Precision treatment in colorectal cancer: Now and the future

Correlation of tumor-associated macrophage density and proportion of M2 subtypes with the pathological stage of colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is a prevalent global malignancy with complex prognostic factors. Tumor-associated macrophages (TAMs) have shown paradoxical associations with CRC survival, particularly concerning the M2 subset.

AIM

We aimed to establish a simplified protocol for quantifying M2-like TAMs and explore their correlation with clinicopathological factors.

METHODS

A cross-sectional study included histopathological assessment of paraffin-embedded tissue blocks obtained from 43 CRC patients. Using CD68 and CD163 immunohistochemistry, we quantified TAMs in tumor stroma and front, focusing on M2 proportion. Demographic, histopathological, and clinical parameters were collected.

RESULTS

TAM density was significantly higher at the tumor front, with the M2 proportion three times greater in both zones. The tumor front had a higher M2 proportion, which correlated significantly with advanced tumor stage (P = 0.04), pathological nodal involvement (P = 0.04), and lymphovascular invasion (LVI, P = 0.01). However, no significant association was found between the M2 proportion in the tumor stroma and clinicopathological factors.

CONCLUSION

Our study introduces a simplified protocol for quantifying M2-like TAMs in CRC tissue samples. We demonstrated a significant correlation between an increased M2 proportion at the tumor front and advanced tumor stage, nodal involvement, and LVI. This suggests that M2-like TAMs might serve as potential indicators of disease progression in CRC, warranting further investigation and potential clinical application.

Feasibility and Tolerability of Anlotinib Plus PD-1 Blockades for Patients with Treatment-Refractory Metastatic Colorectal Cancer: A Retrospective Exploratory Study

Objective

Therapeutic regimens are relatively scarce among patients with treatment-refractory metastatic colorectal cancer (CRC). This study aimed to determine the feasibility and tolerability of anlotinib plus PD-1 blockades in patients with treatment-refractory metastatic CRC retrospectively.

Methods

A total of 68 patients with previously treated metastatic CRC who received anlotinib plus PD-1 blockades in clinical practice were included in this study retrospectively. Demographic and clinical characteristics of the patients, therapeutic outcomes and safety profile during administration were collected and briefly analyzed. All subjects were followed up regularly. Therapeutic outcomes, including drug response and prognosis, were presented, and a safety profile was depicted to illustrate the adverse reactions.

Results

A total of 68 patients with treatment-refractory metastatic CRC who received anlotinib plus PD-1 blockades in clinical practice were included in the final analysis. Best therapeutic response during treatment indicated that partial response was observed in 11 patients, stable disease was noted in 41 patients, and progressive disease was found in 16 patients, producing an objective response rate of 16.2% (95% CI: 8.4%-27.1%) and a disease control rate of 76.5% (95% CI: 64.6%-85.9%). Prognostic analysis suggested that the median progression-free survival (PFS) of the 68 patients was 5.3 months (95% CI: 3.01-7.59), and the median overall survival (OS) was 12.5 months (95% CI: 9.40-15.60). Of the 11 patients who responded, the median duration of response was 6.7 months (95% CI: 2.89-10.53). Safety profile during treatment showed that patients experienced adverse reactions regardless of grade, and grade ≥3 adverse reactions were found in 61 patients (89.7%) and 41 patients (60.3%), respectively. Common adverse reactions were hypertension, myelosuppression (including leukopenia, neutropenia, thrombocytopenia, and anemia), fatigue, and hand-foot syndrome.

Conclusion

Anlotinib plus PD-1 blockades demonstrated encouraging efficacy and acceptable safety profile in patients with treatment-refractory metastatic CRC preliminarily in clinical practice. This conclusion should be confirmed in prospective clinical trials.

A Contemporary Review on the Critical Role of Nonsteroidal Anti-inflammatory Agents in Colorectal Cancer Therapy

Nonsteroidal Anti-Inflammatory Drugs (NSAIDs) are widely recognized as effective pain relievers and function by inhibiting the cyclooxygenase enzyme (COXs). Moreover, they have been found to participate in various cellular processes through different signaling pathways, such as WNT, MAPK, NF-κB, and PI3K/AKT/mTOR. This makes them potential candidates for chemoprevention of several malignancies, particularly colorectal cancer (CRC). However, the use of NSAIDs in cancer prevention and treatment is a complex issue due to their adverse effects and gastrointestinal toxicity. Therefore, it is crucial to explore combination therapies that can minimize side effects while maximizing synergistic effects with other agents and to evaluate the success rate of such approaches in both pre-clinical and clinical studies. In this review, we aim to provide an overview of the effects of NSAIDs in the prevention and treatment of CRC. We will focus on elucidating the possible mechanisms of action of these drugs, the signaling pathways involved in CRC, and the potential synergistic effects when combined with other therapeutic agents.

