KRAS, NRAS and BRAF mutations in colorectal cancer and melanoma

RIPK2 promotes colorectal cancer metastasis by protecting YAP degradation from ITCH-mediated ubiquitination

Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide, making the exploration of metastatic mechanisms crucial for therapeutic advancements. In this study, we identified receptor-interacting protein kinase 2 (RIPK2) as an independent risk factor for poor CRC prognosis. Single-cell RNA sequencing and spatial transcriptomics revealed that a tumor cell cluster with high RIPK2 expression exhibited enhanced metastatic potential, closely linked to bacterial invasion. In vitro and in vivo experiments confirmed that RIPK2 specifically promotes tumor cell migration and invasion, rather than proliferation. Proteomic analysis indicated that RIPK2 knockdown leads to increased proteolysis mediated by ubiquitin, particularly affecting the oncoprotein YAP. Additionally, bacterial invasion of epithelial cells was significantly suppressed in RIPK2 knockdown cells, suggesting a connection to the NOD2-RIPK2 pathway, stimulated by bacterial muramyl dipeptide (MDP). We demonstrated that MDP levels are significantly higher in CRC tissues compared to adjacent non-cancerous tissues, correlating with RIPK2 activation. This activation triggers K63-linked ubiquitination of RIPK2, essential for NF-κB and MAPK pathway activation. Mechanistic studies identified the E3 ubiquitin ligase ITCH as a critical mediator, balancing K63-linked ubiquitination of RIPK2 and K48-linked ubiquitination of YAP, leading to YAP degradation and suppressed CRC metastasis. The stability of YAP could also be disrupted by GSK583, a pharmacological inhibitor of RIPK2, effectively suppressing CRC metastasis. Our findings provide deep insights into RIPK2's role in CRC progression and present a promising target for future therapeutic strategies.

Facts, Dogmas, and Unknowns About Mitochondrial Reactive Oxygen Species in Cancer

Cancer metabolism is sustained both by enhanced aerobic glycolysis, characteristic of the Warburg phenotype, and oxidative metabolism. Cell survival and proliferation depends on a dynamic equilibrium between mitochondrial function and glycolysis, which is heterogeneous between tumors and even within the same tumor. During oxidative phosphorylation, electrons from NADH and FADH2 originated in the tricarboxylic acid cycle flow through complexes of the electron transport chain. Single electron leaks at specific complexes of the electron transport chain generate reactive oxygen species (ROS). ROS are a concentration-dependent double-edged sword that plays multifaceted roles in cancer metabolism. ROS serve either as signaling molecules favoring cellular homeostasis and proliferation or damage DNA, protein and lipids, causing cell death. Several aspects of ROS biology still remain unsolved. Among the unknowns are the actual levels at which ROS become cytotoxic and if toxicity depends on specific ROS species or if it is caused by a cumulative effect of all of them. In this review, we describe mechanisms of mitochondrial ROS production, detoxification, ROS-induced cytotoxicity, and the use of antioxidants in cancer treatment. We also provide updated information about critical questions on the biology of ROS on cancer metabolism and discuss dogmas that lack adequate experimental demonstration. Overall, this review brings a comprehensive perspective of ROS as drivers of cancer progression, inducers of cell death, and the potential use of antioxidants as anticancer therapy.

Exploring somatic mutations in BRAF, KRAS, and NRAS as therapeutic targets in Saudi colorectal cancer patients through massive parallel sequencing and variant classification

Background

Colorectal cancer (CRC) is the leading cancer among Saudis, and mutations in BRAF, KRAS, and NRAS genes are therapeutically significant due to their association with pathways critical for cell cycle regulation. This study evaluates the prevalence and frequency of somatic mutations in these actionable genes in Saudi CRC patients and assesses their pathogenicity with bioinformatics methods.

Methodology

The study employed the TruSight Tumor 15 next-generation sequencing (NGS) panel on 86 colorectal cancer (CRC) samples to detect somatic mutations in BRAF, KRAS, and NRAS genes. Bioinformatic analyses of NGS sequences included variant annotation with ANNOVAR, pathogenicity prediction, variant reclassification with CancerVar, and extensive structural analysis. Additionally, molecular docking assessed the binding of Encorafenib to wild-type and mutant BRAF proteins, providing insights into the therapeutic relevance of pathogenic variants.

Results

Out of 86 tumor samples, 40 (46.5%) harbored somatic mutations within actionable genes (BRAF: 2.3%, KRAS: 43%, NRAS: 2.3%). Fourteen missense variants were identified (BRAF: n = 1, KRAS: n = 11, NRAS: n = 2). Variants with strong clinical significance included BRAF V600E (2.32%) and KRAS G12D (18.60%). Variants with potential clinical significance included several KRAS and an NRAS mutation, while variants of unknown significance included KRAS E49K and NRAS R102Q. One variant was novel: NRAS R102Q, and two were rare: KRAS E49K and G138E. We further extended the CancerVar prediction capability by adding new pathogenicity prediction tools. Molecular docking demonstrated that Encorafenib inhibits the V600E variant BRAF protein less effectively compared to its wild-type counterpart.

Conclusion

Overall, this study highlights the importance of comprehensive molecular screening and bioinformatics in understanding the mutational landscape of CRC in the Saudi population, ultimately improving targeted drug treatments.

Correcting for Observation Bias in Cancer Progression Modeling

Tumor progression is driven by the accumulation of genetic alterations, including both point mutations and copy number changes. Understanding the temporal sequence of these events is crucial for comprehending the disease but is not directly discernible from cross-sectional genomic data. Cancer progression models, including Mutual Hazard Networks (MHNs), aim to reconstruct the dynamics of tumor progression by learning the causal interactions between genetic events based on their co-occurrence patterns in cross-sectional data. Here, we highlight a commonly overlooked bias in cross-sectional datasets that can distort progression modeling. Tumors become clinically detectable when they cause symptoms or are identified through imaging or tests. Detection factors, such as size, inflammation (fever, fatigue), and elevated biochemical markers, are influenced by genomic alterations. Ignoring these effects leads to "conditioning on a collider" bias, where events making the tumor more observable appear anticorrelated, creating false suppressive effects or masking promoting effects among genetic events. We enhance MHNs by incorporating the effects of genetic progression events on the inclusion of a tumor in a dataset, thus correcting for collider bias. We derive an efficient tensor formula for the likelihood function and apply it to two datasets from the MSK-IMPACT study. In colon adenocarcinoma, we observe a significantly higher rate of clinical detection for TP53-positive tumors, while in lung adenocarcinoma, the same is true for EGFR-positive tumors. Compared to classical MHNs, this approach eliminates several spurious suppressive interactions and uncovers multiple promoting effects.

Association between thyroid disorders and extra-thyroidal cancers, a review

Thyroid hormone has been shown to have both tumor-promoting and tumor-suppressing actions, which has led to significant debate over its involvement in the development of cancer. Proliferation, apoptosis, invasiveness, and angiogenesis are all aspects of cancer that are affected by the thyroid hormones T3 and T4, according to research conducted in animal models and in vitro experiments. The effects of thyroid hormones on cancer cells are mediated by many non-genomic mechanisms, one of which involves the activation of the plasma membrane receptor integrin αvβ3. Typically, abnormal amounts of thyroid hormones are linked to a higher occurrence of cancer. Both benign and malignant thyroid disorders were found to be associated with an increased risk of extra-thyroidal malignancies, specifically colon, breast, prostate, melanoma, and lung cancers. The purpose of this review was to shed light on this link to define which types of cancer are sensitive to thyroid hormones and, as a result, are anticipated to respond favorably to treatment of the thyroid hormone axis.

Prioritizing cervical cancer candidate genes using chaos game and fractal-based time series approach

Cervical cancer is one of the most severe threats to women worldwide and holds fourth rank in lethality. It is estimated that 604, 127 cervical cancer cases have been reported in 2020 globally. With advancements in high throughput technologies and bioinformatics, several cervical candidate genes have been proposed for better therapeutic strategies. In this paper, we intend to prioritize the candidate genes that are involved in cervical cancer progression through a fractal time series-based cross-correlations approach. we apply the chaos game representation theory combining a two-dimensional multifractal detrended cross-correlations approach among the known and candidate genes involved in cervical cancer progression to prioritize the candidate genes. We obtained 16 candidate genes that showed cross-correlation with known cancer genes. Functional enrichment analysis of the candidate genes shows that they involve GO terms: biological processes, cell-cell junction assembly, cell-cell junction organization, regulation of cell shape, cortical actin cytoskeleton organization, and actomyosin structure organization. KEGG pathway analysis revealed genes' role in Rap1 signaling pathway, ErbB signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, mTOR signaling pathway, Acute myeloid leukemia, chronic myeloid leukemia, Breast cancer, Thyroid cancer, Bladder cancer, and Gastric cancer. Further, we performed survival analysis and prioritized six genes CDH2, PAIP1, BRAF, EPB41L3, OSMR, and RUNX1 as potential candidate genes for cervical cancer that has a crucial role in tumor progression. We found that our study through this integrative approach an efficient tool and paved a new way to prioritize the candidate genes and these genes could be evaluated experimentally for potential validation. We suggest this may be useful in analyzing the nucleotide sequences and protein sequences for clustering, classification, class affiliation, etc.

