Metastatic Gene Research Articles

Identifying KRT20 as a Potential Key Gene in Lymphatic Metastasis of Head and Neck Squamous Cell Carcinoma.

Background: Head and neck squamous cell carcinoma (HNSCC) was the seventh most common cancer worldwide in 2018. Lymphatic metastasis (LM) is closely related to HNSCC prognosis and recurrence. However, the underlying mechanism of LM remains unclear. Therefore, this study aimed to identify the key genes in the LM of HNSCC. Methods: We used The Cancer Genome Atlas (TCGA) to identify differentially expressed genes (DEGs) between LM and non-LM cases. A random forest model, the Search Tool for the Retrieval of Interacting Genes, Cytoscape, and cytoHubba were used to identify hub genes among DEGs, including KRT20 (Cytokeratins 20). We analyzed the survival of KRT20 in TCGA, and we overexpressed KRT20 in HNSCC cell lines to investigate its effects on migration and invasion. We also correlated the expression of KRT20 in HNSCC tissue microarrays with survival and clinicopathological features. Results: We identified 243 DEGs—143 upregulated genes and 100 downregulated genes. Further analysis revealed that KRT20 is a potential key gene associated with LM and overall survival rates among patients with HNSCC. Overexpression of KRT20 increased the migration and invasion ability of HNSCC cell lines Tu686 and FD-LSC-1. Tissue microarray studies demonstrated an overexpression of KRT20 among N1+ patients (including N1-N3 patients). Survival analysis results and the clinicopathological features of HNSCC tissue microarrays were consistent with our analysis of TCGA. Thus, a high KRT20 expression level might suggest an adverse HNSCC prognosis. Our gene set enrichment analysis showed that KRT20 participates in many metabolic pathways, including those related to tumorigenesis and cancer development. Conclusions: We propose that KRT20 may be a key gene in HNSCC with LM.

Pro-apoptotic, anti-metastatic, and anti-telomerase activity of Tinospora cordifolia and its active polysaccharide arabinogalactan during Benzo(a)pyrene-induced lung carcinogenesis.

BACKGROUND:The present study aims to unravel the pro-apoptotic, anti-metastatic, and anti-telomerase activity of aqueous extract of Tinospora cordifolia stem (Aq.Tc) and its active component arabinogalactan (AG) during Benzo(a)pyrene [B(a)P]-induced lung tumorigenesis in mice.MATERIALS AND METHODS:Lung tumors were induced in male BALB/c mice using B(a)P as a carcinogen. Animals were administered twice with 50 mg/kg b.wt (i.p.) dosage of B(a)P at the 2nd and 4th week of the study. Mice were orally treated with Aq.Tc and AG on alternate days at a dose of 200 mg/kg b.wt and 7.5 mg/kg b.wt, respectively, for continuous 22 weeks.RESULTS:Oral administration of animals with Aq.Tc and AG suppressed the development of lung carcinogenesis by modulating the mRNA and protein expressions of different apoptotic genes; bcl-2, bax, caspase 3, and caspase 9. The pro-apoptotic proficiency of Aq.Tc and AG was further confirmed by DNA agarose gel electrophoresis showing fragmentation in B(a)P + Aq.Tc group and smear formation in B(a)P + AG group. In contrast to the control group, an increase in tumor invasion factors such as matrix metalloproteinases-2 (MMP-2) and MMP-9 was also observed in B(a)P treated animals. Nevertheless, Aq.Tc and AG treatment effectively mitigated the B(a)P-induced upregulation of MMP-2 and MMP-9. The activity of the telomerase enzyme was also observed to be upregulated in B(a)P treated animals which consecutively found to get normalized with the parallel administration of Aq.Tc and AG.CONCLUSION:Aq.Tc and AG successfully mitigated the altered expression of apoptosis, metastasis, and telomerase activity-associated genes during pulmonary carcinogenesis.

In silico Prediction of Deleterious Single Nucleotide Polymorphism in S100A4 Metastatic Gene: Potential Early Diagnostic Marker.