LncRNA MEG3 inhibits the proliferation and migration abilities of colorectal cancer cells by competitively suppressing MiR-31 and reducing the binding of MiR-31 to target gene SFRP1

To explore the potential mechanism of long-chain non-coding ribonucleic acid (lncRNA) maternal expression gene 3 (MEG3) in colorectal cancer (CRC). The relationship between MEG3 and miR-31 was detected by dual-luciferase assay. Quantitative polymerase chain reaction was utilized to determine the expression of MEG3 in CRC cell lines. Cell Counting Kit-8 assay was performed to detect cell proliferation. Transwell, cell scratch wound assay, and monoclonal proliferation assay were used to detect the proliferation, migration, and invasion of cells. In addition, cell motility was evaluated by detecting the expression of cellular pseudopodia protein α-actinin via immunofluorescence assay, and cell proliferation and motility were judged by determining the expressions of Ki-67, MMP2 and MMP9 via Western blotting. The effect of MEG3 and miR-31 on the development of colorectal cancer was verified by nude mouse tumor-bearing assay and HE staining. Transient transfection with MEG3 overexpression plasmid revealed that MEG3 inhibited the proliferation and motility of cells. The results of dual-luciferase assay showed that MEG3 could specifically inhibit the expression of miR-31, which inhibits the development of colorectal cancer. Transwell, cell scratch wound assay, and monoclonal proliferation experiment showed that miR-31 enhanced cell proliferation, migration and invasion. MEG3 overexpression plasmid was capable of reversing the proliferation and motility of CRC cells enhanced by miR-31. MEG3 can inhibit the proliferation and motility of CRC cells by competitively suppressing the binding of miR-31 to the target gene SFRP1, thus playing an inhibitory role in the pathogenesis of CRC.

Prospects of new targeted nanotherapy combining liponiosomes with berberine to combat colorectal cancer development: An in vivo experimental model

Colorectal cancer (CRC) is one of the most identified and deadly malignancies worldwide. It presents a serious challenge due to its quick growth, which finally culminates in severe malignancy. It is critical to improve the efficacy of berberine (BR) as an anticancer agent to overcome its limited bioavailability. Implementation of a novel, effective nanocarrier system of liponiosomes for BR (LipoNio.BR) can support mechanistic actions associated with its anti-CRC role. Following CRC induction in rats using 1,2 Dimethylhydrazine (40 mg DMH/kg/week), the potency and mechanistic actions of LipoNio.BR were assessed by evaluating the lesion severity and molecular mechanisms controlling oxidative stress, apoptosis, autophagy, and inflammatory responses, and conducting histopathological and immunohistochemistry examinations of colonic tissues. The results indicated that the severity of clinical signs comprising weight gain loss, increased diarrhea and rectal bleeding, and reduced survivability were greatly restored in the LipoNio.BR-treated group. LipoNio.BR remarkably reduced CRC development compared to FBR (free berberine), as it induced apoptosis via upregulating apoptotic genes (Bax and caspase3, increased up to 7.89 and 6.25-fold, respectively) and downregulating the anti-apoptotic gene Bcl-2 by 2.25-fold. LipoNio.BR mitigated the oxidative stress associated with CRC and maintained redox homeostasis. Notably, the excessive inflammatory response associated with CRC was prominently reduced following administration of LipoNio.BR [which decreased iterleukin (IL-B, IL-6), tumor necrosis factor-alpha (TNF-α), cyclooxygenase-2 (COX2), inducible nitric oxide synthase (iNOS), proliferating cell nuclear antigen (PCNA), follistatin, and activin BA (beta-A) expression]. LipoNio.BR modulated the expression of nuclear factor kappa B (NF-κB) and mammalian target of rapamycin (mTOR), which impacted tumor vascularity (decreased Vascular endothelial growth factor (VEGF) expression by 2.36-fold). The severity of the histopathological alterations in the colonic tissues, including the development of neoplastic epithelium and the invasion of some neoplastic masses, was greatly reduced in the LipoNio.BR group compared to the FBR-(free berberine) administrated group. Following CRC induction, immunohistochemical staining revealed that the overexpression of cyclin and COX-2 in colonic tissues were suppressed in the LipoNio.BR group. Taken together, these findings suggest that LipoNio.BR has a potential role in reducing CRC progression to a greater extent compared to free BR and could be considered a promising and potent therapy against CRC.

Development of a novel modified vaccine (TheraVacM) for curative treatment of mouse solid tumors

Monotherapy with immune checkpoint blockade (ICB) antibodies (anti-CTLA4 and anti-PD1/PDL-1) is only effective for 20% to 30% of patients with certain cancers. Patients with cancers harboring few effector T cells (Teffs) are insensitive to ICB therapy. The lack of tumor-specific Teffs is predominantly caused by the paralysis of tumor-infiltrating dendritic cells (TiDCs) resulting from immunosuppression in the tumor microenvironment. We have identified a potent combination of high mobility group nucleosome binding domain 1 (HMGN1, N1) and fibroblast stimulating lipopeptide-1 (FSL-1) that can synergistically trigger maturation of both mouse and human DCs. Accordingly, we designed a combinational anti-cancer immunotherapy with two arms: an immune-activating arm consisting of N1 and FSL-1 to stimulate the generation of Teffs by triggering full maturation of TiDCs, and an ICB arm using anti-PDL-1 or anti-CTLA4 to prevent Teffs from being silenced in the tumor tissue. This combinational immunotherapeutic vaccination regimen dubbed modified TheraVac (TheraVacM) has proved particularly effective as it cured 100% of mice bearing established ectopic CT26 colon and RENCA kidney tumors. The resultant tumor-free mice were resistant to subsequent re-challenge with the same tumors, indicating the generation of long-term tumor specific protective immunity. Since the immune-activating arm also induces full maturation of human DCs, and anti-PDL-1 or anti-CTLA4 have been FDA-approved, this combinational immunotherapy has the potential to be an effective clinical therapy for patients with solid tumors.