Tumor- and Fibroblast-Derived Cell-Free DNAs Differently Affect the Progression of B16 Melanoma In Vitro and In Vivo

It is widely postulated that the majority of pathologically elevated extracellular or cell-free DNA (cfDNA) in cancer originates from tumor cells; however, evidence has emerged regarding the significant contributions of other cells from the tumor microenvironment. Here, the effect of cfDNA originating from murine B16 melanoma cells and L929 fibroblasts on B16 cells was investigated. It was found that cfDNAL929 increased the viability and migration properties of B16 cells in vitro and their invasiveness in vivo. In contrast, cfDNAB16 exhibited a negative effect on B16 cells, reducing their viability and migration in vitro, which in vivo led to decreased tumor size and metastasis number. It was shown that cell treatment with both cfDNAs resulted in an increase in the expression of genes encoding DNases and the oncogenes Braf, Kras, and Myc. cfDNAL929-treated cells were shown to experience oxidative stress. Gene expression changes in the case of cfDNAB16 treatment are well correlated with the observed decrease in proliferation and migration of B16 cells. The obtained data may indicate the possible involvement of fibroblast DNA in the tumor microenvironment in tumor progression and, potentially, in the formation of new tumor foci due to the transformation of normal cells.

Exploring the multifaceted role of RASGRP1 in disease: immune, neural, metabolic, and oncogenic perspectives

RAS guanyl releasing protein 1 (RASGRP1) is a guanine nucleotide exchange factor (GEF) characterized by the presence of a RAS superfamily GEF domain. It functions as a diacylglycerol (DAG)-regulated nucleotide exchange factor, specifically activating RAS through the exchange of bound GDP for GTP. Activation of RAS by RASGRP1 has a wide range of downstream effects at the cellular level. Thus, it is not surprising that many diseases are associated with RASGRP1 disorders. Here, we present an overview of the structure and function of RASGRP1, its crucial role in the development, expression, and regulation of immune cells, and its involvement in various signaling pathways. This review comprehensively explores the relationship between RASGRP1 and various diseases, elucidates the underlying molecular mechanisms of RASGRP1 in each disease, and identifies potential therapeutic targets. This study provides novel insights into the role of RASGRP1 in insulin secretion and highlights its potential as a therapeutic target for diabetes. The limitations and challenges associated with studying RASGRP1 in disease are also discussed.

Metastatic Undifferentiated Melanoma Mimicking a Primary Bone Tumor: A Potential Diagnostic Pitfall

ABSTRACT

Undifferentiated melanoma (UM) is defined by the loss of classic morphologic and immunohistochemical melanocytic markers. Reports in the literature are rare and show that UM usually occurs as a metastasis in the setting of a known primary cutaneous melanoma. The most common mutations in UM include those involving BRAF , NRAS , and KIT , which are almost invariably present in the parent melanoma. In this study, we report a case of a primary sinonasal melanoma with metastatic UM presenting with osteoclast-like giant cells and resembling a primary bone tumor. The retention of an unusual KRAS mutation in UM that was also present in the primary lesion provided critical information for the diagnosis. Our report highlights the importance of considering mutational analysis to identify undifferentiated melanomas in patients with metastatic tumors which do not have the typical histopathologic and immunohistochemical features of melanoma.

Computational insights into KRAS G12C inhibition: exploring possible repurposing of Azacitidine and Ribavirin

Kirsten rat sarcoma (KRAS) stands out as the most prevalent mutated oncogene, playing a crucial role in the initiation and progression of various cancer types, including colorectal, lung and pancreatic cancer. The oncogenic modifications of KRAS are intricately linked to tumor development and are identified in 22% of cancer patients. This has spurred the necessity to explore inhibition mechanisms, with the aim of investigating and repurposing existing drugs for diagnosing cancers dependent on KRAS G12C In this investigation, 26 nucleoside-based drugs were collected from literature to assess their effectiveness against KRAS G12C. The study incorporates in-silico molecular simulations and molecular docking examinations of these nucleoside-derived drugs with the KRAS G12C protein using Protein Data Bank (PDB) ID: 5V71. The docking outcomes indicated that two drugs, Azacitidine and Ribavirin, exhibited substantial binding affinities of -8.7 and -8.3 kcal/mol, respectively. These drugs demonstrated stability in binding to the active site of the protein during simulation studies. Root mean square deviation (RMSD) analyses indicated that the complexes closely adhered to an equilibrium RMSD value ranging from 0.17 to 0.2 nm. Additionally, % occupancies, bond angles and the length of hydrogen bonds were calculated. These findings suggest that Azacitidine and Ribavirin may potentially serve as candidates for repurposing in individuals with KRAS-dependent cancers.

Current Status of Cancer Genomics and Imaging Phenotypes: What Radiologists Need to Know

Ongoing discoveries in cancer genomics and epigenomics have revolutionized clinical oncology and precision health care. This knowledge provides unprecedented insights into tumor biology and heterogeneity within a single tumor, among primary and metastatic lesions, and among patients with the same histologic type of cancer. Large-scale genomic sequencing studies also sparked the development of new tumor classifications, biomarkers, and targeted therapies. Because of the central role of imaging in cancer diagnosis and therapy, radiologists need to be familiar with the basic concepts of genomics, which are now becoming the new norm in oncologic clinical practice. By incorporating these concepts into clinical practice, radiologists can make their imaging interpretations more meaningful and specific, facilitate multidisciplinary clinical dialogue and interventions, and provide better patient-centric care. This review article highlights basic concepts of genomics and epigenomics, reviews the most common genetic alterations in cancer, and discusses the implications of these concepts on imaging by organ system in a case-based manner. This information will help stimulate new innovations in imaging research, accelerate the development and validation of new imaging biomarkers, and motivate efforts to bring new molecular and functional imaging methods to clinical radiology. Keywords: Oncology, Cancer Genomics, Epignomics, Radiogenomics, Imaging Markers Supplemental material is available for this article. © RSNA, 2023.

Quinazolin-4-one/3-cyanopyridin-2-one Hybrids as Dual Inhibitors of EGFR and BRAFV600E: Design, Synthesis, and Antiproliferative Activity

A novel series of hybrid compounds comprising quinazolin-4-one and 3-cyanopyridin-2-one structures has been developed, with dual inhibitory actions on both EGFR and BRAFV600E. These hybrid compounds were tested in vitro against four different cancer cell lines. Compounds 8, 9, 18, and 19 inhibited cell proliferation significantly in the four cancer cells, with GI50 values ranging from 1.20 to 1.80 µM when compared to Doxorubicin (GI50 = 1.10 µM). Within this group of hybrids, compounds 18 and 19 exhibited substantial inhibition of EGFR and BRAFV600E. Molecular docking investigations provided confirmation that compounds 18 and 19 possess the capability to inhibit EGFR and BRAFV600E. Moreover, computational ADMET prediction indicated that most of the newly synthesized hybrids have low toxicity and minimal side effects.

Different oncological features of colorectal cancer codon-specific KRAS mutations: Not codon 13 but codon 12 have prognostic value

BACKGROUND

Approximately 40% of colorectal cancer (CRC) cases are linked to Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations. KRAS mutations are associated with poor CRC prognosis, especially KRAS codon 12 mutation, which is associated with metastasis and poorer survival. However, the clinicopathological characteristics and prognosis of KRAS codon 13 mutation in CRC remain unclear.

AIM

To evaluate the clinicopathological characteristics and prognostic value of codon-specific KRAS mutations, especially in codon 13.

METHODS

This retrospective, single-center, observational cohort study included patients who underwent surgery for stage I-III CRC between January 2009 and December 2019. Patients with KRAS mutation status confirmed by molecular pathology reports were included. The relationships between clinicopathological characteristics and individual codon-specific KRAS mutations were analyzed. Survival data were analyzed to identify codon-specific KRAS mutations as recurrence-related factors using the Cox proportional hazards regression model.

RESULTS

Among the 2203 patients, the incidence of KRAS codons 12, 13, and 61 mutations was 27.7%, 9.1%, and 1.3%, respectively. Both KARS codons 12 and 13 mutations showed a tendency to be associated with clinical characteristics, but only codon 12 was associated with pathological features, such as stage of primary tumor (T stage), lymph node involvement (N stage), vascular invasion, perineural invasion, tumor size, and microsatellite instability. KRAS codon 13 mutation showed no associations (77.2% vs 85.3%, P = 0.159), whereas codon 12 was associated with a lower 5-year recurrence-free survival rate (78.9% vs 75.5%, P = 0.025). In multivariable analysis, along with T and N stages and vascular and perineural invasion, only codon 12 (hazard ratio: 1.399; 95% confidence interval: 1.034-1.894; P = 0.030) among KRAS mutations was an independent risk factor for recurrence.

