Metabolomics Profiling on Different Stages of Colorectal Cancer: A Systematic Review

Metabolomics analyses of cancer tissue from patients with colorectal cancer

The alteration of metabolism is essential for the initiation and progression of numerous types of cancer, including colorectal cancer (CRC). Metabolomics has been used to study CRC. At present, the reprogramming of the metabolism in CRC remains to be fully elucidated. In the present study, comprehensive untargeted metabolomics analysis was performed on the paired CRC tissues and adjacent normal tissues from patients with CRC (n=35) using ultra‑high‑performance liquid chromatography‑mass spectrometry. Subsequently, bioinformatic analysis was performed on the differentially expressed metabolites. The changes in these differential metabolites were compared among groups of patients based on sex, anatomical tumor location, grade of tumor differentiation and stage of disease. A total of 927 metabolites were detected in the tissue samples, and 24 metabolites in the CRC tissue were significantly different compared with the adjacent normal tissue. The present study revealed that the levels of three amino acid metabolites were increased in the CRC tissue, specifically, N‑α‑acetyl‑ε‑(2‑propenal)‑Lys, cyclo(Glu‑Glu) and cyclo(Phe‑Glu). The metabolites with decreased levels in the CRC tissue included quinaldic acid (also referred to as quinoline‑2‑carboxilic acid), 17α‑ and 17β‑estradiol, which are associated with tumor suppression activities, as well as other metabolites such as, anhydro‑β‑glucose, Asp‑Arg, lysophosphatidylcholine, lysophosphatidylethanolamine (lysoPE), lysophosphatidylinositol, carnitine, 5'‑deoxy‑5'‑(methylthio) adenosine, 2'‑deoxyinosine‑5'‑monophosphate and thiamine monophosphate. There was no difference in the levels of the differential metabolites between male and female patients. The differentiation of CRC also showed no impact on the levels of the differential metabolites. The levels of lysoPE were increased in the right side of the colon compared with the left side of the colon and rectum. Analysis of the different tumor stages indicated that 2‑aminobenzenesulfonic acid, P‑sulfanilic acid and quinoline‑4‑carboxylic acid were decreased in stage I CRC tissue compared with stage II, III and IV CRC tissue. The levels of N‑α‑acetyl‑ε‑(2‑propenal)‑Lys, methylcysteine and 5'‑deoxy‑5'‑(methylthio) adenosine varied at different stages of tumorigenesis. These differential metabolites were implicated in multiple metabolism pathways, including carbohydrate, amino acid, lipid, nucleotide and hormone. In conclusion, the present study demonstrated that CRC tumors had altered metabolites compared with normal tissue. The data from the metabolic profile of CRC tissues in the present study provided supportive evidence to understand tumorigenesis.

IDH2, a novel target of OGT, facilitates glucose uptake and cellular bioenergy production via NF-κB signaling to promote colorectal cancer progression

BACKGROUND

Although isocitrate dehydrogenase 2 (IDH2) mutations have been the hotspots in recent anticancer studies, the impact of wild-type IDH2 on cancer cell growth and metabolic alterations is still elusive.

METHODS

IDH2 expression in CRC tissues was evaluated by immunohistochemistry, and the correlation between the expression level and the patient's survival rate was analyzed. Cell functional assays included CCK8 and colony formation for cell proliferation in vitro and ectopic xenograft as in vivo experimental model for tumor progression. A targeted metabolomic procedure was performed by liquid chromatography/tandem mass spectrometry to profile the metabolites from glycolysis and tricarboxylic acid (TCA) cycle. Mitochondrial function was assessed by measuring cellular oxygen consumption (OCR) and mitochondrial membrane potential (ΔΨ). Confocal microscope analysis and Western blotting were applied to detect the expression of GLUT1 and NF-κB signaling. O-GlcNAcylation and the interaction of IDH2 with OGT were confirmed by co-immunoprecipitation, followed by Western blotting analysis.

RESULTS

IDH2 protein was highly expressed in CRC tissues, and correlated with poor survival of CRC patients. Wild-type IDH2 promoted CRC cell growth in vitro and tumor progression in xenograft mice. Overexpression of wild-type IDH2 significantly increased glycolysis and TCA cycle metabolites, the ratios of NADH/NAD⁺ and ATP/ADP, OCR and mitochondrial membrane potential (ΔΨ) in CRC cells. Furthermore, α-KG activated NF-κB signaling to promote glucose uptake by upregulating GLUT1. Interesting, O-GlcNAcylation enhanced the protein half-time of IDH2 by inhibiting ubiquitin-mediated proteasome degradation. The O-GlcNAc transferase (OGT)-IDH2 axis promoted CRC progression.