Restoration of miR-650 leads to down-regulation of KISS1, a possible route involved in overcoming 5-FU resistance and induction of apoptosis in CRC cells in-vitro

BACKGROUND

Colorectal cancer (CRC) is one of the most common cancers and the fourth leading cause of cancer-related deaths worldwide. We aimed to determine the role of miR-650 in CRC pathogenesis.

METHODS

In this study, we examined the expression of miR-650 and KISS1 in 80 CRC patients who either received or did not receive chemo agents. For this aim, we assessed the miR-650 and KISS1 expression levels in 80 CRC tissues, 30 of which had no history of chemotherapy. The effect of miR-650 and 5-FU on KISS1 expression was measured using qPCR and Western blotting. Also, the 5- FU effect on miR-650 expression in the CRC cell lines was measured by qRT-PCR. Next, MTT assay and Flowcytometry assays were conducted to determine the role of miR-650 in cell viability and apoptosis.

RESULTS

The results showed that miR-650 was down-regulated in CRC tissues. However, patients who received 5-FU before surgery showed increased expression of miR-650. The results for KISS1 were insignificant while administering 5-FU to patients preoperatively increased its expression. In-vitro studies showed that 5-FU led to the up-regulation of miR-650 in the SW480 CRC cell line. Furthermore, the administration of miR-650 and 5-FU downregulated KISS1, especially when combined. Moreover, miR-650 with 5-FU significantly reduced cell viability in CRC cell lines by inducing apoptosis.

CONCLUSIONS

These results indicate that miR-650 has a tumor suppressive function, overcoming 5-FU chemoresistance in CRC, and induces apoptosis probably by alleviating KISS1. These results suggest that miR-650 is a potential contributor to CRC pathogenesis.

miR-509-5p promotes colorectal cancer cell ferroptosis by targeting SLC7A11

BACKGROUND/AIM

Colorectal cancer (CRC), is characterized by aberrant microRNA (miRNA) expression during their development and progression. Recently, miR-509-5p's role as a regulator of several malignancies has been highlighted. Its function in CRC, however, is exposed. This research aimed to determine the relative abundance of miR-509-5p and its biological function in colorectal cancer.

METHODS

The expression of miR-509-5p in CRC cell lines and tissues, as well as neighboring normal tissues, was evaluated using real-time quantitative polymerase chain reaction (RT-PCR). 3-(4,5-dimethylthiazol-2-yl)- 2,5-diphenyl-2 H-tetrazolium bromide (MTT) was used to assess cell viability. The association between miR-509-5p and its predicted target in CRC cells was analyzed using bioinformatics tools. The levels of Solute carrier family seven number 11 (SLC7A11) were assessed using enzyme-linked immunosorbent assay (ELISA), while malondialdehyde (MDA) and iron content levels were determined colorimetrically.

RESULTS

Compared to adjacent normal tissue and normal colorectal cell, there was a significant reduction in miR-509-5p expression in both CRC tissues and cells. miR-509-5p upregulation inhibited Caco-2 cell viability. SLC7A11 was predicted to be the cellular target of miR-509-5p. Interestingly, miR-509-5p's overexpression suppressed both mRNA and protein levels of SLC7A11, whereas its downregulation boosted SLC7A11 gene expression. Finally, overexpressing miR-509-5p resulted in increased MDA and iron levels.

CONCLUSION

Our results demonstrate that miR-509-5p has CRC tumor suppressor functions through controlling the expression of SLC7A11 and promotion of ferroptosis providing a new therapeutic target for the treatment of CRC.

MKX-AS1 Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients

Oxaliplatin (OXAL) is a commonly used chemotherapy for treating colorectal cancer (CRC). A recent genome wide association study (GWAS) showed that a genetic variant (rs11006706) in the lncRNA gene MKX-AS1 and partnered sense gene MKX could impact the response of genetically varied cell lines to OXAL treatment. This study found that the expression levels of MKX-AS1 and MKX in lymphocytes (LCLs) and CRC cell lines differed between the rs11006706 genotypes, indicating that this gene pair could play a role in OXAL response. Further analysis of patient survival data from the Cancer Genome Atlas (TCGA) and other sources showed that patients with high MKX-AS1 expression status had significantly worse overall survival (HR = 3.2; 95%CI = (1.17-9); p = 0.024) compared to cases with low MKX-AS1 expression status. Alternatively, high MKX expression status had significantly better overall survival (HR = 0.22; 95%CI = (0.07-0.7); p = 0.01) compared to cases with low MKX expression status. These results suggest an association between MKX-AS1 and MKX expression status that could be useful as a prognostic marker of response to OXAL and potential patient outcomes in CRC.