CONCLUSION

This study provides evidence that KRAS codon 13 mutation is less likely to serve as a prognostic biomarker than codon 12 mutation for CRC in a large-scale cohort.

Computed tomography-based radiomics nomogram for the pre-operative prediction of BRAF mutation and clinical outcomes in patients with colorectal cancer: a double-center study

OBJECTIVE

To develop and validate a radiomics nomogram based on CT for the pre-operative prediction of BRAF mutation and clinical outcomes in patients with colorectal cancer (CRC).

METHODS

A total of 451 CRC patients (training cohort = 190; internal validation cohort = 125; external validation cohort = 136) from 2 centers were retrospectively included. Least absolute shrinkage and selection operator regression was used to select radiomics features and the radiomics score (Radscore) was calculated. Nomogram was constructed by combining Radscore and significant clinical predictors. Receiver operating characteristic curve analysis, calibration curve and decision curve analysis were used to evaluate the predictive performance of the nomogram. Kaplan‒Meier survival curves based on the radiomics nomogram were used to assess overall survival (OS) of the entire cohort.

RESULTS

The Radscore consisted of nine radiomics features which were the most relevant to BRAF mutation. The radiomics nomogram integrating Radscore and clinical independent predictors (age, tumor location and cN stage) showed good calibration and discrimination with AUCs of 0.86 (95% CI: 0.80-0.91), 0.82 (95% CI: 0.74-0.90) and 0.82 (95% CI: 0.75-0.90) in the training cohort, internal validation and external validation cohorts, respectively. Furthermore,the performance of nomogram was significantly better than that of the clinical model (p < 0.05). The radiomics nomogram-predicted BRAF mutation high-risk group had a worse OS than the low-risk group (p < 0.0001).

CONCLUSION

The radiomics nomogram showed good performance in predicting BRAF mutation and OS of CRC patients, which could provide valuable information for individualized treatment.

ADVANCES IN KNOWLEDGE

The radiomics nomogram could effectively predict BRAF mutation and OS in patients with CRC. High-risk BRAF mutation group identified by the radiomics nomogram was independently associated with poor OS.

Identification of BRAF, CCND1, and MYC mutations in a patient with multiple primary malignant tumors: a case report and review of the literature

BACKGROUND

Multiple primary malignant tumors (MPMTs), usually associated with worse malignant behavior and prognosis comparing to a single primary tumor, and have recently been found to have an increasing incidence globally. However, the pathogenesis of MPMTs remains to be clarified. Here, we report a unique case of the coexistence of malignant melanoma (MM), papillary thyroid carcinoma (PTC), and clear-cell renal cell carcinoma (ccRCC) along with our perceptions on its pathogenesis.

CASE PRESENTATION

The case reported is of a 59-year-old male patient with unilateral nasal obstruction as well as a renal occupying lesion. Positron emission tomography-computed tomography (PET-CT) revealed a palpable mass of 32 × 30 mm on the posterior and left walls of the nasopharynx. In addition, an isodense nodule was observed in the right superior renal pole, approximately 25 mm in diameter, as well as a slightly hypodense shadow in the right leaf of the thyroid, approximately 13 mm in diameter. Nasal endoscopy and magnetic resonance imaging (MRI) confirmed the existence of a nasopharyngeal neoplasm. Afterward, biopsies of the nasopharyngeal neoplasm, thyroid gland and kidney were performed, and the patient was diagnosed with MM, PTC, and ccRCC according to the pathological and immunohistochemical results. Moreover, mutation of BRAF^V600E was detected in bilateral thyroid tissues, and amplification of both CCND1 and MYC oncogenes were detected in the nasopharyngeal melanoma. After chemotherapy, the patient is now in good overall condition.

CONCLUSIONS

This is the first reported case of a patient with the co-existence of MM, PTC and ccRCC undergoing chemotherapy with a favorable prognosis. Herein, we suggest that such a combination may be non-random, as for mutation of BRAF^V600E might account for the co-occurrence of PTC and MM, while mutations of CCND1 and MYC cause the coexistence of MM and ccRCC. This finding may provide valuable guidance on the diagnosis and treatment of such disease, as well as the prevention of developing a second or third tumor for patients with a single primary.

Design, Synthesis, Antiproliferative Actions, and DFT Studies of New Bis-Pyrazoline Derivatives as Dual EGFR/BRAFV600E Inhibitors

Some new Bis-pyrazoline hybrids 8-17 with dual EGFR and BRAFV600E inhibitors have been developed. The target compounds were synthesized and tested in vitro against four cancer cell lines. Compounds 12, 15, and 17 demonstrated strong antiproliferative activity with GI50 values of 1.05 µM, 1.50 µM, and 1.20 µM, respectively. Hybrids showed dual inhibition of EGFR and BRAFV600E. Compounds 12, 15, and 17 inhibited EGFR-like erlotinib and exhibited promising anticancer activity. Compound 12 is the most potent inhibitor of cancer cell proliferation and BRAFV600E. Compounds 12 and 17 induced apoptosis by increasing caspase 3, 8, and Bax levels, and resulted in the downregulation of the antiapoptotic Bcl2. The molecular docking studies verified that compounds 12, 15, and 17 have the potential to be dual EGFR/BRAFV600E inhibitors. Additionally, in silico ADMET prediction revealed that most synthesized bis-pyrazoline hybrids have low toxicity and adverse effects. DFT studies for the two most active compounds, 12 and 15, were also carried out. The values of the HOMO and LUMO energies, as well as softness and hardness, were computationally investigated using the DFT method. These findings agreed well with those of the in vitro research and molecular docking study.

Genomic profiling of a metastatic anaplastic melanocytic neuroectodermal tumor arising from a mature thymic teratoma as part of a mediastinal germ cell tumor

Following chemotherapy, a mediastinal germ cell tumor can lead to a mature teratoma that is composed of tissues derived from all three germ layers. Although teratoma is usually curable, in rare cases it can give rise to various somatic tumors and exceptionally it undergoes melanocytic neuroectodermal tumor (MNT) transformation, a process that is not well-described. We report a patient with a postchemotherapy thymic teratoma associated with an MNT component who, 10 years later, additionally presented a vertebral metastasis corresponding to an anaplastic MNT. Using exome sequencing of the mature teratoma, the MNT and its metastatic vertebral anaplastic MNT components, we identified 19 somatic mutations shared by at least two components. Six mutations were common to all three components, and three of them were located in the known cancer-related genes KRAS (p.E63K), TP53 (p.P222X), and POLQ (p.S447P). Gene set enrichment analysis revealed that the melanoma tumorigenesis pathway was enriched in mutated genes including the four major driver genes KRAS, TP53, ERBB4, and KDR, indicating that these genes may be involved in the development of the anaplastic MNT transformation of the teratoma. To our knowledge, this is the first molecular study realized on MNT. Understanding the clinicopathological and molecular characteristics of these tumors is essential to better understand their development and to improve therapeutics.

EPIDEMIOLOGICAL AND MOLECULAR EVALUATION OF BRAF, KRAS, NRAS GENES, AND MSI IN THE DEVELOPMENT OF COLORECTAL CANCER

BACKGROUND AND OBJECTIVES

KRAS, NRAS, BRAF Mutations and microsatellite instability (MSI) can be associated with Colorectal Cancer (CRC) development.

MATERIAL AND METHODS

We evaluated 828 medical records of CRC patients from a school hospital from January/2016 to December/2020. Variables such as age, gender, ethnicity, literacy level, smoking, alcoholism, primary anatomical site, tumor staging, presence of BRAFV600E, KRAS, NRAS and MSI mutations, survival and metastasis were identified. The statistical analyses were performed (p<0.05 is significant.

RESULTS

There was a predominance of males (51.93%), whites (90.70%), low education (72.34%), smokers (73.79%), and non- alcoholics (79.10%). Rectum was the most affected site (42.14%), advanced tumor stage was most prevalent (62.07%), and metastasis occurred in (64.61%). Of the enrolled patients; 204 were investigated for BRAF mutation and detected in (2.94%); 216 for KRAS gene and detected in (26.08%); 210 for NRAS gene, and detected in (25.36%); 370 for MSI, and detected in (44.68%). A significant association of CRC with NRAS mutation and alcohol habit (p = 0.043) was observed. The presence of MSI was associated with primary site proximal colon (p<0.000), distal colon (p=0.001) and rectum (p=0.010).

CONCLUSION

Patients with CRC are male, over 64 years old, white, with low education, smokers and non-alcoholics. The most affected primary site is rectum in advanced stage with metastasis. CRC is associated with NRAS mutation and alcohol habit, there is increased risk for primary site of proximal colon and MSI; decreased risk for distal colon and rectum in the presence of MSI mutation.

