High throughput RNA sequencing utility for diagnosis and prognosis in colon diseases

Transcriptome-wide association studies associated with Crohn's disease: challenges and perspectives

Crohn's disease (CD) is regarded as a lifelong progressive disease affecting all segments of the intestinal tract and multiple organs. Based on genome-wide association studies (GWAS) and gene expression data, transcriptome-wide association studies (TWAS) can help identify susceptibility genes associated with pathogenesis and disease behavior. In this review, we overview seven reported TWASs of CD, summarize their study designs, and discuss the key methods and steps used in TWAS, which affect the prioritization of susceptibility genes. This article summarized the screening of tissue-specific susceptibility genes for CD, and discussed the reported potential pathological mechanisms of overlapping susceptibility genes related to CD in a certain tissue type. We observed that ileal lipid-related metabolism and colonic extracellular vesicles may be involved in the pathogenesis of CD by performing GO pathway enrichment analysis for susceptibility genes. We further pointed the low reproducibility of TWAS associated with CD and discussed the reasons for these issues, strategies for solving them. In the future, more TWAS are needed to be designed into large-scale, unified cohorts, unified analysis pipelines, and fully classified databases of expression trait loci.

Glutathione peroxidase 2: A key factor in the development of microsatellite instability in colon cancer

BACKGROUND

Much research has focused on detecting microsatellite instability (MSI), which is frequently employed in the diagnosis and treatment of patients with colon cancer. However, the causes and progression of MSI in colon cancer have not yet been thoroughly elucidated. In this study, we screened and validated the genes associated with MSI in colorectal adenocarcinoma (COAD) using bioinformatics analysis.

METHODS

MSI-related genes of COAD were obtained from the Gene Expression Omnibus dataset, Search Tool for the Retrieval of Interaction Gene/Proteins, Gene Set Enrichment Analysis, and Human Protein Atlas. The function, prognostic value, and immune connection of MSI-related genes in COAD were examined using Cytoscape 3.9.1, the Human Gene Database, and the Tumor IMmune Estimation Resource. Key genes were verified using The Cancer Genome Atlas database and immunohistochemistry of clinical tumor samples.

RESULTS

We identified 59 MSI-related genes in patients with colon cancer. The protein interaction network of these genes was developed, and numerous functional modules associated with MSI were discovered. Pathways related to MSI were identified using KEGG enrichment analysis, and these included chemokine signaling, thyroid hormone synthesis, cytokine receptor interaction, estrogen signaling, and Wnt signaling pathways. Further analyses were used to identify the MSI-related gene, glutathione peroxidase 2 (GPX2), which was closely related to the occurrence of COAD and tumor immunity.

CONCLUSIONS

In COAD, GPX2 may be crucial for the establishment of MSI and tumor immunity, and its deficiency may result in MSI and immune cell infiltration in colon cancer.

Extracellular matrix-based gene signature for predicting prognosis in colon cancer and immune microenvironment

Background

The extracellular matrix (ECM) plays a vital role in progression, expansion, and prognosis of malignancies. In this study, we aimed to explore a novel ECM-based prognostic model for patients with colon cancer (CC).

Methods

ECM-related genes were obtained from Molecular Signatures database. Differential expression analysis was performed using the CC dataset from The Cancer Genome Atlas (TCGA) database. Four ECM-related genes related to overall survival were identified using the Cox regression and LASSO analysis. Then an ECM-related signature was developed and verified in three independent CC cohorts (GSE33882, GSE39582 and GSE29621) from the Gene Expression Omnibus (GEO). A prognostic nomogram was developed incorporating the ECM-related gene signature with clinical risk factors. CIBERSORT was used to explore the immune cell infiltration level. Human Protein Atlas (HPA) database was utilized to validate the expression levels of identified prognostic ECM genes.