Principles of Molecular Utility for CMS Classification in Colorectal Cancer Management

Colorectal cancer (CRC) is the second cause of cancer-related deaths in both sexes globally and presents different clinical outcomes that are described by a range of genomic and epigenomic alterations. Despite the advancements in CRC screening plans and treatment strategies, the prognosis of CRC is dismal. In the last two decades, molecular biomarkers predictive of prognosis have been identified in CRC, although biomarkers predictive of treatment response are only available for specific biological drugs used in stage IV CRC. Translational clinical trials mainly based on "omic" strategies allowed a better understanding of the biological heterogeneity of CRCs. These studies were able to classify CRCs into subtypes mainly related to prognosis, recurrence risk, and, to some extent, also to treatment response. Accordingly, the comprehensive molecular characterizations of CRCs, including The Cancer Genome Atlas (TCGA) and consensus molecular subtype (CMS) classifications, were presented to improve the comprehension of the genomic and epigenomic landscapes of CRCs for a better patient management. The CMS classification obtained by the CRC subtyping consortium categorizes CRC into four consensus molecular subtypes (CMS1-4) characterized by different prognoses. In this review, we discussed the CMS classification in different settings with a focus on its relationships with precursor lesions, tumor immunophenotype, and gut microbiota, as well as on its role in predicting prognosis and/or response to pharmacological treatments, as a crucial step towards precision medicine.

What Personalized Medicine Humans Need and Way to It --also on the Practical Significance and Scientific Limitations of Precision Medicine

The rise of precision medicine has opened up a broad space for the development of modern medicine and has also given practical significance to the concept of personalised medicine. Precision medicine is establishing a personalized disease classification system that differs from the traditional system. However, the research progress of precision medicine in recent years is far from satisfactory: There are few disease types that can be attributed to the abnormality of a single target; the effects of current'precision' medications are not ideal, and various side effects remain unavoidable. The methodology of precision medicine is still reductionist, and it would not solve the integration problem of clinical treatment but rather would increase the difficulty of integration. Therefore, the precision medicine approach is not a feasible way to build a personalised medicine system. Based on the analysis and demonstration of the scientific limitations of precision medicine and the consistency of traditional Chinese medicine (TCM) and complexity science methods, this paper draws on the concepts and methods of cybernetics and complexity science, and proposes a fresh set of ideas and methods for the development of personalised medicine. The conclusion is as follows: Along the path of precision medicine, ideal personalised medicine cannot be achieved; what people ultimately need is personalised medicine that can achieve holistic integration. On the basis of TCM with the characteristics of holistic integration and personalisation, and according to scientific norms and the principle of evidence, building a theoretical model and state description system grounded in empirical evidence is the best way to establish a personalised medicine system.

BRAF and MLH1 Analysis Algorithm for the Evaluation of Lynch Syndrome Risk in Colorectal Carcinoma Patients: Evidence-Based Data from the Analysis of 100 Consecutive Cases

Several causes may lead to CRC, either extrinsic (sporadic forms) or genetic (hereditary forms), such as Lynch syndrome (LS). Most sporadic deficient mismatch repair (dMMR) CRC cases are characterized by the methylation of the MLH1 promoter gene and/or BRAF gene mutations. Usually, the first test performed is the mismatch repair deficiency analysis. If a tumor shows a dMMR, BRAF mutations and then the MLH1 promoter methylation status have to be assessed, according to the ACG/ASCO screening algorithm. In this study, 100 consecutive formalin-fixed and paraffin-embedded samples of dMMR CRC were analyzed for both BRAF mutations and MLH1 promoter methylation. A total of 47 (47%) samples were BRAF p.V600E mutated, while MLH1 promoter methylation was found in 77 cases (77.0%). The pipeline “BRAF-followed-by-MLH1-analysis” led to a total of 153 tests, while the sequence “MLH1-followed-by-BRAF-analysis” resulted in a total of 123 tests. This study highlights the importance of performing MLH1 analysis in LS screening of BRAF-WT specimens before addressing patients to genetic counseling. We show that MLH1 analysis performs better as a first-line test in the screening of patients with LS risk than first-line BRAF analysis. Our data indicate that analyzing MLH1 methylation as a first-line test is more cost-effective.

Yusof NF, Mohd Yunos RI, Ishak M, Saidin S, Rose IM, Sagap I, Mazlan L, Mohd Azman ZA, Mazlan M, Ab Rahim S, Wan Ngah WZ, Nathan S, Hashim NAA, Mohamed-Hussein ZA, Jamal R. TCGA-My: A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer

Colorectal cancer (CRC) ranks second among the most commonly occurring cancers in Malaysia, and unfortunately, its pathobiology remains unknown. CRC pathobiology can be understood in detail with the implementation of omics technology that is able to generate vast amounts of molecular data. The generation of omics data has introduced a new challenge for data organization. Therefore, a knowledge-based repository, namely TCGA-My, was developed to systematically store and organize CRC omics data for Malaysian patients. TCGA-My stores the genome and metabolome of Malaysian CRC patients. The genome and metabolome datasets were organized using a Python module, pandas. The variants and metabolites were first annotated with their biological information using gene ontologies (GOs) vocabulary. The TCGA-My relational database was then built using HeidiSQL PorTable 9.4.0.512, and Laravel was used to design the web interface. Currently, TCGA-My stores 1,517,841 variants, 23,695 genes, and 167,451 metabolites from the samples of 50 CRC patients. Data entries can be accessed via search and browse menus. TCGA-My aims to offer effective and systematic omics data management, allowing it to become the main resource for Malaysian CRC research, particularly in the context of biomarker identification for precision medicine.