CONCLUSION

Wild-type IDH2 reprogrammed glucose metabolism and bioenergetic production via the NF-κB signaling pathway to promote CRC development and progression. O-GlcNAcylation of IDH2 elevated the stability of IDH2 protein. And the axis of OGT-IDH2 played an essential promotive role in tumor progression, suggesting a novel potential therapeutic strategy in CRC treatment.

Microbial metabolites in colorectal tumorigenesis and cancer therapy

Trillions of microbes are indigenous to the human gastrointestinal tract, together forming an ecological community known as the gut microbiota. The gut microbiota is involved in dietary digestion to produce various metabolites. In healthy condition, microbial metabolites have unneglectable roles in regulating host physiology and intestinal homeostasis. However, increasing studies have reported the correlation between metabolites and the development of colorectal cancer (CRC), with the identification of oncometabolites. Meanwhile, metabolites can also influence the efficacy of cancer treatments. In this review, metabolites derived from microbes-mediated metabolism of dietary carbohydrates, proteins, and cholesterol, are introduced. The roles of pro-tumorigenic (secondary bile acids and polyamines) and anti-tumorigenic (short-chain fatty acids and indole derivatives) metabolites in CRC development are then discussed. The impacts of metabolites on chemotherapy and immunotherapy are further elucidated. Collectively, given the importance of microbial metabolites in CRC, therapeutic approaches that target metabolites may be promising to improve patient outcome.

Chemotherapeutic resistant cholangiocarcinoma displayed distinct intratumoral microbial composition and metabolic profiles

Background

Cholangiocarcinoma (CCA) is a malignancy of the cholangiocytes. One of the major issues regarding treatment for CCA patients is the development of chemotherapeutic resistance. Recently, the association of intratumoral bacteria with chemotherapeutic response has been reported in many cancer types.

Method

In the present study, we aimed to investigate the association between the intratumoral microbiome and its function on gemcitabine and cisplatin response in CCA tissues using 16S rRNA sequencing and 1H NMR spectroscopic analysis.

Result

The results of 16S rRNA sequencing demonstrated that Gammaproteobacteria were significantly higher in both gemcitabine- and cisplatin-resistance groups compared to sensitive groups. In addition, intratumoral microbial diversity and abundance were significantly different compared between gemcitabine-resistant and sensitive groups. Furthermore, the metabolic phenotype of the low dose gemcitabine-resistant group significantly differed from that of low dose gemcitabine-sensitive group. Increased levels of acetylcholine, adenine, carnitine and inosine were observed in the low dose gemcitabine-resistant group, while the levels of acetylcholine, alpha-D-glucose and carnitine increased in the low dose cisplatin-resistant group. We further performed the intergrative microbiome-metabolome analysis and revealed a correlation between the intratumoral bacterial and metabolic profiles which reflect the chemotherapeutics resistance pattern in CCA patients.

Conclusion

Our results demonstrated insights into the disruption of the microbiome and metabolome in the progression of chemotherapeutic resistance. The altered microbiome-metabolome fingerprints could be used as predictive markers for drug responses potentially resulting in the development of an appropriate chemotherapeutic drug treatment plan for individual CCA patients.

Metallic Nanoparticles for the Modulation of Tumor Microenvironment; A New Horizon

Cancer is one of the most critical human challenges which endangers many people’s lives every year with enormous direct and indirect costs worldwide. Unfortunately, despite many advanced treatments used in cancer clinics today, the treatments are deficiently encumbered with many side effects often encountered by clinicians while deploying general methods such as chemotherapy, radiotherapy, surgery, or a combination thereof. Due to their low clinical efficacy, numerous side effects, higher economic costs, and relatively poor acceptance by patients, researchers are striving to find better alternatives for treating this life-threatening complication. As a result, Metal nanoparticles (Metal NPs) have been developed for nearly 2 decades due to their important therapeutic properties. Nanoparticles are quite close in size to biological molecules and can easily penetrate into the cell, so one of the goals of nanotechnology is to mount molecules and drugs on nanoparticles and transfer them to the cell. These NPs are effective as multifunctional nanoplatforms for cancer treatment. They have an advantage over routine drugs in delivering anticancer drugs to a specific location. However, targeting cancer sites while performing anti-cancer treatment can be effective in improving the disease and reducing its complications. Among these, the usage of these nanoparticles (NPs) in photodynamic therapy and sonodynamic therapy are notable. Herein, this review is aimed at investigating the effect and appliances of Metal NPs in the modulation tumor microenvironment which bodes well for the utilization of vast and emerging nanomaterial resources.