Results

Four ECM-related genes (CXCL13, CXCL14, SFRP5 and THBS4) were identified to develop an ECM-based gene signature and demarcated CC patients into the high- and low-risk groups. In training and validation datasets, patients in the low-risk group had better overall survival outcomes than those in the high-risk group (log-rank P<0.001). In addition, ECM-related signature was significantly associated with consensus molecular subtype 4 (CMS4) as well as other known clinical risk factors such as a higher Tumor, Nodal Involvement, Metastasis (TNM) stage. Moreover, the risk score derived from the ECM-based gene signature could be utilized as an independent prognostic factor for CC patients. A nomogram including the ECM-related gene signature, age and stage was developed to serve clinical practice. CIBERSORT analysis showed immune cell infiltration was different between high- and low-risk groups. The immunohistochemical results derived from HPA indicated differential expression of prognosis-related ECM genes in CC and normal tissues.

Conclusions

In the present study, a novel risk model based on ECM-signature could effectively reflect individual risk classification and provide potential therapeutic targets for CC patients. Moreover, the prognostic nomogram may help predict individualized survival.

A pseudo-value regression approach for differential network analysis of co-expression data

BACKGROUND

The differential network (DN) analysis identifies changes in measures of association among genes under two or more experimental conditions. In this article, we introduce a pseudo-value regression approach for network analysis (PRANA). This is a novel method of differential network analysis that also adjusts for additional clinical covariates. We start from mutual information criteria, followed by pseudo-value calculations, which are then entered into a robust regression model.

RESULTS

This article assesses the model performances of PRANA in a multivariable setting, followed by a comparison to dnapath and DINGO in both univariable and multivariable settings through variety of simulations. Performance in terms of precision, recall, and F1 score of differentially connected (DC) genes is assessed. By and large, PRANA outperformed dnapath and DINGO, neither of which is equipped to adjust for available covariates such as patient-age. Lastly, we employ PRANA in a real data application from the Gene Expression Omnibus database to identify DC genes that are associated with chronic obstructive pulmonary disease to demonstrate its utility.

CONCLUSION

To the best of our knowledge, this is the first attempt of utilizing a regression modeling for DN analysis by collective gene expression levels between two or more groups with the inclusion of additional clinical covariates. By and large, adjusting for available covariates improves accuracy of a DN analysis.

RNA expression profiling from the liquid fraction of synovial fluid in knee joint osteoarthritis patients

OBJECTIVE

To investigate the RNA profile of synovial fluid (SF) from osteoarthritis (OA) patients and carry out cluster analysis of OA-related genes.

METHODS

RNA of SF from OA patients was isolated using RNA-specific Trizol. A cDNA library was built and subjected to the second-generation sequencing using HisSeq4000 with a data size of 8G. The sequencing reads were aligned to the UCSC human reference genome (hg38) using Tophat with default parameters. Gene function enrichment was generated using DAVID.

RESULTS

The minimum weight 0.096 µg RNA of SF sample was used for sequencing analysis, which produced 66,154,562 clean reads, 91.28% of which were matched to the reference with 2,682 genes identified. Some of the unmatchable reads matched RNAs of bacteria, mainly Pseudomonas. The detected human RNAs in samples fell into different categories of genes, including protein-coding ones, processed and unprocessed pseudogenes, and long noncoding, antisense and miscellaneous RNAs that mediate various biological functions. Interestingly, 80% of the expressed genes belonged to the mitochondrial genome.

CONCLUSION

These results suggest that less than 0.1 µg RNA is sufficient for establishing a cDNA library and deep sequencing, and that the liquid fraction of SF contains a whole RNA repertoire that may reflect a history of previous microorganism infections.

Microbial and human transcriptome in vaginal fluid at midgestation: Association with spontaneous preterm delivery

BACKGROUND

Intrauterine infection and inflammation caused by microbial transfer from the vagina are believed to be important factors causing spontaneous preterm delivery (PTD). Multiple studies have examined the relationship between the cervicovaginal microbiome and spontaneous PTD with divergent results. Most studies have applied a DNA-based assessment, providing information on the microbial composition but not transcriptional activity. A transcriptomic approach was applied to investigate differences in the active vaginal microbiome and human transcriptome at midgestation between women delivering spontaneously preterm versus those delivering at term.