Metal-Phenolic Networks as Versatile Coating Materials for Biomedical Applications

Polyphenols are naturally derived organic compounds that have long been used as food additives, antioxidants, and adhesives owing to their intrinsic physicochemical properties. Recently, there has been growing interest in the fabrication of coordination networks based on the self-assembly of polyphenols and metal ions, termed metal-phenolic networks (MPNs), for multiple biological applications including bioimaging, drug delivery, and cell encapsulation. The as-synthesized MPN complexes feature pH responsiveness, controllable size and rigidity, and tunable permeability based on the choice of polyphenol-metal ion pairs. The aim of this Review is to introduce the physicochemical properties of MPNs, highlight their recent biological applications in cancer theranostics and single-cell encapsulation, and discuss the future utility of MPNs for biomedical applications.

Berberine as a Potential Agent for the Treatment of Colorectal Cancer

Colorectal cancer (CRC) is one of the most commonly diagnosed and deadly malignancies worldwide. The incidence of CRC has been increasing, especially in young people. Although great advances have been made in managing CRC, the prognosis is unfavorable. Numerous studies have shown that berberine (BBR) is a safe and effective agent presenting significant antitumor effects. Nevertheless, the detailed underlying mechanism in treating CRC remains indistinct. In this review, we herein offer beneficial evidence for the utilization of BBR in the management and treatment of CRC, and describe the underlying mechanism(s). The review emphasizes several therapeutic effects of BBR and confirms that BBR could suppress CRC by modulating gene expression, the cell cycle, the inflammatory response, oxidative stress, and several signaling pathways. In addition, BBR also displays antitumor effects in CRC by regulating the gut microbiota and mucosal barrier function. This review emphasizes BBR as a potentially effective and safe drug for CRC therapy.

Characteristics and Clinical Implication of UGT1A1 Heterozygous Mutation in Tumor

BACKGROUND

The literature recommends that reduced dosage of CPT-11 should be applied in patients with UGT1A1 homozygous mutations, but the impact of UGT1A1 heterozygous mutations on the adverse reactions of CPT-11 is still not fully clear.

METHODS

A total of 107 patients with UGT1A1 heterozygous mutation or wild-type, who were treated with CPT-11 from January 2018 to September 2021 in Peking University Third Hospital, were retrospectively enrolled. The adverse reaction spectra of patients with UGT1A1*6 and UGT1A1*28 mutations were analyzed. Adverse reactions were evaluated according to National Cancer Institute Common Terminology Criteria for Adverse Events (NCI-CTCAE) 5.0. The efficacy was evaluated according to Response Evaluation Criteria in Solid Tumors (RECIST) 1.1. The genotypes of UGT1A1*6 and UGT1A1*28 were detected by digital fluorescence molecular hybridization.

RESULTS

There were 43 patients with UGT1A1*6 heterozygous mutation, 26 patients with UGT1A1*28 heterozygous mutation, 8 patients with UGT1A1*6 and UGT1A1*28 double heterozygous mutations, 61 patients with heterozygous mutation at any gene locus of UGT1A1*6 and UGT1A1*28. Logistic regression analysis showed that the presence or absence of vomiting (P=0.013) and mucositis (P=0.005) was significantly correlated with heterozygous mutation of UGT1A1*28, and the severity of vomiting (P<0.001) and neutropenia (P=0.021) were significantly correlated with heterozygous mutation of UGT1A1*6. In colorectal cancer, UGT1A1*6 was significantly correlated to diarrhea (P=0.005), and the other adverse reactions spectrum was similar to that of the whole patient cohort, and efficacy and prognosis were similar between patients with different genotypes and patients treated with reduced CPT-11 dosage or not.

CONCLUSIONS

In clinical use, heterozygous mutations of UGT1A1*6 and UGT1A1*28 are related to the risk and severity of vomiting, diarrhea, neutropenia and mucositis in patients with Pan-tumor and colorectal cancer post CPT-11 therpy. In colorectal cancer, UGT1A1*6 is significantly related to diarrhea post CPT-11 use, efficacy and prognosis is not affected by various genotypes or CPT-11 dosage reduction.