In silico identification of the specific pathways in each stage of colorectal cancer and the association of their top genes with drug resistance and sensitivity

Investigating the specific pathways and their relation with survival, mutation, sensitivity, and resistance to various drugs in different stages of colorectal cancer (CRC) could be effective in cancer treatment. In this study, identifying the specific pathways in each stage of CRC compared to other stages was considered via meta-analytic methodology. The Cancer Genome Atlas (TCGA) data with gene set enrichment analysis (GSEA) software, and CRC RNA-Seq data were used to enrich and determine specific pathways as well as to evaluate the expression level of TOP RANK genes. In addition, The Cancer Cell Line Encyclopedia (CCLE) data were used to correlate candidate genes with drug resistance. Finally, using Gene Expression Omnibus (GEO) data, drugs that could affect the expression level of these genes were identified. Three specific molecular pathways, including oxidative phosphorylation (OXPHOS), regulation of transporter activity (RTA), and negative regulation of transmembrane receptor protein serine threonine kinase (NRSTK) have been identified as hub pathways for stages II, III, and IV, respectively (P < 0.01). The expression level of TOP RANK genes in each stage increased on average twice compared to other stages (P < 0.01), and CCNB1, DKK1, NOG genes were associated with survival in stages II and IV, respectively (P < 0.01). The expression of some selected genes had a correlation with drug resistance and sensitivity (P < 0.05). GEO data revealed that gamma-tocotrienol (g-T3), NSC319726, and Casiopeina Cas-II-gly may reduce the expression of, NDUFAF1, CCNB1, DKK1 genes, respectively (P < 0.01). Specific pathways and TOP RANK genes could lead to cancer progression and malignancy, resistance to chemotherapy drugs, poor survival in patients, and metastasis. Therefore, identification and targeting these pathways at each stage could be crucial in inhibiting progression at different stages of CRC.

The Application of Metabolomics in Recent Colorectal Cancer Studies: A State-of-the-Art Review

Simple Summary

Colorectal Cancer (CRC) is one of the leading causes of cancer-related death in the United States. Current diagnosis techniques are either highly invasive or lack sensitivity, suggesting the need for alternative techniques for biomarker detection. Metabolomics represents one such technique with great promise in identifying CRC biomarkers with high sensitivity and specificity, but thus far is rarely employed in a clinical setting. In order to provide a framework for future clinical usage, we characterized dysregulated metabolites across recent literature, identifying metabolites dysregulated across a variety of biospecimens. We additionally put special focus on the interplay of the gut microbiome and perturbed metabolites in CRC. We were able to identify many metabolites showing consistent dysregulation in CRC, demonstrating the value of metabolomics as a promising diagnostic technique.

Abstract

Colorectal cancer (CRC) is a highly prevalent disease with poor prognostic outcomes if not diagnosed in early stages. Current diagnosis techniques are either highly invasive or lack sufficient sensitivity. Thus, identifying diagnostic biomarkers of CRC with high sensitivity and specificity is desirable. Metabolomics represents an analytical profiling technique with great promise in identifying such biomarkers and typically represents a close tie with the phenotype of a specific disease. We thus conducted a systematic review of studies reported from January 2012 to July 2021 relating to the detection of CRC biomarkers through metabolomics to provide a collection of knowledge for future diagnostic development. We identified thirty-seven metabolomics studies characterizing CRC, many of which provided metabolites/metabolic profile-based diagnostic models with high sensitivity and specificity. These studies demonstrated that a great number of metabolites can be differentially regulated in CRC patients compared to healthy controls, adenomatous polyps, or across stages of CRC. Among these metabolite biomarkers, especially dysregulated were certain amino acids, fatty acids, and lysophosphatidylcholines. Additionally, we discussed the contribution of the gut bacterial population to pathogenesis of CRC through their modulation to fecal metabolite pools and summarized the established links in the literature between certain microbial genera and altered metabolite levels in CRC patients. Taken together, we conclude that metabolomics presents itself as a promising and effective method of CRC biomarker detection.

Metabolic Profiling of Praziquantel-mediated Prevention of Opisthorchis viverrini-induced Cholangiocyte Transformation in the Hamster Model of Cholangiocarcinoma

BACKGROUND

Opisthorchis viverrini (Ov) infection-induced cholangiocarcinoma (CCA) is a major public health problem in northeastern Thailand. Praziquantel was shown to prevent CCA development in an Ov-infected hamster model; however, the molecular mechanism remains unknown.

MATERIALS AND METHODS

In this study, we used a hamster model with Ov and N-nitrosodimethylamine-induced CCA to study the mechanisms of praziquantel action. The liver tissues from the hamsters with and without praziquantel treatment were analyzed using ¹H nuclear magnetic resonance spectroscopy.