METHODS

Vaginal swabs were collected in women with a singleton pregnancy at 18 + 0 to 20 + 6 gestational weeks. For each case of spontaneous PTD (delivery <37 + 0 weeks) two term controls were randomized (39 + 0 to 40 + 6 weeks). Vaginal specimens were subject to sequencing of both human and microbial RNA. Microbial reads were taxonomically classified using Kraken2 and RefSeq as a reference. Statistical analyses were performed using DESeq2. GSEA and HUMAnN3 were used for pathway analyses.

RESULTS

We found 17 human genes to be differentially expressed (false discovery rate, FDR < 0.05) in the preterm group (n = 48) compared to the term group (n = 96). Gene expression of kallikrein-2 (KLK2), KLK3 and four isoforms of metallothioneins 1 (MT1s) was higher in the preterm group (FDR < 0.05). We found 11 individual bacterial species to be differentially expressed (FDR < 0.05), most with a low occurrence. No statistically significant differences in bacterial load, diversity or microbial community state types were found between the groups.

CONCLUSIONS

In our mainly white population, primarily bacterial species of low occurrence were differentially expressed at midgestation in women who delivered preterm versus at term. However, the expression of specific human transcripts including KLK2, KLK3 and several isoforms of MT1s was higher in preterm cases. This is of interest, because these genes may be involved in critical inflammatory pathways associated with spontaneous PTD.

Astragalus mongholicus Bunge and Curcuma aromatica Salisb. inhibits liver metastasis of colon cancer by regulating EMT via the CXCL8/CXCR2 axis and PI3K/AKT/mTOR signaling pathway

BACKGROUND

One of the most challenging aspects of colon cancer (CC) prognosis and treatment is liver-tropic metastasis. Astragalus mongholicus Bunge-Curcuma aromatica Salisb. (AC) is a typical medication combination for the therapy of many malignancies. Our previous studies found that AC intervention inhibits liver metastasis of colon cancer (LMCC). Nevertheless, the comprehensive anti-metastasis mechanisms of AC have not been uncovered.

METHODS

In bioinformatics analysis, RNA-seq data of CC and LMCC patients were collected from TCGA and GEO databases, and differentially expressed genes (DEGs) were identified. The biological processes and signaling pathways involved in DEGs were enriched by GO and KEGG. The protein-protein interaction (PPI) network of DEGs was established and visualized using the Cytocape software, followed by screening Hub genes in the PPI network using Degree value as the criterion. Subsequently, the expression and survival relevance of Hub gene in COAD patients were verified. In the experimental study, the effects of AC on the inhibition of colon cancer growth and liver metastasis were comprehensively evaluated by cellular and animal models. Finally, based on the results of bioinformatics analysis, the possible mechanisms of AC inhibition of colon cancer EMT and liver metastasis were explored by in vivo and in vitro pharmacological experiments.

RESULTS

In this study, we obtained 2386 DEGs relevant to LMCC from the COAD (colon adenocarcinoma) and GSE38174 datasets. Results of GO gene function and KEGG signaling pathway enrichment analysis suggested that cellular EMT (Epithelial-mesenchymal transition) biological processes, Cytokine-cytokine receptor interaction and PI3K/Akt signaling pathways might be closely related to LMCC mechanism. We then screened for CXCL8, the core hub gene with the highest centrality within the PPI network of DEGs, and discovered that CXCL8 expression was negatively correlated with the prognosis of COAD patients. In vitro and in vivo experimental evidence presented that AC significantly inhibited colon cancer cell proliferation, migration and invasion ability, and suppressed tumor growth and liver metastasis in colon cancer orthotopic transplantation mice models. Concomitantly, AC significantly reduced CXCL8 expression levels in cell supernatants and serum. Moreover, AC reduced the expression and transcription of genes related to the PI3K/AKT pathway while suppressing the EMT process in colon cancer cells and model mice.

CONCLUSIONS

In summary, our research predicted the potential targets and pathways of LMCC, and experimentally demonstrated that AC might inhibit the growth and liver metastasis in colon cancer by regulating EMT via the CXCL8/CXCR2 axis and PI3K/AKT/mTOR signaling pathway, which may facilitate the discovery of mechanisms and new therapeutic strategies for LMCC.