S100A4 protein overexpression has been reported in different types of cancer and plays a key role by interacting with the tumor suppressor protein Tp53. Single nucleotide polymorphisms (SNP) in S100A4 could directly influence the biomolecular interaction with the tumor suppressor protein Tp53 due to their aberrant conformations. Hence, the study was designed to predict the deleterious SNP and its effect on the S100A4 protein structure and function. Twenty-one SNP data sets were screened for nonsynonymous mutations and subsequently subjected to deleterious mutation prediction using different computational tools. The screened deleterious mutations were analyzed for their changes in functionality and their interaction with the tumor suppressor protein Tp53 by protein-protein docking analysis. The structural effects were studied using the 3DMissense mutation tool to estimate the solvation energy and torsion angle of the screened mutations on the predicted structures. In our study, 21 deleterious nonsynonymous mutations were screened, including F72V, E74G, L5P, D25E, N65S, A28V, A8D, S20L, L58P, and K26N were found to be remarkably conserved by exhibiting the interaction either with the EF-hand 1 or EF-hand 2 domain. The solvation and torsion values significantly deviated for the mutant-type structures with S20L, N65S, and F72L mutations and showed a marked reduction in their binding affinity with the Tp53 protein. Hence, these deleterious mutations might serve as prospective targets for diagnosing and developing personalized treatments for cancer and other related diseases.

Deficient DNASE1L3 facilitates neutrophil extracellular traps-induced invasion via cyclic GMP-AMP synthase and the non-canonical NF-κB pathway in diabetic hepatocellular carcinoma.

ObjectiveDiabetic hepatocellular carcinoma (HCC) patients have high mortality and metastasis rates. Diabetic conditions promote neutrophil extracellular traps (NETs) generation, which mediates HCC metastasis and invasion. However, whether and how diabetes‐induced NETs trigger HCC invasion is largely unknown. Here, we aimed to observe the effects of diabetes‐induced NETs on HCC invasion and investigate mechanisms relevant to a DNA sensor cyclic GMP‐AMP synthase (cGAS).MethodsSerum from diabetic patients and healthy individuals was collected. Human neutrophil‐derived NETs were isolated for stimulating HCC cell invasion. Data from the SEER and TCGA databases were used for bioinformatics analysis. In HCC cells and allograft models, NETs‐triggered invasion was observed.ResultsDiabetic HCC patients had poorer survival than non‐diabetic ones. Either diabetic serum or extracted NETs caused HCC invasion. Induction of diabetes or NETosis elicited HCC allograft invasion in nude mice. HCC cell invasion was attenuated by the treatment with DNase1. In TCGA_LIHC, an extracellular DNase DNASE1L3 was downregulated in tumor tissues, while function terms (the endocytic vesicle membrane, the NF‐κB pathway and extracellular matrix disassembly) were enriched. DNASE1L3 knockdown in LO2 hepatocytes or H22 cell‐derived allografts facilitated HCC invasion in NETotic or diabetic nude mice. Moreover, exposure of HCC cells to NETs upregulated cGAS and the non‐canonical NF‐κB pathway and induced expression of metastasis genes (MMP9 and SPP1). Both cGAS inhibitor and NF‐κB RELB knockdown diminished HCC invasion caused by NETs DNA. Also, cGAS inhibitor was able to retard translocation of NF‐κB RELB.ConclusionDefective DNASE1L3 aggravates NETs DNA‐triggered HCC invasion on diabetic conditions via cGAS and the non‐canonical NF‐κB pathway.

N6-Methyladenosine Reader YTHDF1 Promotes ARHGEF2 Translation and RhoA Signaling in Colorectal Cancer