Cordycepin and kinase inhibition in cancer

Cordycepin, a nucleoside from Cordyceps mushrooms, has many beneficial properties for health, including anticancer activities. In cancer cells, cordycepin targets various signaling molecules. Here, we review the possible anticancer mechanisms of cordycepin involving the targeting of kinases. Abnormal kinase expression is involved in cancer development and progression through different molecular mechanisms, including phosphorylation, amplification, genetic mutations, and epigenetic regulation. Research suggests that kinases, such as the c-Jun N-terminal kinase (JNK), mitogen-activated protein kinase (MAPK), AMP kinase (AMPK), phosphoinositide 3-kinase (PI3K)/Akt, extracellular signal-regulated kinase (ERK), mammalian target of rapamycin (mTOR), glycogen synthase kinase (GSK)-3β, and focal adhesion kinase (FAK) pathways, can be targeted by cordycepin and disrupting their activity. Given that kinase inhibitors can have crucial roles in cancer treatment, targeting kinases might be one of the molecular mechanisms involved in the anticancer potential of cordycepin.

Molecular Aspects and Therapeutic Implications of Herbal Compounds Targeting Different Types of Cancer

Due to genetic changes in DNA (deoxyribonucleic acid) sequences, cancer continues to be the second most prevalent cause of death. The traditional target-directed approach, which is confronted with the importance of target function in healthy cells, is one of the most significant challenges in anticancer research. Another problem with cancer cells is that they experience various mutations, changes in gene duplication, and chromosomal abnormalities, all of which have a direct influence on the potency of anticancer drugs at different developmental stages. All of these factors combine to make cancer medication development difficult, with low clinical licensure success rates when compared to other therapy categories. The current review focuses on the pathophysiology and molecular aspects of common cancer types. Currently, the available chemotherapeutic drugs, also known as combination chemotherapy, are associated with numerous adverse effects, resulting in the search for herbal-based alternatives that attenuate resistance due to cancer therapy and exert chemo-protective actions. To provide new insights, this review updated the list of key compounds that may enhance the efficacy of cancer treatment.

Options of Therapeutics and Novel Delivery Systems of Drugs for the Treatment of Melanoma

Melanoma is one of the most severe cancerous diseases. The cells employ multiple signaling pathways, such as ERK, HGF/c-MET, WNT, and COX-2 to cause the cell proliferation, survival, and metastasis. Treatment of melanoma, including surgery, chemotherapy, immunotherapy, radiation, and targeted therapy, is based on 4 major or 11 substages of the disease. Fourteen drugs, including dacarbazine, interferon α-2b, interleukin-12, ipilimumab, peginterferon α-2b, vemurafenib, trametinib, talimogene laherparepvec, cobimetinib, pembrolizumab, dabrafenib, binimetinib, encorafenib, and nivolumab, have been approved by the FDA for the treatment of melanoma. All of them are in conventional dosage forms of injection solutions, suspensions, oral tablets, or capsules. Major drawbacks of the treatment are side effects of the drugs and patients' incompliance to them. These are consequences of high doses and long-term treatments for the diseases. Currently more than 350 NCI-registered clinical trials are being carried out to treat advanced and/or metastatic melanoma using novel treatment methods, such as immune cell therapy, cancer vaccines, and new therapeutic targets. In addition, novel delivery systems using biomaterials of the approved drugs have been developed attempting to increase the drug delivery, targeting, stability, bioavailability, thus potentially reducing the toxicity and increasing the treatment effectiveness. Nanoparticles and liposomes have been emerging as advanced delivery systems which can improve drug stability and systemic circulation time. In this review, the most recent findings in the options for treatment and development of novel drug delivery systems for the treatment of melanoma are comprehensively discussed.

Genetic risk, incident colorectal cancer, and the benefits of adhering to a healthy lifestyle: A prospective study using data from UK Biobank and FinnGen

Background

Genetic factors increase the individual risk of colorectal cancer (CRC); however, the extent to which a healthy lifestyle can offset increased genetic risk is unknown. This study investigated whether a healthy lifestyle is associated with lower CRC risk, regardless of genetic risk.

Methods

We recruited 390,365 participants without cancer at baseline (2006-2010) from the UK Biobank. The primary outcome was CRC incidence. A healthy lifestyle score constructed using 16 factors of six dimensions (smoking, drinking, body mass index, diet, exercise, and sleep) was categorized into three risk categories: favorable, intermediate, and unfavorable. To calculate the polygenic risk scores (PRSs) of UK Biobank participants, we extracted 454,678 single nucleotide polymorphisms (SNPs) from the UK Biobank and FinnGen Biobank after quality control. Cox proportional hazards regression was performed to evaluate the associations and was expressed as hazard ratios (HRs) with 95% confidence intervals (CIs).

Results

During a median follow-up of 10.90 years, 4,090 new CRC cases were reported in the UK Biobank. The "best-fit" PRSs were constructed using 59 SNPs based on the UK Biobank cohort and FinnGen genome-wide association study summary data (R² = 0.23%) and were divided into low (lowest quintile), intermediate (including second-fourth quintile), and high (highest quintile) genetic risk categories. The multivariate-adjusted Cox model revealed that participants with favorable lifestyles had HRs of 0.66 (95% CI = 0.60-0.72) for developing CRC vs. those with unfavorable lifestyles; low genetic risk was associated with a decreased risk of CRC (HR = 0.67, 95% CI =0.61-0.74) compared with those with high genetic risk. The HRs for low genetic risk participants with favorable lifestyles were 0.44 (95% CI =0.36-0.55) vs. participants with high genetic risk and unfavorable lifestyles. Among the participants with low, intermediate, or high genetic risk, the HRs of favorable vs. unfavorable lifestyles were 0.74, 0.64, and 0.72 (all p< 0.05).

Conclusions

Low genetic risk and a favorable lifestyle were significantly associated with a decreased risk of CRC. A favorable lifestyle was associated with a lower CRC risk, regardless of genetic risk.

Is Melanoma Progression Affected by Thyroid Diseases?

Clinical and epidemiological evidence indicate a relationship between thyroid diseases and melanoma. In particular, the hypothyroidism condition appears to promote melanoma spread, which suggests a protective role of thyroid hormones against disease progression. In addition, experimental data suggest that, in addition to thyroid hormones, other hormonal players of the hypothalamic–pituitary–thyroid (HPT) axis, namely the thyrotropin releasing hormone and the thyrotropin, are likely to affect melanoma cells behavior. This information warrants further clinical and experimental studies in order to build a precise pattern of action of the HPT hormones on melanoma cells. An improved knowledge of the involved molecular mechanism(s) could lead to a better and possibly personalized clinical management of these patients.

iRhom2 regulates ERBB signalling to promote KRAS-driven tumour growth of lung cancer cells

Dysregulation of the ERBB/EGFR signalling pathway causes multiple types of cancer. Accordingly, ADAM17, the primary shedding enzyme that releases and activates ERBB ligands, is tightly regulated. It has recently become clear that iRhom proteins, inactive members of the rhomboid-like superfamily, are regulatory cofactors for ADAM17. Here, we show that oncogenic KRAS mutants target the cytoplasmic domain of iRhom2 (also known as RHBDF2) to induce ADAM17-dependent shedding and the release of ERBB ligands. Activation of ERK1/2 by oncogenic KRAS induces the phosphorylation of iRhom2, recruitment of the phospho-binding 14-3-3 proteins, and consequent ADAM17-dependent shedding of ERBB ligands. In addition, cancer-associated mutations in iRhom2 act as sensitisers in this pathway by further increasing KRAS-induced shedding of ERBB ligands. This mechanism is conserved in lung cancer cells, where iRhom activity is required for tumour xenograft growth. In this context, the activity of oncogenic KRAS is modulated by the iRhom2-dependent release of ERBB ligands, thus placing the cytoplasmic domain of iRhom2 as a central component of a positive feedback loop in lung cancer cells. This article has an associated First Person interview with the first authors of the paper.