Traditional chinese medicine syndromes classification associates with tumor cell and microenvironment heterogeneity in colorectal cancer: a single cell RNA sequencing analysis

BACKGROUND

Colorectal cancer (CRC) is one of the common gastrointestinal malignancies, tumor heterogeneity is the main cause of refractory CRC. Syndrome differentiation is the premise of individualized treatment of traditional Chinese medicine (TCM), but TCM syndrome lacks objective identification in CRC. This study is to investigate the correlation and significance of tumor heterogeneity and TCM syndromes classification in CRC.

METHODS

In this study, we using scRNA-seq technology, investigate the significance of tumor heterogeneity in TCM syndromes classification on CRC.

RESULTS

The results showed that 662 cells isolated from 11 primary CRC tumors are divided into 14 different cell clusters, and each cell subtype and its genes have different functions and signal transduction pathways, indicating significant heterogeneity. CRC tumor cell clusters have different proportions in Excess, Deficiency and Deficiency-Excess syndromes, and have their own characteristic genes, gene co-expression networks, gene functional interpretations as well as monocle functional evolution. Moreover, there were significant differences between the high expressions of MUC2, REG4, COL1A2, POSTN, SDPR, GPX1, ELF3, KRT8, KRT18, KRT19, FN1, SERPINE1, TCF4 and ZEB1 genes in Excess and Deficiency syndrome classification in CRC (P < 0.01).

CONCLUSIONS

The Excess and Deficiency syndromes classification may be related to tumor heterogeneity and its microenvironment in CRC.

High-throughput sequencing profile of laryngeal cancers: analysis of co-expression and competing endogenous RNA networks of circular RNAs, long non-coding RNAs, and messenger RNAs

Background

Circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) have been recently identified as new classes of non-coding RNAs which participate in carcinogenesis and tumor progression. However, the functions of these non-coding RNAs and gene expression patterns are largely unknown.

Methods

We carried out high-throughput sequencing to analyze the differential expression of RNAs in 5 coupled laryngeal cancer (LC) and corresponding adjacent noncancerous tissues. Bioinformatics analyses were performed to predict the functions of these non-coding RNAs via co-expression, competing endogenous RNA networks and pathway enrichment analysis. The differential expression of the selected RNAs were confirmed using RT-qPCR. The CCK8, EDU, Transwell, and wound healing assays were conducted to validate the biological functions of SNHG29 in LC. Western blot assay was performed to identify the effects of SNHG29 having on the epithelial to mesenchymal transition process. Kaplan-Meier analysis was used to investigate whether the expression level of SNHG29 correlated with survival in LC patients. One-way ANOVA was used to analyze the correlation between the expression of SNHG29 and clinicopathological parameters of the included patients.

Results

Compared to normal laryngeal tissues, 31,763 non-coding RNAs were upregulated and 11,557 non-coding RNAs were downregulated in cancer tissues. SNHG29 expression was low in the LC cell lines and tissues predicting a better clinical prognosis. SNHG29 was also found to inhibit the proliferation, migration, and invasion ability of LC, exerting a suppressive role in the epithelial to mesenchymal transition process as well. SNHG29 downregulation was significantly correlated with differentiation (P=0.026), T-stage (P=0.041), lymphatic metastasis (P=0.044), and clinical stage (P=0.037). We found that the biological functions of differentially expressed transcripts included cell adhesion, biological adhesion, and migration and invasion related to adherens junction pathways.

Conclusions

Our study was the first to describe the non-coding RNA profile of LC, and suggested that dysregulated non-coding RNAs could be involved in LC tumorigenesis. SNHG29 was demonstrated to play crucial roles in inhibiting the pathogenesis and progression of LC. Our findings provide a new approach for further analyses of pathogenetic mechanisms, the detection of novel transcripts, and the identification of valuable biomarkers for this tumor.