N6-methyladenosine (m6A) governs the fate of RNAs through m6A readers. Colorectal cancer (CRC) exhibits aberrant m6A modifications and expression of m6A regulators. However, how m6A readers interpret oncogenic m6A methylome to promote malignant transformation remains to be illustrated. YTH N6-methyladenosine RNA binding protein 1 (Ythdf1) knockout mouse was generated to determine the effect of Ythdf1 in CRC tumorigenesis invivo. Multiomic analysis of RNA-sequencing, m6A methylated RNA immunoprecipitation sequencing, YTHDF1 RNA immunoprecipitation sequencing, and proteomics were performed to unravel targets of YTHDF1 in CRC. The therapeutic potential of targeting YTHDF1-m6A-Rho/Rac guanine nucleotide exchange factor 2 (ARHGEF2) was evaluated using small interfering RNA (siRNA) encapsulated by lipid nanoparticles (LNP). DNA copy number gain of YTHDF1 is a frequent event in CRC and contributes to its overexpression. High expression of YTHDF1 is significantly associated with metastatic gene signature in patient tumors. Ythdf1 knockout in mice dampened tumor growth in an inflammatory CRC model. YTHDF1 promotes cell growth in CRCcell lines and primary organoids and lung and liver metastasis invivo. Integrative multiomics analysis identified RhoA activator ARHGEF2 as a key downstream target of YTHDF1. YTHDF1 binds to m6A sites of ARHGEF2 messenger RNA, resulting in enhanced translation of ARHGEF2. Ectopic expression of ARHGEF2 restored impaired RhoA signaling, cell growth, and metastatic ability both invitro and invivo caused by YTHDF1 loss, verifying that ARHGEF2 is a key target of YTHDF1. Finally, ARHGEF2 siRNA delivered by LNP significantly suppressed tumor growth and metastasis invivo. We identify a novel oncogenic epitranscriptome axis of YTHDF1-m6A-ARHGEF2, which regulates CRC tumorigenesis and metastasis. siRNA-delivering LNP drug validated the therapeutic potential of targeting this axis in CRC.

8-Hydroxydaidzein Downregulates JAK/STAT, MMP, Oxidative Phosphorylation, and PI3K/AKT Pathways in K562 Cells.

A metabolite isolated from fermented soybean, 8-hydroxydaidzein (8-OHD, 7,8,4′-trihydroxyisoflavone, NSC-678112), is widely used in ethnopharmacological research due to its anti-proliferative and anti-inflammatory effects. We reported previously that 8-OHD provoked reactive oxygen species (ROS) overproduction, and induced autophagy, apoptosis, breakpoint cluster region-Abelson murine leukemia viral oncogene (BCR-ABL) degradation, and differentiation in K562 human chronic myeloid leukemia (CML) cells. However, how 8-OHD regulates metabolism, the extracellular matrix during invasion and metastasis, and survival signaling pathways in CML remains largely unexplored. High-throughput technologies have been widely used to discover the therapeutic targets and pathways of drugs. Bioinformatics analysis of 8-OHD-downregulated differentially expressed genes (DEGs) revealed that Janus kinase/signal transducer and activator of transcription (JAK/STAT), matrix metalloproteinases (MMPs), c-Myc, phosphoinositide 3-kinase (PI3K)/AKT, and oxidative phosphorylation (OXPHOS) metabolic pathways were significantly altered by 8-OHD treatment. Western blot analyses validated that 8-OHD significantly downregulated cytosolic JAK2 and the expression and phosphorylation of STAT3 dose- and time-dependently in K562 cells. Zymography and transwell assays also confirmed that K562-secreted MMP9 and invasion activities were dose-dependently inhibited by 8-OHD after 24 h of treatment. RT-qPCR analyses verified that 8-OHD repressed metastasis and OXPHOS-related genes. In combination with DisGeNET, it was found that 8-OHD’s downregulation of PI3K/AKT is crucial for controlling CML development. A STRING protein–protein interaction analysis further revealed that AKT and MYC are hub proteins for cancer progression. Western blotting revealed that AKT phosphorylation and nuclear MYC expression were significantly inhibited by 8-OHD. Collectively, this systematic investigation revealed that 8-OHD exerts anti-CML effects by downregulating JAK/STAT, PI3K/AKT, MMP, and OXPHOS pathways, and MYC expression. These results could shed new light on the development of 8-OHD for CML therapy.