RESULTS

A total of 14 metabolites were found to be significantly different between the two groups. Furthermore, the combination of acetate, inosine and sarcosine was shown to exert an anti-inflammatory effect through interleukin-6 inhibition in a macrophage cell line, suggesting a mechanism by which praziquantel may prevent inflammation caused by Ov, cholangiocyte transformation and further CCA develpoment.

CONCLUSION

These findings might avail the development of a preventive strategy for CCA in high-risk populations.

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.

Untargeted Metabolomics Reveals Major Differences in the Plasma Metabolome between Colorectal Cancer and Colorectal Adenomas

Sporadic colorectal cancer is characterized by a multistep progression from normal epithelium to precancerous low-risk and high-risk adenomas to invasive cancer. Yet, the underlying molecular mechanisms of colorectal carcinogenesis are not completely understood. Within the "Metabolomic profiles throughout the continuum of colorectal cancer" (MetaboCCC) consortium we analyzed data generated by untargeted, mass spectrometry-based metabolomics using plasma from 88 colorectal cancer patients, 200 patients with high-risk adenomas and 200 patients with low-risk adenomas recruited within the "Colorectal Cancer Study of Austria" (CORSA). Univariate logistic regression models comparing colorectal cancer to adenomas resulted in 442 statistically significant molecular features. Metabolites discriminating colorectal cancer patients from those with adenomas in our dataset included acylcarnitines, caffeine, amino acids, glycerophospholipids, fatty acids, bilirubin, bile acids and bacterial metabolites of tryptophan. The data obtained discovers metabolite profiles reflecting metabolic differences between colorectal cancer and colorectal adenomas and delineates a potentially underlying biological interpretation.

Optimisation of Urine Sample Preparation for Headspace-Solid Phase Microextraction Gas Chromatography-Mass Spectrometry: Altering Sample pH, Sulphuric Acid Concentration and Phase Ratio

Headspace-solid phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) can be used to measure volatile organic compounds (VOCs) in human urine. However, there is no widely adopted standardised protocol for the preparation of urine samples for analysis resulting in an inability to compare studies reliably between laboratories. This paper investigated the effect of altering urine sample pH, volume, and vial size for optimising detection of VOCs when using HS-SPME-GC-MS. This is the first, direct comparison of H₂SO₄, HCl, and NaOH as treatment techniques prior to HS-SPME-GC-MS analysis. Altering urine sample pH indicates that H₂SO₄ is more effective at optimising detection of VOCs than HCl or NaOH. H₂SO₄ resulted in a significantly larger mean number of VOCs being identified per sample (on average, 33.5 VOCs to 24.3 in HCl or 12.2 in NaOH treated urine) and more unique VOCs, produced a more diverse range of classes of VOCs, and led to less HS-SPME-GC-MS degradation. We propose that adding 0.2 mL of 2.5 M H₂SO₄ to 1 mL of urine within a 10 mL headspace vial is the optimal sample preparation prior to HS-SPME-GC-MS analysis. We hope the use of our optimised method for urinary HS-SPME-GC-MS analysis will enhance our understanding of human disease and bolster metabolic biomarker identification.

Association between Metabolites and the Risk of Lung Cancer: A Systematic Literature Review and Meta-Analysis of Observational Studies

Globally, lung cancer is the most prevalent cancer type. However, screening and early detection is challenging. Previous studies have identified metabolites as promising lung cancer biomarkers. This systematic literature review and meta-analysis aimed to identify metabolites associated with lung cancer risk in observational studies. The literature search was performed in PubMed and EMBASE databases, up to 31 December 2019, for observational studies on the association between metabolites and lung cancer risk. Heterogeneity was assessed using the I² statistic and Cochran’s Q test. Meta-analyses were performed using either a fixed-effects or random-effects model, depending on study heterogeneity. Fifty-three studies with 297 metabolites were included. Most identified metabolites (252 metabolites) were reported in individual studies. Meta-analyses were conducted on 45 metabolites. Five metabolites (cotinine, creatinine riboside, N-acetylneuraminic acid, proline and r-1,t-2,3,c-4-tetrahydroxy-1,2,3,4-tetrahydrophenanthrene) and five metabolite groups (total 3-hydroxycotinine, total cotinine, total nicotine, total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (sum of concentrations of the metabolite and its glucuronides), and total nicotine equivalent (sum of total 3-hydroxycotinine, total cotinine and total nicotine)) were associated with higher lung cancer risk, while three others (folate, methionine and tryptophan) were associated with lower lung cancer risk. Significant heterogeneity was detected across most studies. These significant metabolites should be further evaluated as potential biomarkers for lung cancer.