Integrative transcriptomic and metabonomic profiling analyses reveal the molecular mechanism of Chinese traditional medicine huankuile suspension on TNBS-induced ulcerative colitis

This study aimed to investigate the therapeutic mechanism of Huankuile suspension (HKL), a typical traditional Chinese medicine, on ulcerative colitis (UC) in a rat model. UC model was established by 2,4,6-trinitrobenzene sulfonic acid (TNBS) enema. Then, the rats were randomly divided into three groups: water treated group, HKL treated group and 5- amino salicylic acid (5-ASA) treated group. After 7 days treatment, the histological score in the HKL treated group was comparable with those in the control group. qRT-PCR and western blot demonstrated that HKL could significantly decreased pro-inflammatory cytokines, including TNF-α, IL-1β and IL-6, while having less effect on anti-inflammatory cytokines, including IL-4 and IL-10. Transcriptomic analysis identified 670 differentially expressed genes (DEGs) between HKL treated UC rats and water treated UC rats. These DEGs were mostly related with immune response. Besides, metabonomic profile revealed 136 differential metabolites which were significantly enriched in “pyrimidine metabolism”, “glutathione metabolism”, “purine metabolism” and “citrate cycle”. Finally, integrated analysis revealed that metabonomic pathways including “steroid hormone biosynthesis”, “pyrimidine metabolism”, “purine metabolism”, and “glutathione metabolism” were altered by HKL at both transcriptomic and metabonomic levels. HKL could inhibit inflammation and regulate bile metabolism, pyrimidine metabolism, purine metabolism, glutathione metabolism and citrate cycle.

An Overview of Gut Microbiota and Colon Diseases with a Focus on Adenomatous Colon Polyps

It is known and accepted that the gut microbiota composition of an organism has an impact on its health. Many studies deal with this topic, the majority discussing gastrointestinal health. Adenomatous colon polyps have a high prevalence as colon cancer precursors, but in many cases, they are hard to diagnose in their early stages. Gut microbiota composition correlated with the presence of adenomatous colon polyps may be a noninvasive and efficient tool for diagnosis with a high impact on human wellbeing and favorable health care costs. This review is meant to analyze the gut microbiota correlated with the presence of adenomatous colon polyps as the first step for early diagnosis, prophylaxis, and treatment.

Prediction of the differentially expressed circRNAs to decipher their roles in the onset of human colorectal cancers

Circular RNAs belong to the class of endogenous long non-coding RNAs that play important roles in many physiological processes including tumorigenesis. One such process is the onset of colorectal cancers (CRC) which is one of the most prevalent cancers in the world. However, the involvement of the circRNAs in CRC progression is still obscure. In this study, we screened the differentially expressed circRNAs in CRC by taking 10 pairs of tumor and non-tumor transcriptomic data. Datasets were downloaded from EBI ENA database and differential expression analysis was performed. For functional characterization and pathway enrichment of differentially expressed circRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed. Interactions with miRNAs and RNA binding proteins (RBPs) were predicted using miRanda, miRTarBase and starBase tools respectively. Our results identified total of 122 differentially expressed circRNAs in CRC onset, including 85 upregulated and 37 downregulated. GO and KEGG analyses revealed these circRNAs to be involved in many tumorigenic pathways. In addition, we predicted many miRNA and RBP targets of significantly expressed circRNAs that could exhibit the functional role in CRC progression. Combined analyses of miRanda, miRTarBase and KEGG pathway suggested that the possibly affected genes by circRNA-miRNA sponge to be associated with many cancer related pathways. From our findings we concluded 16 novel differentially expressed circRNAs that could play important roles in carcinogenesis of CRC. Our findings provide new insights in circRNA research and could therefore be useful in the development of potential biomarker and therapeutic approaches for CRC.

