cell lines. CONCLUSION: The Warburg effect may play an important role in GI cancers, especially in liver cancer.

Characterization of chemical composition and prebiotic effect of a dietary medicinal plant Penthorum chinense Pursh.

Penthorum chinense Pursh is a dietary medicinal plant widely distributed in Asia-Pacific countries. The present study aims to profile the chemical constituents of P. chinense and investigate its prebiotic role in modulating gut microbiota. Fifty polyphenolic compounds were rapidly identified using UPLC-HR-MS. Total flavonoid and phenolic contents of P. chinense were 46.6% and 61.3% (w/w), respectively. Thirteen individual polyphenols were quantified, which accounted for 33.1% (w/w). P. chinense induced structural arrangement of microbial community in mice, showing increased microbiota diversity, elevated Bacteroidetes/Firmicutes ratio and enriched gut health-promoting bacteria. After a one-week drug-free wash, most of these changes were recovered, but the abundance of some beneficial bacteria was further increased. The altered composition of gut microbiota enriched several metabolic pathways. Moreover, P. chinense increased antioxidant capacity in vivo. The results suggest that polyphenol-enriched P. chinense modulates gut microbiota and enhances antioxidant capacity in mice toward a beneficial environment for host health.

Comprehensive understanding of B7 family in gastric cancer: expression profile, association with clinicopathological parameters and downstream targets.

Objectives: B7 family members were identified as co-stimulators or co-inhibitors of the immune response and played important roles in cancer immunotherapy; however, their dysregulation in gastric cancer is still unclear. Methods: Data were obtained from TCGA and GTEX database. B7 mutations, association with DNA methylation and affected proteins were analyzed in cBioportal. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Gene Ontology (GO) project was studied by DAVID to find the downstream signaling pathway and important metabolic process, respectively. Protein-protein interaction network was analyzed in STRING and Cytoscape. A total of 160 paired specimens in tissue microarray from patients with gastric cancer were used to detect the expression levels of seven B7 family members via immunohistochemical analysis. Results: Bioinformatics studies revealed dysregulation of B7 members in gastric cancer. Gene and protein alteration were found in B7 family members. Furthermore, DNA methylation and gene alteration may be both involved in B7 member dysregulation in gastric cancer. Importantly, the high expression of B7-H6 is associated with good overall patient survival. B7 family members primarily affect the EGFR tyrosine kinase inhibitor resistance signaling pathway in gastric cancer and TP53 may be an important target of the family. The low expression of B7-1 and high expression of B7-H3 and B7-H7 were validated by IHC staining. Conclusions: Our results provide insight into B7 family member expression in gastric cancer and stress their importance in stomach tumorigenesis, which may be beneficial for designing future cancer treatments.

Natural killer cells as a double-edged sword in cancer immunotherapy: A comprehensive review from cytokine therapy to adoptive cell immunotherapy.

Natural killer (NK) cells are immune cells which are able to kill tumor and virus-infected cells and play an important role in both innate immunity and acquired immunity. Tumor immunotherapy is an emerging model of tumor treatment in the clinic. It is a re-emerging type of anticancer immunotherapy with the purpose of killing tumor cells by modulating the body's immune function and enhancing the antitumor immunity in tumor microenvironment. At present, many immune cells including lymphokine-activated killer cells, NK cells, cytokine-induced killer cells, and dendritic cells are involved in tumor immunotherapy studies. NK cells, which lyse tumor cells without prior stimulation, has become a research hotspot in cancer immunotherapy for clinical application. In this article, we discussed the surface receptors of NK cells and the anticancer function of NK cells. We also reviewed the biological characteristics and the current research status of NK cells, their clinical application in cancer immunotherapy and its future perspectives.

Cell surface proteomics analysis indicates a neural lineage bias of rat bone marrow mesenchymal stromal cells.

Mesenchymal stromal cells (MSCs) are one of the most intensively studied stem cell types with application aims. However, the molecular characterisation and the relationship between the molecular characterisation and functional properties of MSCs are largely unknown. In this study, we purified the surface proteins from rat bone marrow MSCs (rBMMSCs) and characterised their surface proteome by LC-MS/MS. Moreover, we comparatively analysed the data from this study with the surface proteomics data of mouse and human embryonic stem (ES) cells and human mesenchymal stromal cells (hMSCs). The data showed that, in contrast to ES cells and human mesenchymal stromal cells, rBMMSCs possessed a surface proteomics pattern biased to neural and neural-endocrine lineages, indicating a neural/neural crest bias, and suggested a neural differentiation tendency of these cells. The different surface proteomics pattern between rBMMSCs and hMSCs also suggested that MSCs of different origin might possess a different lineage bias.

Taurine postponed the replicative senescence of rat bone marrow-derived multipotent stromal cells in vitro.

The aging of many mammalian tissues is associated with replicative decline in somatic stem cells. Postponing this decline is a direct way of anti-aging. Bone marrow-derived multipotent stromal cells (BMSCs) hold promise for an increasing list of therapeutic uses due to their multilineage potential. Clinical application of BMSCs requires abundant cells that can be overcome by ex vivo expansion of cells, but often facing the replicative senescence problem. We demonstrated that taurine exhibited anti-replicative senescence effect on rat BMSCs by promoting colony forming unit-fibroblast formation and cell proliferation, shortening cell population doubling time, enormously inhibiting senescence-associated beta-galactosidase activity and slowing the loss of differentiation potential, while having no significant effect on the maximum passage number and total culture time, and slight influences on the cell surface CD molecules expressions. Taurine is a quite safe antioxidant and nutrient extensively used in food addition and clinical treatment. These suggested that taurine is a promising anti-replicative senescence additive for ex vivo expansion of BMSCs in experimental and clinical cell therapies.