Precision Nomothetic Medicine in Depression Research: A New Depression Model, and New Endophenotype Classes and Pathway Phenotypes, and A Digital Self

Machine learning approaches, such as soft independent modeling of class analogy (SIMCA) and pathway analysis, were introduced in depression research in the 1990s (Maes et al.) to construct neuroimmune endophenotype classes. The goal of this paper is to examine the promise of precision psychiatry to use information about a depressed person’s own pan-omics, environmental, and lifestyle data, or to tailor preventative measures and medical treatments to endophenotype subgroups of depressed patients in order to achieve the best clinical outcome for each individual. Three steps are emerging in precision medicine: (1) the optimization and refining of classical models and constructing digital twins; (2) the use of precision medicine to construct endophenotype classes and pathway phenotypes, and (3) constructing a digital self of each patient. The root cause of why precision psychiatry cannot develop into true sciences is that there is no correct (cross-validated and reliable) model of clinical depression as a serious medical disorder discriminating it from a normal emotional distress response including sadness, grief and demoralization. Here, we explain how we used (un)supervised machine learning such as partial least squares path analysis, SIMCA and factor analysis to construct (a) a new precision depression model; (b) a new endophenotype class, namely major dysmood disorder (MDMD), which is a nosological class defined by severe symptoms and neuro-oxidative toxicity; and a new pathway phenotype, namely the reoccurrence of illness (ROI) index, which is a latent vector extracted from staging characteristics (number of depression and manic episodes and suicide attempts), and (c) an ideocratic profile with personalized scores based on all MDMD features.

Toward Overcoming Treatment Failure in Rheumatoid Arthritis

Rheumatoid arthritis (RA) is an autoimmune disorder characterized by inflammation and bone erosion. The exact mechanism of RA is still unknown, but various immune cytokines, signaling pathways and effector cells are involved. Disease-modifying antirheumatic drugs (DMARDs) are commonly used in RA treatment and classified into different categories. Nevertheless, RA treatment is based on a "trial-and-error" approach, and a substantial proportion of patients show failed therapy for each DMARD. Over the past decades, great efforts have been made to overcome treatment failure, including identification of biomarkers, exploration of the reasons for loss of efficacy, development of sequential or combinational DMARDs strategies and approval of new DMARDs. Here, we summarize these efforts, which would provide valuable insights for accurate RA clinical medication. While gratifying, researchers realize that these efforts are still far from enough to recommend specific DMARDs for individual patients. Precision medicine is an emerging medical model that proposes a highly individualized and tailored approach for disease management. In this review, we also discuss the potential of precision medicine for overcoming RA treatment failure, with the introduction of various cutting-edge technologies and big data.

Multiplexed DNA Methylation Analysis in Colorectal Cancer Using Liquid Biopsy and Its Diagnostic and Predictive Value

Early diagnosis of colorectal cancer (CRC) is of high importance as prognosis depends on tumour stage at the time of diagnosis. Detection of tumour-specific DNA methylation marks in cfDNA has several advantages over other approaches and has great potential for solving diagnostic needs. We report here the identification of DNA methylation biomarkers for CRC and give insights in our methylation-sensitive restriction enzyme coupled qPCR (MSRE-qPCR) system. Targeted microarrays were used to investigate the DNA methylation status of 360 cancer-associated genes. Validation was done by qPCR-based approaches. A focus was on investigating marker performance in cfDNA from 88 patients (44 CRC, 44 controls). Finally, the workflow was scaled-up to perform 180plex analysis on 110 cfDNA samples, to identify a DNA methylation signature for advanced colonic adenomas (AA). A DNA methylation signature (n = 44) was deduced from microarray experiments and confirmed by quantitative methylation-specific PCR (qMSP) and by MSRE-qPCR, providing for six genes’ single areas under the curve (AUC) values of >0.85 (WT1, PENK, SPARC, GDNF, TMEFF2, DCC). A subset of the signatures can be used for patient stratification and therapy monitoring for progressed CRC with liver metastasis using cfDNA. Furthermore, we identified a 35-plex classifier for the identification of AAs with an AUC of 0.80.

Addition of V-Stage to Conventional TNM Staging to Create the TNVM Staging System for Accurate Prediction of Prognosis in Colon Cancer: A Multi-Institutional Retrospective Cohort Study

We evaluated the prognostic impact of vascular invasion (VI) compared with nodal (N) stage and developed a new staging system including VI in colon cancer. Patients who underwent curative resection with stage II-III colon cancer were assigned to VI and non-VI groups; the latter was subclassified as N0, N1, and N2; a new TNVM staging was devised by adding the V-stage. Among the 2243 study participants, the VI group independently showed worse oncological outcomes than the N1 group (disease-free survival (DFS), hazard-ratio (HR) 1.704, 1.267–2.291; overall survival (OS), HR 2.301, 1.582–3.348). The 5-year DFS in the VI group was 63.4% [N1b (74.6%), p = 0.003; N2a (69.7%), p = 0.126; and N2b (56.8%), p = 0.276], and the 5-year OS was 76.6% [N1b (84.9%), p = 0.004; N2a (83.0%), p = 0.047; and N2b (76.1%), p = 0.906]. Thus, we considered VI as N2a in TNVM staging; 78 patients (3.5%) underwent upstaging. The 5-year OS rates of stage IIB and IIC increased from 88.6% and 65.9% in TNM staging to 90.5% and 85.7% in TNVM staging, respectively. In stage II–III colon cancer, VI had a similar prognostic impact as the N2 stage without VI. The incorporation of the V-stage into the conventional TNM staging facilitates better prediction of prognosis.