Metabolomics in Radiation Biodosimetry: Current Approaches and Advances

Triage and medical intervention strategies for unanticipated exposure during a radiation incident benefit from the early, rapid and accurate assessment of dose level. Radiation exposure results in complex and persistent molecular and cellular responses that ultimately alter the levels of many biological markers, including the metabolomic phenotype. Metabolomics is an emerging field that promises the determination of radiation exposure by the qualitative and quantitative measurements of small molecules in a biological sample. This review highlights the current role of metabolomics in assessing radiation injury, as well as considerations for the diverse range of bioanalytical and sampling technologies that are being used to detect these changes. The authors also address the influence of the physiological status of an individual, the animal models studied, the technology and analysis employed in interrogating response to the radiation insult, and variables that factor into discovery and development of robust biomarker signatures. Furthermore, available databases for these studies have been reviewed, and existing regulatory guidance for metabolomics are discussed, with the ultimate goal of providing both context for this area of radiation research and the consideration of pathways for continued development.

Metabolomic characterization of colorectal cancer cell lines highlighting stage-specific alterations during cancer progression

Introduction: Metabolomic studies on various colorectal cancer (CRC) cell lines have improved our understanding of the biochemical events underlying the disease. However, the metabolic profile dynamics associated with different stages of CRC progression is still lacking. Such information can provide further insights into the pathophysiology and progression of the disease that will prove useful in identifying specific targets for drug designing and therapeutics. Thus, our study aims to characterize the metabolite profiles in the established cell lines corresponding to different stages of CRC. Methods: Metabolite profiling of normal colon cell lines (CCD 841 CoN) and CRC cell lines corresponding to different stages, i.e., SW 1116 (stage A), HT 29 and SW 480 (stage B), HCT 15 and DLD-1 (stage C), and HCT 116 (stage D), was carried out using liquid chromatography-mass spectrometry (LC-MS). Mass Profiler Professional and Metaboanalyst 4.0 software were used for statistical and pathway analysis. METLIN database was used for the identification of metabolites. Results: We identified 72 differential metabolites compared between CRC cell lines of all the stages and normal colon cells. Principle component analysis and partial least squares discriminant analysis score plot were used to segregate normal and CRC cells, as well as CRC cells in different stages of the disease. Variable importance in projection score identified unique differential metabolites in CRC cells of the different stages. We identified 7 differential metabolites unique to stage A, 3 in stage B, 5 in stage C, and 5 in stage D. Conclusion: This study highlights the differential metabolite profiling in CRC cell lines corresponding to different stages. The identification of the differential metabolites in CRC cells at individual stages will lead to a better understanding of the pathophysiology of CRC development and progression and, hence, its application in treatment strategies.

A gas chromatography-mass spectrometry (GC-MS) metabolomic approach in human colorectal cancer (CRC): the emerging role of monosaccharides and amino acids

Background

Colorectal cancer (CRC) has been confirmed to be the third most commonly diagnosed cancer in males and the second in females. We investigated the blood plasma metabolome in CRC patients and in healthy adults to elucidate the role of monosaccharides, amino acids, and their respective metabolic pathways as prognostic factors in patients with CRC.

Methods

Fifteen patients with CRC and nine healthy adults were enrolled in the study and their blood plasma samples analyzed by gas chromatography-mass spectrometry (GC-MS). Univariate Student's t-test, multivariate principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA) were conducted on MetaboAnalyst 4.0. The analysis of metabolic profiles was carried out by the web-based extension Metabolite Sets Enrichment Analysis (MSEA).

Results

Overall, 125 metabolites were identified in plasma samples by GC-MS. In CRC patient samples, nine metabolites, including D-mannose and fructose, were significantly more abundant than in controls; conversely, eleven amino derivatives were less abundant, including methionine, valine, lysine, and proline. Methionine was significantly less abundant in died patients compared with survivors. The most significantly altered metabolic pathways in CRC patients are those involving monosaccharides (primarily the catabolic pathway of fructose and D-mannose), and amino acids (primarily methionine, valine, leucine, and isoleucine).

Conclusions

The abundance of D-mannose in CRC patient samples contributes to inhibiting the growth of cancer cells, while the abundance of fructose may be consistent either with low consumption of fructose by aerobic glycolysis within cancer cells or with a high bioavailability of fructose from diet. The reduction in methionine concentration may be related to increased activity of the threonine and methionine catabolic pathways, confirmed by high levels of α-hydroxybutyrate.