N-acetyl-L-cysteine enhances the osteogenic differentiation and inhibits the adipogenic differentiation through up regulation of Wnt 5a and down regulation of PPARG in bone marrow stromal cells.

Nowadays, the treatment of osteoporosis is still a great challenge in the medical field. The combination of enhancement of osteogenesis and the inhibition of adipogenesis of bone marrow stromal cells (BMSCs) is considered an efficient therapeutic strategy for the treatment of osteoporosis. In the present study, we investigated the effects of N-acetyl-L-cysteine (NAC) on the proliferation, osteogenesis and adipogenesis of BMSCs. NAC treatment enhanced the alkaline phosphatase activity, mineral deposition and mRNA expression levels of osteogenesis markers collagen I, osteopontin, and signal pathway related protein Wingless-type family member 5a in addition to Wingless-type family member 3a during osteogenic induction, and inhibited the accumulation of lipid droplets and the expression levels of lipoprotein lipase, fatty acid binding protein 4 and peroxisome proliferator-activated receptor gamma mRNA during adipogenic induction. Meanwhile, NAC had the same effects as enhancing mineral deposition in regular culture condition. In addition, cell proliferation was also promoted by NAC treatment in regular culture condition. These results suggested that NAC may enhance osteogenic differentiation and inhibit adipogenic differentiation of BMSCs, which is at least partially mediated by up regulating Wnt 5a and down regulating PPARG. Taking into account the extensive protective effects of NAC and that the maintenance of BMSCs number is an important factor in osteoporosis prevention and treatment, these observations suggested that NAC is a promising potential drug for the prevention and treatment of osteoporosis and its associated diseases.

Preparing nano-calcium phosphate particles via a biologically friendly pathway.

It is widely agreed that nano-calcium phosphates (CaP) play an important role in tissue engineering and medical application due to their unique biological characteristics. However, the properties of nano-CaP, including bioactivity, biocompatibility and mechanical properties, are tailored over wide ranges by controlling the size and morphology of particles. Therefore, it is important to develop synthesis methods which can control the particle size distribution and shape uniformly. In this study, we report that polyacrylic acid (PAA) can act as an efficient agent to modulate nano-CaP formation. The dimension of the resultant sphere-like nanoparticles (5-60 nm) can readily be regulated by changing PAA concentrations (75-200 microg ml(-1)). In contrast to other additives, PAA is a water-soluble polymer that has already been used as an excellent biocompatible implant material in vivo. Our in vitro proliferation experiments of bone marrow mesenchymal stem cells (BMSCs) demonstrate that the involvement of PAA does not change the bioactivity of the resultant nano-CaP. In contrast, the nano-CaP fabricated by using another typical control agent, hexadecyl (cetyl) trimethyl ammonium bromide, suppressed the cell proliferation of BMSCs. Thus, we suggest that the biopolymer, PAA, can provide a more biologically friendly pathway to prepare biological nano-CaP for biomedical application.

Generation and characterisation of rabbit monoclonal antibodies against the native cell surface antigens of embryonic stem cells.

Embryonic stem (ES) cells are potent resources for cell therapy, and monoclonal antibodies (mAbs) against native cell surface markers of ES cells could be useful tools for therapeutic applications. Here, we report the development of a feasible approach, which could be used in mass production, for experimentally producing rabbit mAbs against native cell surface antigens on the cell surface. Two of the 14 mAbs, which were selected at random, could be bound to the cell surface antigens of mES cells. The immunocytochemistry (ICC) and Western blot results showed that mAb 39 recognises conformational epitopes. The target antigen of mAb 39 was then successfully purified using an improved immunoprecipitation approach in which mAb was bounded to intact mES cells before the cells were lysed. The LC-LTQ mass spectrum analysis showed that the target antigen of mAb 39 was Glut3. This result was further confirmed by Western blot using commercially available antibodies against Glut3. Further experiments showed that mAb 39 exhibited an antiproliferative effect on mES cells. We also found that Glut3 was differentially expressed among the mES cell population as detected by flow cytometry.

In vitro effects of nanophase hydroxyapatite particles on proliferation and osteogenic differentiation of bone marrow-derived mesenchymal stem cells.

Coculturing scaffolds with seeded cells in vitro is an indispensable process for construction of engineered tissues. It is essential to understand effects of the constituent particles of scaffold on seeded cells. In this study, we investigated the influence of nano-sized hydroxyapatite (nHAP) particles on the proliferation and osteogenic differentiation of bone marrow-derived mesenchymal stem cells (MSCs). nHAP particles were cocultured with MSCs separated from rabbit. Cellular effects of particles were determined by cell counts, Vonkossa stains, and reverse transcription-polymerase chain reaction (RT-PCR) examinations. Results showed that nHAP particles could promote the MSCs growth when particle concentrations were lower than 20 microg/10(4) cells. This effect disappeared when the particles and the cells were cocultured in serum-free media. Higher particle concentrations could significantly inhibit the cell growth. Under the standard culture condition, the only effect of nHAP particles on osteogenic differentiation of MSCs was to enhance the expression of collagen I. Under the osteogenic-inductive culture condition, nHAP particles could inhibit mineralization of cells but promote their osteogenic differentiation. These cellular effects of particles still existed when the particles and the cells were cultured in indirect coculture system. nHAP particles could decrease calcium and phosphate concentrations of culture media, which possibly contributed to the cellular effects of nHAP particles.