Molecular Imaging, How Close to Clinical Precision Medicine in Lung, Brain, Prostate and Breast Cancers

Precision medicine is playing a pivotal role in strategies of cancer therapy. Unlike conventional one-size-fits-all chemotherapy or radiotherapy modalities, precision medicine could customize an individual treatment plan for cancer patients to acquire superior efficacy, while minimizing side effects. Precision medicine in cancer therapy relies on precise and timely tumor biological information. Traditional tissue biopsies, however, are often inadequate in meeting this requirement due to cancer heterogeneity, poor tolerance, and invasiveness. Molecular imaging could detect tumor biology characterization in a noninvasive and visual manner, and provide information about therapeutic targets, treatment response, and pharmacodynamic evaluation. This summates to significant value in guiding cancer precision medicine in aspects of patient screening, treatment monitoring, and estimating prognoses. Although growing clinical evidences support the further application of molecular imaging in precision medicine of cancer, some challenges remain. In this review, we briefly summarize and discuss representative clinical trials of molecular imaging in improving precision medicine of cancer patients, aiming to provide useful references for facilitating further clinical translation of molecular imaging to precision medicine of cancers.

Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning

Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person's variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e., precision oncology). Machine learning (ML), a subfield of artificial intelligence in which computers learn through experience, has a great potential to be used in precision oncology chiefly to help physicians make diagnostic decisions based on tumor images. A promising venue of ML in precision oncology is the integration of all available data from images to multi-omics big data for the holistic care of patients and high-risk healthy subjects. In this review, we provide a focused overview of precision oncology and ML with attention to breast cancer and glioma as well as the Bayesian networks that have the flexibility and the ability to work with incomplete information. We also introduce some state-of-the-art attempts to use and incorporate ML and genetic information in precision oncology.

The Role of microRNAs in Development of Colitis-Associated Colorectal Cancer

Colorectal cancer (CRC) is the third most deadly cancer worldwide, and inflammatory bowel disease (IBD) is one of the critical factors in CRC carcinogenesis. IBD is responsible for an unphysiological and sustained chronic inflammation environment favoring the transformation. MicroRNAs (miRNAs) belong to a class of highly conserved short single-stranded segments (18-25 nucleotides) non-coding RNA and have been extensively discussed in both CRC and IBD. However, the role of miRNAs in the development of colitis-associated CRC (CAC) is less clear. The aim of this review is to summarize the major upregulated (miR-18a, miR-19a, miR-21, miR-31, miR-155 and miR-214) and downregulated (miR-124, miR-193a-3p and miR-139-5p) miRNAs in CAC, and their roles in genes' expression modulation in chronic colonic-inflammation-induced carcinogenesis, including programmed cell-death pathways. These miRNAs dysregulation could be applied for early CAC diagnosis, to predict therapy efficacy and for precision treatment.

A selective p53 activator and anticancer agent to improve colorectal cancer therapy

Impairment of the p53 pathway is a critical event in cancer. Therefore, reestablishing p53 activity has become one of the most appealing anticancer therapeutic strategies. Here, we disclose the p53-activating anticancer drug (3S)-6,7-bis(hydroxymethyl)-5-methyl-3-phenyl-1H,3H-pyrrolo[1,2-c]thiazole (MANIO). MANIO demonstrates a notable selectivity to the p53 pathway, activating wild-type (WT)p53 and restoring WT-like function to mutant (mut)p53 in human cancer cells. MANIO directly binds to the WT/mutp53 DNA-binding domain, enhancing the protein thermal stability, DNA-binding ability, and transcriptional activity. The high efficacy of MANIO as an anticancer agent toward cancers harboring WT/mutp53 is further demonstrated in patient-derived cells and xenograft mouse models of colorectal cancer (CRC), with no signs of undesirable side effects. MANIO synergizes with conventional chemotherapeutic drugs, and in vitro and in vivo studies predict its adequate drug-likeness and pharmacokinetic properties for a clinical candidate. As a single agent or in combination, MANIO will advance anticancer-targeted therapy, particularly benefiting CRC patients harboring distinct p53 status.

APOD: accurate sequence-based predictor of disordered flexible linkers

MOTIVATION

Disordered flexible linkers (DFLs) are abundant and functionally important intrinsically disordered regions that connect protein domains and structural elements within domains and which facilitate disorder-based allosteric regulation. Although computational estimates suggest that thousands of proteins have DFLs, they were annotated experimentally in <200 proteins. This substantial annotation gap can be reduced with the help of accurate computational predictors. The sole predictor of DFLs, DFLpred, trade-off accuracy for shorter runtime by excluding relevant but computationally costly predictive inputs. Moreover, it relies on the local/window-based information while lacking to consider useful protein-level characteristics.