Molecular and pathological subtypes related to prostate cancer disparities and disease outcomes in African American and European American patients

Prostate cancer (PCa) disproportionately affects African American (AA) men, yet present biomarkers do not address the observed racial disparity. The objective of this study was to identify biomarkers with potential benefits to AA PCa patients. Differentially expressed genes (DEG) analysis coupled with gene set enrichment analysis (GSEA) and leading-edge genes analysis showed that the keratin family of genes, including KRT8, KRT15, KRT19, KRT34, and KRT80, constituted the single most prominent family of genes enriched in AA compared to European American (EA) PCa cell lines. In PCa patients (TCGA and MSKCC patient cohorts), KRT8, KRT15, and KRT19 expression were relatively higher in AA than in EA patients. The differences in the expression of KRT15 and KRT19, but not KRT8, were enhanced by Gleason score and ERG fusion status; in low Gleason (Gleason ≤ 6 [TCGA cohort] and Gleason ≤ 7 [MSKCC cohort]), the expression of KRT15 and KRT19 was significantly (p ≤ 0.05) higher in AA than in EA patients. Survival analysis revealed that high expression of KRT15 and KRT19 was associated with increased risk of biochemical recurrence in low Gleason category patients in the TCGA patient cohort. Interestingly, KRT15 and KRT19 expression were also associated with an increased risk of death in the metastatic prostate adenocarcinoma cohort, suggesting the potential to predict the risks of disease recurrence and death in the low Gleason category and advanced disease conditions respectively. Gene set enrichment analysis revealed known oncogenic gene signatures, including KRAS and ERBB2, to be enriched in patients expressing high KRT15 and KRT19. Furthermore, high KRT15 and KRT19 were linked to the basal and LumA PCa subtypes, which are associated with poor postoperative androgen deprivation therapy (ADT) response compared to the LumB subtype. Taken together, the present study identifies genes with high expression in AA than in EA PCa. The identified genes are linked to oncogenic gene signatures, including KRAS and ERBB2, and to basal and LumA PCa subtypes that are associated with poor postoperative ADT response. This study, therefore, reveals biomarkers with the potential to address biomarker bias in PCa risk stratification and/or prognosis.

Targeting ferroptosis in ischemia/reperfusion renal injury

Renal I/R injury is a severe medical condition contributing to acute kidney injury (AKI), leading to rapid kidney dysfunction and high mortality rates. It is generally observed during renal transplantation, shock, trauma, and urologic and cardiovascular surgery, for which there is no effective treatment. Cell death and damage are commonly linked to I/R. Cell death triggered by iron-dependent lipid peroxidation, such as ferroptosis, has been demonstrated to have a significant detrimental effect in renal IRI models, making it a new type of cell death currently being researched. Ferroptosis is a nonapoptotic type of cell death that occurs when free iron enters the cell and is a critical component of many biological processes. In ferroptosis-induced renal I/R injury, iron chelators such as Deferasirox, Deferiprone, and lipophilic antioxidants are currently suppressed lipid peroxidation Liproxstatin-1 (Lip-1), Ferrostatin-1 along with antioxidants like vitamin and quercetin. Ferroptosis has been considered a potential target for pharmaceutical intervention to alleviate renal IRI-associated cell damage. Thus, this review emphasized the role of ferroptosis and its inhibition in renal IRI. Also, Pharmacological modulation of ferroptosis mechanism in renal I/R injury has been conferred. Graphical abstract.

ERK2 signaling regulates cell-cell adhesion of epithelial cells and enhances growth factor-induced cell scattering

The ERK signaling pathway, consisting of core protein kinases Raf, MEK and effector kinases ERK1/2, regulates various biological outcomes such as cell proliferation, differentiation, apoptosis, or cell migration. Signal transduction through the ERK signaling pathway is tightly controlled at all levels of the pathway. However, it is not well understood whether ERK pathway signaling can be modulated by the abundance of ERK pathway core kinases. In this study, we investigated the effects of low-level overexpression of the ERK2 isoform on the phenotype and scattering of cuboidal MDCK epithelial cells growing in discrete multicellular clusters. We show that ERK2 overexpression reduced the vertical size of lateral membranes that contain cell-cell adhesion complexes. Consequently, ERK2 overexpressing cells were unable to develop cuboidal shape, remained flat with increased spread area and intercellular adhesive contacts were present only on the basal side. Interestingly, ERK2 overexpression was not sufficient to increase phosphorylation of multiple downstream targets including transcription factors and induce global changes in gene expression, namely to increase the expression of pro-migratory transcription factor Fra1. However, ERK2 overexpression enhanced HGF/SF-induced cell scattering as these cells scattered more rapidly and to a greater extent than parental cells. Our results suggest that an increase in ERK2 expression primarily reduces cell-cell cohesion and that weakened intercellular adhesion synergizes with upstream signaling in the conversion of the multicellular epithelium into single migrating cells. This mechanism may be clinically relevant as the analysis of clinical data revealed that in one type of cancer, pancreatic adenocarcinoma, ERK2 overexpression correlates with a worse prognosis.

Molecular Targets and Mechanisms of Hedyotis diffusa-Scutellaria barbata Herb Pair for the Treatment of Colorectal Cancer Based on Network Pharmacology and Molecular Docking

Objective: Hedyotis diffusa-Scutellaria barbata herb pair (HS) has therapeutic effects on a variety of cancers, and this study aims to systematically explore the multiple mechanisms of HS in the treatment of colorectal cancer (CRC). Methods. The active ingredients of HS were obtained from TCMSP, and the potential targets related to these ingredients were screened from the STITCH, SuperPred, and Swiss TargetPrediction databases. Targets associated with CRC were retrieved by Drugbank, TTD, DisGeNET, and GeneCards. We used a Venn diagram to screen the intersection targets and used Cytoscape to construct the herb-ingredient-target-disease network, and the core targets were selected. The Go analysis and KEGG pathway annotation were performed by R language software. We used PyMol and Autodock Vina to achieve molecular docking of core ingredients and targets. Results: A total of 33 active ingredients were obtained from the HS, and 762 CRC-related targets were reserved from the four databases. We got 170 intersection targets to construct the network and found that the four ingredients with the most targets were quercetin, luteolin, baicalein, and dinatin, which were the core ingredients. The PPI analysis showed that the core targets were STAT3, TP53, MAPK3, AKT1, JUN, EGFR, MYC, VEGFA, EGF, and CTNNB1. Molecular docking results showed that these core ingredients had good binding potential with core targets, especially the docking of each component with MAPK obtained the lowest binding energy. HS acts simultaneously on various signaling pathways related to CRC, including the PI3K-Akt signaling pathway, proteoglycans in cancer, and the MAPK signaling pathway. Conclusions: This study systematically analyzed the active ingredients, core targets, and central mechanisms of HS in the treatment of CRC. It reveals the role of HS targeting PI3K-Akt signaling and MAPK signaling pathways in the treatment of CRC. We hope that our research could bring a new perspective to the therapy of CRC and find new anticancer drugs.

High-Selectivity Single-Nucleotide Variant Capture Technology Based on the DNA Reaction Network

The extremely low abundance of circulating tumor DNA in blood samples has limited the development of liquid biopsy techniques for the early diagnosis of major diseases. In this study, we demonstrate a DRN-based screening technique, SCREEN, which achieves the specific capture and enrichment of low abundance SNV nucleic acid samples without selective amplification. The SCREEN technique achieved a 108-fold increase in the abundance of single-nucleotide variant (SNV) nucleic acids from highly homologous mixtures (from 0.01% to 1.08%) and has been shown to significantly increase the abundance of SNV nucleic acids from 0.1% to 51% further through two rounds of capture. As a highly effective pre-enrichment technique, SCREEN has demonstrated the ability to enhance NGS in detecting an ultralow abundance SNV nucleic acid powerfully and has high compatibility with existing molecular diagnostic methods.

The Systematic Analysis of Exercise Mechanism in Human Diseases

Background

As a part of a healthy lifestyle, exercise has been proven to be beneficial for the treatment of diseases and the prognosis of patients. Based on this, our research focuses on the impact of exercise on human health.

Methods

To study and analyze the samples in the GSE18966 gene expression profile, we first performed an analysis on the differential expressed genes (DEGs) through GEO2R, and then the DEGs enrichment in Gene Ontology functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways through the Database for Annotation, Visualization and Integrated Discovery database was conducted. Then, we delved into the gene set enrichment in KEGG through gene set enrichment analysis. After that, we achieved the construction of the protein-protein interaction (PPI) network of DEGs based on the Search Tool for the Retrieval of Interacting Genes online database, and the hub genes were screened and identified.

Results

We identified 433 upregulated DEGs and 186 downregulated DEGs from the samples before and after exercise in GSE18966. Through analysis, it was found that these DEGs-enriched pathways, such as the VEGF signaling pathway, the Wnt signaling pathway, and the insulin signaling pathway, were all involved in the regulation of various diseases. Then, GSEA analysis revealed that glycosaminoglycan biosynthesis chondroitin sulfate, type II diabetes mellitus, and basal cell carcinoma were related with exercise samples. The effects of these pathways on various diseases could be improved through exercise. Finally, 3 upregulated hub genes (VEGFA, POMC, and NRAS) and 3 downregulated hub genes (HRAS, NCOR1, and CAV1) were identified through the PPI network.

Conclusions

The bioinformatic analysis of samples before and after exercise provides key pathways and genes related to exercise to regulate various diseases, which confirms that exercise has an important influence on the treatment of many diseases.

NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction

Gene expression can serve as a powerful predictor for disease progression and other phenotypes. Consequently, microarrays, which capture gene expression genome-wide, have been used widely over the past two decades to derive biomarker signatures for tasks such as cancer grading, prognosticating the formation of metastases, survival, and others. Each of these signatures was selected and optimized for a very specific phenotype, tissue type, and experimental set-up. While all of these differences may naturally contribute to very heterogeneous and different biomarker signatures, all cancers share characteristics regardless of particular cell types or tissue as summarized in the hallmarks of cancer. These commonalities could give rise to biomarker signatures, which perform well across different phenotypes, cell and tissue types. Here, we explore this possibility by employing a network-based approach for pan-cancer biomarker discovery. We implement a random surfer model, which integrates interaction, expression, and phenotypic information to rank genes by their suitability for outcome prediction. To evaluate our approach, we assembled 105 high-quality microarray datasets sampled from around 13,000 patients and covering 13 cancer types. We applied our approach (NetRank) to each dataset and aggregated individual signatures into one compact signature of 50 genes. This signature stands out for two reasons. First, in contrast to other signatures of the 105 datasets, it is performant across nearly all cancer types and phenotypes. Second, It is interpretable, as the majority of genes are linked to the hallmarks of cancer in general and proliferation specifically. Many of the identified genes are cancer drivers with a known mutation burden linked to cancer. Overall, our work demonstrates the power of network-based approaches to compose robust, compact, and universal biomarker signatures for cancer outcome prediction.

Circular RNA-microRNA-mRNA network identified circ_0007618 and circ_0029426 as new valuable biomarkers for lung adenocarcinoma

Circular RNAs (circRNAs) are involved in multiple physiological processes. However, whether circRNAs function as the indicators of lung adenocarcinoma (LUAD) remains unclear. Three LUAD-related microarray datasets were downloaded from the Gene Expression Omnibus database, and overlapping differentially expressed circRNAs (DECs) in LUAD were identified. circ_0007618 and circ_0029426 were revealed to be significantly dysregulated in LUAD and verified in LUAD tissues and serum obtained in this study. Subsequently, the overall survival curve and receiver operating characteristics curve analyses were performed to evaluate the prognosis, sensitivity, and specificity of circ_0007618 and circ_0029426 for LUAD diagnosis. The results indicate that the combination of circ_0007618 and circ_0029426 is a potential biomarker for LUAD diagnosis and prognosis. TargetScan and miRDB were used to predict interactions between microRNAs (miRNAs) and circRNAs/mRNAs. A circRNA–miRNA–mRNA network was established for LUAD diagnosis. The Kyoto Encyclopedia of Genes and Genomes and protein–protein interaction network identified four hub genes. In conclusion, circ_0007618 and circ_0029426 may be novel biomarkers for LUAD diagnosis and prognosis. For LUAD diagnosis, PIK3CA and NRAS, and KRAS and ETS1, were targeted by circ_0007618 and circ_0029426, respectively.

EMBER-Embedding Multiple Molecular Fingerprints for Virtual Screening

In recent years, the debate in the field of applications of Deep Learning to Virtual Screening has focused on the use of neural embeddings with respect to classical descriptors in order to encode both structural and physical properties of ligands and/or targets. The attention on embeddings with the increasing use of Graph Neural Networks aimed at overcoming molecular fingerprints that are short range embeddings for atomic neighborhoods. Here, we present EMBER, a novel molecular embedding made by seven molecular fingerprints arranged as different “spectra” to describe the same molecule, and we prove its effectiveness by using deep convolutional architecture that assesses ligands’ bioactivity on a data set containing twenty protein kinases with similar binding sites to CDK1. The data set itself is presented, and the architecture is explained in detail along with its training procedure. We report experimental results and an explainability analysis to assess the contribution of each fingerprint to different targets.

Molecular Genetic Investigation of Digital Melanoma in Dogs

Canine digital melanoma, in contrast to canine oral melanoma, is still largely unexplored at the molecular genetic level. The aim of this study was to detect mutant genes in digital melanoma. Paraffin-embedded samples from 86 canine digital melanomas were examined for the BRAF V595E variant by digital droplet PCR (ddPCR), and for exon 11 mutations in c-kit. Furthermore, exons 2 and 3 of KRAS and NRAS were analysed by Sanger sequencing. Copy number variations (CNV) of KITLG in genomic DNA were analysed from nine dogs. The BRAF V595E variant was absent and in c-kit, a single nucleotide polymorphism was found in 16/70 tumours (23%). The number of copies of KITLG varied between 4 and 6. KRAS exon 2 codons 12 and 13 were mutated in 22/86 (25.6%) of the melanomas examined. Other mutually exclusive RAS mutations were found within the hotspot loci, i.e., KRAS exon 3 codon 61: 2/55 (3.6%); NRAS exon 2 codons 12 and 13: 2/83 (2.4%); and NRAS exon 3 codon 61: 9/86 (10.5%). However, no correlation could be established between histological malignancy criteria, survival times and the presence of RAS mutations. In summary, canine digital melanoma differs from molecular genetic data of canine oral melanoma and human melanoma, especially regarding the proportion of RAS mutations.

Association Between Tumor Mutation Profile and Clinical Outcomes Among Hispanic-Latino Patients With Metastatic Colorectal Cancer

In the United States, CRC is the third most common type of cancer and the second leading cause of cancer-related death. Although the incidence of CRC among the Hispanic population has been declining, recently, a dramatic increase in CRC incidents among HL younger than 50 years of age has been reported. The incidence of early-onset CRC is more significant in HL population (45%) than in non-Hispanic Whites (27%) and African-Americans (15%). The reason for these racial disparities and the biology of CRC in the HL are not well understood. We performed this study to understand the biology of the disease in HL patients. We analyzed formalin-fixed paraffin-embedded tumor tissue samples from 52 HL patients with mCRC. We compared the results with individual patient clinical histories and outcomes. We identified commonly altered genes in HL patients (APC, TP53, KRAS, GNAS, and NOTCH). Importantly, mutation frequencies in the APC gene were significantly higher among HL patients. The combination of mutations in the APC, NOTCH, and KRAS genes in the same tumors was associated with a higher risk of progression after first-line of chemotherapy and overall survival. Our data support the notion that the molecular drivers of CRC might be different in HL patients.

Application and prospects of single cell sequencing in tumors

Cancer is an intricate disease with inherent intra-tumor heterogeneity at the cellular level because of genetic changes and environmental differences. Cellular heterogeneity exists even within the same tumor type. Small deviations in a genome or transcriptome can lead to significant differences in function. Conventional bulk population sequencing, which produces admixed populations of cells, can only provide an average expression signal for one cell population, ignoring differences between individual cells. Important advances in sequencing have been made in recent years. Single cell sequencing starts in a single cell, thereby increasing our capability to characterize intratumor heterogeneity. This technology has been used to analyze genetic variation, specific metabolic activity, and evolutionary processes in tumors, which may help us understand tumor occurrence and development and improve our understanding of the tumor microenvironment. In addition, it provides a theoretical basis for the development of clinical treatments, especially for personalized medicine. In this article, we briefly introduce Single cell sequencing technology, summarize the application of Single cell sequencing to study the tumor microenvironment, as well as its therapeutic application in different clinical procedures.

Development of Potential Prognostic Biomarkers Based on DNA Methylation-Driven Genes for Patients with Endometrial Cancer

Background

Endometrial cancer (EC) is a multifactorial disease, and its progression may be driven by abnormal genetic methylation. To clarify the underlying molecular mechanisms and sensitive biomarkers for EC, this study used an integrated bioinformatic analysis to explore the methylation-driven genes of EC.

Methods

The mRNA expression data, methylation data and corresponding clinical information of EC samples were downloaded from The Cancer Genome Atlas (TCGA) database. MethylMix algorithm was used to screen out methylation-driven genes in EC. Functional and pathway enrichment analysis and the protein–protein interaction (PPI) analysis were conducted to demonstrate the functions and interactions between these genes. Then, prognosis-related methylated genes were screened out by using univariate and multivariate Cox analyses, and a prognostic risk assessment model for EC was constructed. The methylation sites and expression profiles of candidate genes were further investigated.

Results

A total of 127 methylated genes were identified in EC. Four genes (RP11-968O1.5, DCAF12L1, MSX1 and ALS2CR11) were selected as candidate genes to construct a reliable prognostic risk model. The univariate and multivariate Cox proportional hazards regression analyses showed that the risk score based on four genes was an independent prognostic indicator for OS among EC patients. A nomogram was established and the calibration plot analysis indicated the good performance and clinical utility of the nomogram. In addition, the methylation and expression of MSX1 and DCAF12L1 were significantly associated with EC survival rate. The joint ROC analysis revealed that the AUC of DCAF12L1-MSX1 was 0.867, which suggested both have a good EC-diagnosing efficiency. We then coped DCAF12L1 and MSX1 with GESA analysis, finding both were mainly associated with the KRAS signaling pathway.