Identification of key genes involved in the development and progression of early-onset colorectal cancer by co-expression network analysis

A number of studies have revealed that there is an increasing incidence of early-onset colorectal cancer (CRC) in young adults (before the age of 50 years) and a progressive decline in CRC among older patients, after the age of 50 years (late-onset CRC). However, the etiology of early-onset CRC is not fully understood. The aim of the present study was to identify key genes associated with the development of early-onset CRC through weighted gene co-expression network analysis (WGCNA). The GSE39582 dataset was downloaded from the Gene Expression Omnibus database, and the data profiles of tissues from patients diagnosed before the age of 50 years were selected. The top 10,000 genes with the highest variability were used to construct the WGCNA. Hub genes were identified from the modules associated with clinical traits using gene significance >0.2 and module membership >0.8 as the cut-off criteria. Gene Ontology and pathway analyses were subsequently performed on the hub genes and a protein-protein interaction network (PPI) was constructed. The diagnostic value of module hub genes with a degree score >5 in the PPI network was verified in samples from patients with CRC diagnosed before the age of 50 years obtained from The Cancer Genome Atlas. Eight co-expressed gene modules were identified in the WGCNA and two modules (blue and turquoise) were associated with the tumor-node-metastasis stage. A total of 140 module hub genes were identified and found to be enriched in 'mitochondrial large ribosomal subunit', 'structural constituent of ribosome', 'poly (A) RNA binding', 'collagen binding', 'protein ubiquitination' and 'ribosome pathway'. Twenty-six module hub genes were found to have a degree score >5 in the PPI network, seven of which [secreted protein acidic and cysteine rich (SPARC), decorin (DCN), fibrillin 1 (FBN1), WW domain containing transcription regulator 1 (WWTR1), transgelin (TAGLN), DEAD-box helicase 28 (DDX28) and cold shock domain containing C2 (CSDC2)], had good prognostic values for patients with early-onset CRC, but not late-onset CRC. Therefore, SPARC, DCN, FBN1, WWTR1, TAGLN, DDX28 and CSDC2 may contribute to the development of early-onset CRC and may serve as potential diagnostic biomarkers.

Integrated analysis highlights multiple long non‑coding RNAs and their potential roles in the progression of human esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is a prevalent aggressive malignant tumor with poor prognosis. Investigations into the molecular changes that occur as a result of the disease, as well as identification of novel biomarkers for its diagnosis and prognosis, are urgently required. Long non‑coding RNAs (lncRNAs) have been reported to play a critical role in tumor progression. The present study performed data mining analyses for ESCC via an integrated study of accumulated datasets and identification of the differentially expressed lncRNAs from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. The identified intersection of differentially expressed genes (lncRNAs, miRNAs and mRNAs) in ESCC tissues between the GEO and TCGA datasets was investigated. Based on these intersected lncRNAs, the present study constructed a competitive endogenous RNA (ceRNA) network of lncRNAs in ESCC. A total of 81 intersection lncRNAs were identified; 67 of these were included in the ceRNA network. Functional analyses revealed that these 67 key lncRNAs primarily dominated cellular biological processes. The present study then analyzed the associations between the expression levels of these 67 key lncRNAs and the clinicopathological characteristics of the ESCC patients, as well as their survival time using TCGA. The results revealed that 31 of these lncRNAs were associated with tumor grade, tumor‑node‑metastasis (TNM) stage and lymphatic metastasis status (P<0.05). In addition, 15 key lncRNAs were demonstrated to be associated with survival time (P<0.05). Finally, 5 key lncRNAs were selected for validation of their expression levels in 30 patients newly diagnosed with ESCC via reverse transcription‑quantitative PCR (RT‑qPCR). The results suggested that the fold changes in the trends of up‑ and downregulation between GEO, TCGA and RT‑qPCR were consistent. In addition, it was also demonstrated that a select few of these 5 key lncRNAs were significantly associated with TNM stage and lymph node metastasis (P<0.05). The results of the clinically relevant analysis and the aforementioned bioinformatics were similar, hence proving that the bioinformatics analysis used in the present study is credible. Overall, the results from the present study may provide further insight into the functional characteristics of lncRNAs in ESCC through bioinformatics integrative analysis of the GEO and TCGA datasets, and reveal potential diagnostic and prognostic biomarkers for ESCC.