RESULTS

We conceptualize, design and test APOD (Accurate Predictor Of DFLs), the first highly accurate predictor that utilizes both local- and protein-level inputs that quantify propensity for disorder, sequence composition, sequence conservation and selected putative structural properties. Consequently, APOD offers significantly more accurate predictions when compared with its faster predecessor, DFLpred, and several other alternative ways to predict DFLs. These improvements stem from the use of a more comprehensive set of inputs that cover the protein-level information and the application of a more sophisticated predictive model, a well-parametrized support vector machine. APOD achieves area under the curve = 0.82 (28% improvement over DFLpred) and Matthews correlation coefficient = 0.42 (180% increase over DFLpred) when tested on an independent/low-similarity test dataset. Consequently, APOD is a suitable choice for accurate and small-scale prediction of DFLs.

AVAILABILITY AND IMPLEMENTATION

https://yanglab.nankai.edu.cn/APOD/.

GABRD promotes progression and predicts poor prognosis in colorectal cancer

Little is known about the functional roles of gamma-aminobutyric acid type A receptor subunit delta (GABRD) in colorectal cancer (CRC). The expression of GABRD between CRCs and adjacent normal tissues (NTs), metastasis and primary tumors was compared using public transcriptomic datasets. A tissue microarray and immunohistochemical staining (IHC) were used to determine the clinical and prognostic significance of the GABRD in CRC. We used gain-of-function and loss-of-function experiments to investigate the in vitro roles of GABRD in cultured CRC cells. We characterized the potential mechanism of GABRD’s activities in CRC using a Gene Set Enrichment Analysis (GSEA) with The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) dataset. We found that the GABRD expression was significantly increased in CRCs compared to that in NTs, but was similar between metastasis and primary tumors. Overexpression of GABRD was significantly associated with later pTNM stages and unfavorable patient survival. Overexpression of GABRD accelerated while knock-down of GABRD inhibited cell growth and migration. Mechanistically, the function of GABRD might be ascribed to its influence on major oncogenic events such as epithelial–mesenchymal transition (EMT), angiogenesis, and hedgehog signaling. Collectively, GABRD could be a novel prognostic predictor for CRC that deserves further investigation.

Non-Invasive Colorectal Cancer Screening: An Overview

Background

Colorectal cancer (CRC) follows a protracted stepwise progression, from benign adenomas to malignant adenocarcinomas. If detected early, 90% of deaths are preventable. However, CRC is asymptomatic in its early-stage and arises sporadically within the population. Therefore, CRC screening is a public health priority.

Summary

Faecal immunochemical test (FIT) is gradually replacing guaiac faecal occult blood test and is now the most commonly used screening tool for CRC screening program globally. However, FIT is still limited by the haemoglobin degradation and the intermittent bleeding patterns, so that one in four CRC cases are still diagnosed in a late stage, leading to poor prognosis. A multi-target stool DNA test (Cologuard, a combination of NDRG4 and BMP3 DNA methylation, KRAS mutations, and haemoglobin) and a plasma SEPT9 DNA methylation test (Epi proColon) are non-invasive tools also approved by the US FDA, but those screening approaches are not cost-effective, and the detection accuracies remain unsatisfactory. In addition to the approved tests, faecal-/blood-based microRNA and CRC-related gut microbiome screening markers are under development, with work ongoing to find the best combination of molecular biomarkers which maximise the screening sensitivity and specificity.

Key Message

Maximising the detection accuracy with a cost-effective approach for non-invasive CRC screening is urgently needed to further reduce the incidence of CRC and associated mortality rates.

Faecal microRNAs as a non-invasive tool in the diagnosis of colonic adenomas and colorectal cancer: A meta-analysis

MicroRNAs (miRNAs) are proposed as potential biomarkers for the diagnosis of numerous diseases. Here, we performed a meta-analysis to evaluate the utility of faecal miRNAs as a non-invasive tool in colorectal cancer (CRC) screening. A systematic literature search, according to predetermined criteria, in five databases identified 17 research articles including 6475, 783 and 5569 faecal-based miRNA tests in CRC, adenoma patients and healthy individuals, respectively. Sensitivity, specificity, positive/negative likelihood and diagnostic odds ratios, area under curve (AUC), summary receiver operator characteristic (sROC) curves, association of individual or combinations of miRNAs to cancer stage and location, subgroup, meta-regression and Deeks' funnel plot asymmetry analyses were employed. Pooled miRNAs for CRC had an AUC of 0.811, with a sensitivity of 58.8% (95% confidence interval [CI]: 51.7-65.5%) and specificity of 84.8% (95% CI: 81.1-87.8%), whilst for colonic adenoma, it was 0.747, 57.3% (95% CI: 40.8-72.3%) and 76.1% (95% CI: 66.1-89.4%), respectively. The most reliable individual miRNA was miR-21, with an AUC of 0.843, sensitivity of 59.3% (95% CI: 26.3-85.6%) and specificity of 85.6% (95% CI: 72.2-93.2%). Paired stage analysis showed a better diagnostic accuracy in late stage CRC and sensitivity higher in distal than proximal CRC. In conclusion, faecal miR-21, miR-92a and their combination are promising non-invasive biomarkers for faecal-based CRC screening.