Conclusion

This bioinformatic study combs the methylated genes involved in EC development for the first time, finding that MSX1 and DCAF12L1 could serve as EC prognostic markers and drug targets.

Relevance of BRAF Subcellular Localization and Its Interaction with KRAS and KIT Mutations in Skin Melanoma

Although skin melanoma (SKM) represents only one-quarter of newly diagnosed skin malignant tumors, it presents a high mortality rate. Hence, new prognostic and therapeutic tools need to be developed. This study focused on investigating the prognostic value of the subcellular expression of BRAF, KRAS, and KIT in SKM in correlation with their gene-encoding interactions. In silico analysis of the abovementioned gene interactions, along with their mRNA expression, was conducted, and the results were validated at the protein level using immunohistochemical (IHC) stains. For IHC expression, the encoded protein expressions were checked on 96 consecutive SKMs and 30 nevi. The UALCAN database showed no prognostic value for the mRNA expression level of KRAS and BRAF and demonstrated a longer survival for patients with low mRNA expression of KIT in SKMs. IHC examinations of SKMs confirmed the UALCAN data and showed that KIT expression was inversely correlated with ulceration, Breslow index, mitotic rate, and pT stage. KRAS expression was also found to be inversely correlated with ulceration and perineural invasion. When the subcellular expression of BRAF protein was recorded (nuclear vs. cytoplasmatic vs. mixed nucleus + cytoplasm), a direct correlation was emphasized between nuclear positivity and lymphovascular or perineural invasion. The independent prognostic value was demonstrated for mixed expression of the BRAF protein in SKM. BRAF cytoplasmic predominance, in association with KIT's IHC positivity, was more frequently observed in early-stage nonulcerated SKMs, which displayed a low mitotic rate and a late death event. The present study firstly verified the possible prognostic value of BRAF subcellular localization in SKMs. A low mRNA expression or IHC cytoplasmic positivity for KIT and BRAF might be used as a positive prognostic parameter of SKM. SKM's BRAF nuclear positivity needs to be evaluated in further studies as a possible indicator of perineural and lymphovascular invasion.

Prioritizing the candidate genes related to cervical cancer using the moment of inertia tensor

It is well known that cervical cancer poses the fourth most malignancy threat to women worldwide among all cancer types. There is a tremendous improvement in realizing the underlying molecular associations in cervical cancer. Several studies reported pieces of evidence for the involvement of various genes in the disease progression. However, with the ever-evolving bioinformatics tools, there has been an upsurge in predicting numerous genes responsible for cervical cancer progression and making it highly complex to target the genes for further evaluation. In this article, we prioritized the candidate genes based on the sequence similarity analysis with known cancer genes. For this purpose, we used the concept of the moment of inertia tensor, which reveals the similarities between the protein sequences more efficiently. Tensor for moment of inertia explores the similarity of the protein sequences based on the physicochemical properties of amino acids. From our analysis, we obtained 14 candidate cervical cancer genes, which are highly similar to known cervical cancer genes. Further, we analyzed the GO terms and prioritized these genes based on the number of hits with biological process, molecular functions, and their involvement in KEGG pathways. We also discussed the evidence-based involvement of the prioritized genes in other cancers and listed the available drugs for those genes.

Identification of prognostic long intergenic non-coding RNAs as competing endogenous RNAs with KRAS mutations in colorectal cancer

Colorectal cancer (CRC) is recognized as a common type of human cancer, and KRAS mutations are correlated with poor CRC survival outcomes. The evaluation and prediction of CRC results remain challenging. In the present study, RNA sequencing and clinical data from The Cancer Genome Atlas were used to identify KRAS mutation-related prognostic long intergenic non-coding RNAs (lincRNAs) in CRC. Significantly dysregulated lincRNAs and independent prognostic lincRNAs with KRAS mutations in CRC were identified. Two lincRNAs with KRAS mutations, LINC00265 and AL390719.2, were selected as key prognostic lincRNAs for both 10- and 5-year survival rates. In addition, competing endogenous (ce)RNA models were constructed to comprehensively assess the oncogenic performance of the two key lincRNAs. The ceRNA models suggested that LINC00265 and AL390719.2 are critical for the cell cycle and cancer pathways. Finally, reverse transcription-quantitative PCR was used to validate the ceRNA models in 12 pairs of CRC tissue samples. These prognostic lincRNAs may provide novel biomarkers for the prognostic prediction of CRC. The ceRNA model may also demonstrate the underlying mechanism of these lincRNAs in CRC.

The pan-cancer landscape of crosstalk between epithelial-mesenchymal transition and immune evasion relevant to prognosis and immunotherapy response

An emerging body of evidence has recently recognized the coexistence of epithelial-mesenchymal transition (EMT) and immune response. However, a systems-level view and survey of the interplay between EMT and immune escape program, and their impact on tumor behavior and clinical outcome across various types of cancer is lacking. Here, we performed comprehensive multi-omics analyses to characterize the landscape of crosstalk between EMT and immune evasion and their clinical relevance across 17 types of solid cancer. Our study showed the presence of complex and dynamic immunomodulatory crosstalk between EMT and immune evasion shared by pan-cancer, and the crosstalk was significantly associated with cancer prognosis and immunotherapy response. Integrative quantitative analyses of genomics and immunogenomics revealed that cellular composition of immune infiltrates, non-synonymous mutation burden, chromosomal instability and oncogenic gene alterations are associated with the balance between EMT and immune evasion. Finally, we proposed a scoring model termed EMT-CYT Index (ECI) to quantify the EMT-immunity axis, which was a superior predictor of prognosis and immunotherapy response across different malignancies. By providing a systematic overview of crosstalk between EMT and immune evasion, our study highlights the potential of pan-cancer EMT-immunity crosstalk as a paradigm for dissecting molecular mechanisms underlying cancer progression and guiding more effective and generalized immunotherapy strategies.

Malignant Melanoma within a Cellular Blue Nevi Presenting as a Vascular Malformation and the Connection to Sporadic KRAS Mutations

We present a case of malignant melanoma (MM) developing within a vascular malformation showing features of cellular blue nevi. A 47-year-old male presented with acute symptoms of a temporal and zygomatic mass, which were both previously asymptomatic upon development 30 years ago. These masses were diagnosed as vascular malformations upon imaging and were treated with sclerotherapy. Embolization and surgical excision were performed 3 years later due to symptomatic growth. Final pathology reports showed MM with congenital blue nevi. We hypothesize a possible linkage to a sporadic KRAS mutation, linking both presentations of vascular malformation, MM, and cellular blue nevi. A literature search for similar cases is also reported.

Frequency detection of BRAF V600E mutation in a cohort of pediatric langerhans cell histiocytosis patients by next-generation sequencing

BACKGROUND

Langerhans cell histiocytosis (LCH) is a rare neoplastic disease that occurs in both children and adults, and BRAF V600E is detected in up to 64% of the patients. Several studies have discussed the associations between BRAF V600E mutation and clinicopathological manifestations, but no clear conclusions have been drawn regarding the clinical significance of the mutation in pediatric patients.

RESULTS

We retrieved the clinical information for 148 pediatric LCH patients and investigated the BRAF V600E mutation using next-generation sequencing alone or with droplet digital PCR. The overall positive rate of BRAF V600E was 60/148 (41%). The type of sample (peripheral blood and formalin-fixed paraffin-embedded tissue) used for testing was significantly associated with the BRAF V600E mutation status (p-value = 0.000 and 0.000). The risk of recurrence declined in patients who received targeted therapy (p-value = 0.006; hazard ratio 0.164, 95%CI: 0.046 to 0.583). However, no correlation was found between the BRAF V600E status and gender, age, stage, specific organ affected, TP53 mutation status, masses close to the lesion or recurrence.

CONCLUSIONS

This is the largest pediatric LCH study conducted with a Chinese population to date. BRAF V600E in LCH may occur less in East Asian populations than in other ethnic groups, regardless of age. Biopsy tissue is a more sensitive sample for BRAF mutation screening because not all of circulating DNA is tumoral. Approaches with low limit of detection or high sensitivity are recommended for mutation screening to avoid type I and II errors.

High expression of spermatogenesis associated serine rich 2 promotes tumorigenicity in esophageal squamous cell carcinoma cells and is associated with poor patient prognosis

Spermatogenesis associated serine rich 2 (SPATS2), recognized as a cytoplasmic RNA-binding protein, is implicated in the tumorgenicity of several cancers. However, the potential role of SPATS2 in esophageal squamous cell carcinoma (ESCC) is yet to be elucidated. The present study aimed to explore the functional implication of SPATS2 in ESCC. The ESCC cell lines Eca109 and KYSE-150 were used to conduct loss-of-function experiments. The expression patterns of SPATS2 in patients with ESCC were obtained from Oncomine, The Cancer Genome Atlas and Genotype-Tissue Expression databases. Reverse transcription-quantitative PCR and western blot analysis were applied to determine the expression levels of SPATS2 in ESCC cells. The proliferation of ESCC cells was measured via cell proliferation and colony-formation assays. Subsequently, the migration and invasion capacities of ESCC cells were observed using Transwell assays. Finally, the expression levels of P53, cyclin E, matrix metalloproteinase (MMP)-9 and neuronal-cadherin were determined via western blot analysis. SPATS2 was expressed at higher levels in ESCC tissues compared with the controls, and high expression of SPATS2 was associated with poor prognosis. ESCC cell line proliferation, migration and invasion abilities were suppressed after silencing SPATS2. Moreover, following knockdown of SPATS2, the proteins cyclin E, MMP-9 and N-cadherin were expressed at markedly decreased levels, while P53 expression was increased. In summary, the results of the present study suggest that SPATS2 promotes ESCC development and progression, providing potential insights into future ESCC targeted treatment.