Single-cell transcriptional profiling reveals the heterogenicity in colorectal cancer

BACKGROUND

Colorectal Cancer (CRC) is a highly heterogeneous disease. RNA profiles of bulk tumors have enabled transcriptional classification of CRC. However, such ways of sequencing can only target a cell colony and obscure the signatures of distinct cell populations. Alternatively, single-cell RNA sequencing (scRNA-seq), which can provide unbiased analysis of all cell types, opens the possibility to map cellular heterogeneity of CRC unbiasedly.

METHODS

In this study, we utilized scRNA-seq to profile cells from cancer tissue of a CRC patient. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to understand the roles of genes within the clusters.

RESULTS AND CONCLUSION

The 2824 cells were analyzed and categorized into 5 distinct clusters by scRNA-seq. For every cluster, specific cell markers can be applied, indicating each 1 of them different from another. We discovered that the tumor of CRC displayed a clear sign of heterogenicity, while genes within each cluster serve different functions. GO term analysis also stated that different cluster's relatedness towards the tumor of CRC differs. Three clusters participate in peripheral works in cells, including, energy transport, extracellular matrix generation, etc; Genes in other 2 clusters participate more in immunology processes. Lastly, trajectory plot analysis also supports the viewpoint, in that some clusters present in different states and pseudo-time, while others present in a single state or pseudo time. Our analysis provides more insight into the heterogeneity of CRC, which can provide assistance to further researches on this topic.

Harnessing the potential of gene editing technology using CRISPR in inflammatory bowel disease

The molecular scalpel of clustered regularly interspersed short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) technology may be sharp enough to begin cutting the genes implicated in inflammatory bowel disease (IBD) and consequently decrease the 6.3 billion dollar annual financial healthcare burden in the treatment of IBD. For the past few years CRISPR technology has drastically revolutionized DNA engineering and biomedical research field. We are beginning to see its application in gene manipulation of sickle cell disease, human immunodeficiency virus resistant embryologic twin gene modification and IBD genes such as Gatm (Glycine amidinotransferase, mitochondrial), nucleotide-binding oligomerization domain-containing protein 2, KRT12 and other genes implicated in adaptive immune convergence pathways have been subjected to gene editing, however there are very few publications. Furthermore, since Crohn’s disease and ulcerative colitis have shared disease susceptibility and share genetic gene profile, it is paramount and is more advantageous to use CRISPR technology to maximize impact. Although, currently CRISPR does have its limitations due to limited number of specific Cas enzymes, off-target activity, protospacer adjacent motifs and crossfire between different target sites. However, these limitations have given researchers further insight on how to augment and manipulate enzymes to enable precise gene excision and limit crossfire between target sites.

A Gene-Related Nomogram for Preoperative Prediction of Lymph Node Metastasis in Colorectal Cancer

Purpose: To develop and validate a gene-related nomogram for predicting the risk of lymph node (LN) metastasis preoperatively in patients with colorectal cancer (CRC). Methods: RNA-seq data of 581 CRC and 51 normal cases with clinical features were downloaded from TCGA database. In the evaluation cohort with 381 CRC cases, the LASSO regression was used to reduce dimensionality of gene signatures extracted to build gene score. A gene-related nomogram was performed based on the multivariable logistic regression analysis. The performance of the nomogram was assessed by the discrimination, calibration, and clinical usefulness not only in the evaluation, but also in the validation cohort with 200 CRC cases. Results: A total of 12,590 differentially expressed genes were selected, in which 59 candidates associated with LN metastasis in differentially expressed genes set were screened by LASSO to form the gene score. Based on the analysis of multivariate logistic regression, the gene-related nomogram showed good calibration and discrimination not only in the evaluation cohort (concordance-index 0.93; 95%CI 0.91-0.96), but also in the validation cohort (concordance-index 0.70; 95%CI 0.63-0.78). The decision curve analysis of the gene-related nomogram also provides constructive guidance for the design of operation plan, preoperatively. Conclusions: The presented genes nomogram may predict the LN metastasis in CRC patients, preoperatively. And 59 hub genes were defined related to LN metastasis of CRC, which can serve as treatment targets for the further study. Preoperative biopsy and gene analysis are needed to develop the operation plan in clinical practice.