A panel of eight mRNA signatures improves prognosis prediction of osteosarcoma patients

Genetic alterations are vital to the progression of osteosarcoma carcinoma. The present study investigated a panel of gene signatures that could evaluate prognosis in osteosarcoma based on data from the Therapeutically Applicable Research To Generate Effective Treatments initiative. Osteosarcoma messenger RNA (mRNA) profiles and clinical data were downloaded from the therapeutically applicable research to generate effective treatments database. Patients with osteosarcoma were divided into two groups based on findings at diagnosis: with and without metastasis. Differentially expressed mRNAs were compared and analyzed between groups. Univariate and multivariate Cox regression analyses identified a set of eight mRNAs with the ability to classify patients into high-risk and low-risk groups with significantly different overall survival times. Further analysis indicated that the eight-mRNA signature was an independent prognostic factor after adjusting for other clinical factors. Receiver operating characteristic curve analysis demonstrated a good performance of the eight-mRNA signature. Further, the biological processes and signaling pathways of the eight-mRNA signature were reviewed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes resources. Finally, the results of the TCGA analysis were verified by other cohorts from Gene Expression Omnibus database. The identification of an eight-mRNA signature not only provides a prognostic biomarker of osteosarcoma but also offers the potential of novel therapeutic targets for its treatment.

Downregulation of lncRNA TSLNC8 promotes melanoma resistance to BRAF inhibitor PLX4720 through binding with PP1α to re-activate MAPK signaling

PURPOSE

Approximately 60% of patients with melanoma harbor BRAF mutation and targeting BRAF offers enormous advance in the treatment of those patients. Unfortunately, the efficacy of the BRAF inhibitors is usually restricted by the onset of drug resistance. Therefore, better understanding of the adaptive drug resistance mechanisms is essential for the development of alternative therapeutic strategies, and offers more promising measures to promote the short duration of response to BRAF inhibitors.

METHODS

The levels of tumor suppressive long noncoding RNA on chromosome 8p12 (TSLNC8) were evaluated by qPCR. The MTT assay, colony formation assay, apoptosis assay, and in vivo xenograft tumor model were performed to assess the functions of TSLNC8 on drug resistance. Western blotting, RNA pull-down, and RNA immunoprecipitation (RIP) assays were applied to investigate the mechanisms of TSLNC8 in melanoma.

RESULTS

Herein, our findings demonstrate that TSLNC8 is significantly downregulated in BRAF inhibitor-resistant melanoma tissues and cells. Moreover, downregulation of TSLNC8 in BRAF inhibitor sensitive cells reduces the toxicity response to BRAF inhibitor PLX4720, and inhibits apoptosis of melanoma cells-treated with PLX4720. Further assay elucidates that TSLNC8 can bind with the catalytic subunit of protein phosphatase 1α (PP1α) to regulate its distribution, and Downregulation of TSLNC8 results in PP1α cytoplasmic accumulation, thus re-activating the MAPK signaling. Eventually, the overexpression of TSLNC8 in BRAF inhibitor PLX4720-resistant melanoma cells restores the sensitive to BRAF inhibitor.

CONCLUSION

Collectively, our research provides a compelling rationale for resistance to BRAF inhibitor in melanoma, and the patient might benefit from the combinatorial therapy of BRAF inhibitors and lncRNA TSLNC8.

22β-hydroxytingenone induces apoptosis and suppresses invasiveness of melanoma cells by inhibiting MMP-9 activity and MAPK signaling

ETHNOPHARMACOLOGICAL RELEVANCE

22β-hydroxytingenone (22-HTG) is a quinonemethide triterpene isolated from Salacia impressifolia (Miers) A. C. Smith (family Celastraceae), which has been used in traditional medicine to treat a variety of diseases, including dengue, renal infections, rheumatism and cancer. However, the anticancer effects of 22-HTG and the underlying molecular mechanisms in melanoma cells have not yet been elucidated.

AIM OF THE STUDY

The present study investigated apoptosis induction and antimetastatic potencial of 22-HTG in SK-MEL-28 human melanoma cells.

MATERIALS AND METHODS

First, the in vitro cytotoxic activity of 22-HTG in cultured cancer cells was evaluated. Then, cell viability was determined using the trypan blue assay in melanoma cells (SK-MEL-28), which was followed by cell cycle, annexin V-FITC/propidium iodide assays (Annexin/PI), as well as assays to evaluate mitochondrial membrane potential, production of reactive oxygen species (ROS) using flow cytometry. Fluorescence microscopy using acridine orange/ethidium bromide (AO/BE) staining was also performed. RT-qPCR was carried out to evaluate the expression of BRAF, NRAS, and KRAS genes. The anti-invasiveness potential of 22-HTG was evaluated in a three-dimensional (3D) model of reconstructed human skin.

RESULTS

22-HTG reduced viability of SK-MEL-28 cells and caused morphological changes, as cell shrinkage, chromatin condensation, and nuclear fragmentation. Furthermore, 22-HTG caused apoptosis, which was demonstrated by increased staining with AO/BE and Annexin/PI. The apoptosis may have been caused by mitochondrial instability without the involvement of ROS production. The expression of BRAF, NRAS, and KRAS, which are important biomarkers in melanoma development, was reduced by the 22-HTG treatment. In the reconstructed skin model, 22-HTG was able to decrease the invasion capacity of melanoma cells in the dermis.

CONCLUSIONS

Our data indicate that 22-HTG has anti-tumorigenic properties against melanoma cells through the induction of cell cycle arrest, apoptosis and inhibition of invasiveness potential, as observed in the 3D model. As such, the results provide new insights for future work on the utilization of 22-HTG in malignant melanoma treatment.

Poor Prognosis of Pulmonary Adenosquamous Carcinoma with NRAS and HRAS Double Mutation

RAS mutations constitute one of the major tumorigenic mechanisms and are detected in approximately 20% of lung cancers. The most frequent mutated and well-studied RAS isoform is KRAS, which is associated with an overall poor prognosis in non-small-cell lung cancer (NSCLC). However, the clinical significances of NRAS and HRAS in NSCLC are rarely reported. Here, we present a 58-year-old male smoker who was diagnosed with stage IV lung adenosquamous carcinoma. A rare NRAS and HRAS double mutation was detected in the primary tumor and lymph node samples using next-generation sequencing (NGS). The patient showed rapid disease progression and passed away due to respiratory failure after 15 days of osimertinib in combination with cisplatin. To the best of our knowledge, this is the first report associating NRAS and HRAS double mutation in the poor prognosis of NSCLC.

New Insights into the Link between Melanoma and Thyroid Cancer: Role of Nucleocytoplasmic Trafficking

Cancer remains a major public health concern, mainly because of the incompletely understood dynamics of molecular mechanisms for progression and resistance to treatments. The link between melanoma and thyroid cancer (TC) has been noted in numerous patients. Nucleocytoplasmic transport of oncogenes and tumor suppressor proteins is a common mechanism in melanoma and TC that promotes tumorigenesis and tumor aggressiveness. However, this mechanism remains poorly understood. Papillary TC (PTC) patients have a 1.8-fold higher risk for developing cutaneous malignant melanoma than healthy patients. Our group and others showed that patients with melanoma have a 2.15 to 2.3-fold increased risk of being diagnosed with PTC. The BRAF V600E mutation has been reported as a biological marker for aggressiveness and a potential genetic link between malignant melanoma and TC. The main mechanistic factor in the connection between these two cancer types is the alteration of the RAS-RAF-MEK-ERK signaling pathway activation and translocation. The mechanisms of nucleocytoplasmic trafficking associated with RAS, RAF, and Wnt signaling pathways in melanoma and TC are reviewed. In addition, we discuss the roles of tumor suppressor proteins such as p53, p27, forkhead O transcription factors (FOXO), and NF-_KB within the nuclear and cytoplasmic cellular compartments and their association with tumor aggressiveness. A meticulous English-language literature analysis was performed using the PubMed Central database. Search parameters included articles published up to 2021 with keyword search terms melanoma and thyroid cancer, BRAF mutation, and nucleocytoplasmic transport in cancer.