Identification of potential core genes in colorectal carcinoma and key genes in colorectal cancer liver metastasis using bioinformatics analysis

Colorectal carcinoma (CRC) is one of the most prevalent malignant tumors worldwide. Meanwhile, the majority of CRC related deaths results from liver metastasis. Gene expression profile of CRC patients with liver Metastasis was identified using 4 datasets. The data was analyzed using GEO2R tool. GO and KEGG pathway analysis were performed. PPI network of the DEGs between 1 and 2 gene sets was also constructed. The set 1 is named between primary CRC tissues and metastatic CRC tissues. The set 2 is named between primary CRC tissues and normal tissues. Finally, the prognostic value of hub genes was also analyzed. 35 DEGs (set 1) and 142 DEGs (set 2) were identified between CRC liver metastatic cancer patients. The PPI network was constructed using the top 10 set 1 hub genes which included AHSG, SERPINC1, FGA, F2, CP, ITIH2, APOA2, HPX, PLG, HRG and set 2 hub genes which included TIMP1, CXCL1, COL1A2, MMP1, AURKA, UBE2C, CXCL12, TOP2A, ALDH1A1 and PRKACB. Therefore, ITIH2 might represent the potential core gene for colon cancer liver metastasis. COL1A2 behaves as a key gene in colorectal carcinoma.

Knockdown of lncRNA ZEB2NAT suppresses epithelial mesenchymal transition, metastasis and proliferation in breast cancer cells.

Breast cancer is the second most common cause of cancer-related mortality in women. Breast cancer metastasis which usually is observed at the last stage is the major cause of breast cancer-related death. Long non-coding RNAs (lncRNAs) are member of the non-coding RNA family. It is known that lncRNAs have important functions in the genes regulation of different processes and pathways such as EMT (Epithelial mesenchymal transition), metastasis and apoptosis. Therefore, it is inevitable that lncRNAs have potential contribution for the understanding of cancer pathogenesis. lncRNA-ZEB2NAT is the natural antisense transcript of ZEB2. Herein, we investigated the effects of lncRNA-ZEB2NAT on process of EMT, metastasis and apoptosis in MCF7 and MDA-MB-231 breast cancer cells. The effect of ZEB2NAT on the expression of important genes in EMT, metastasis and apoptosis, and some protein levels was determined by qRT-PCR and western blot analysis, respectively. The effects of ZEB2NAT on cell proliferation, apoptosis, invasion and colony formation were evaluated using XTT, annexin V, invasion and colony assays, respectively. The ZEB2NAT knockdown caused anti-metastatic and apoptotic effects. The ZEB2NAT knockdown resulted in a decrease in ZEB2 and N-cadherin but an increase in E-cadherin protein levels. In addition, it was determined that ZEB2NAT knockdown significantly decreased cell proliferation and stimulated apoptosis in both cells. It was found that ZEB2NAT knockdown significantly decreased invasion and colony formation in both cells. ZEB2NAT knockdown showed anti-metastatic and apoptotic effect by affecting the important genes in both cells. These results have suggested that ZEB2NAT has an important role in EMT, metastasis and apoptosis in breast cancer and ZEB2NAT knockdown caused significant anti-cancer activities.

Triptonide effectively inhibits triple-negative breast cancer metastasis through concurrent degradation of Twist1 and Notch1 oncoproteins

BackgroundTriple-negative breast cancer (TNBC) is highly metastatic and lethal. Due to a lack of druggable targets for this disease, there are no effective therapies in the clinic.MethodsWe used TNBC cells and xenografted mice as models to explore triptonide-mediated inhibition of TNBC metastasis and tumor growth. Colony formation assay was used to quantify the tumorigenesis of TNBC cells. Wound-healing and cell trans-well assays were utilized to measure cell migration and invasion. Tube formation assay was applied to access tumor cell-mediated vasculogenic mimicry. Western blot, quantitative-PCR, immunofluorescence imaging, and immunohistochemical staining were used to measure the expression levels of various tumorigenic genes in TNBC cells.ResultsHere, we showed that triptonide, a small molecule from the traditional Chinese medicinal herb Tripterygium wilfordii Hook F, potently inhibited TNBC cell migration, invasion, and vasculogenic mimicry, and effectively suppressed TNBC tumor growth and lung metastasis in xenografted mice with no observable toxicity. Molecular mechanistic studies revealed that triptonide strongly triggered the degradation of master epithelial-mesenchymal transition (EMT)-inducing protein Twist1 through the lysosomal system and reduced Notch1 expression and NF-κB phosphorylation, which consequently diminished the expression of pro-metastatic and angiogenic genes N-cadherin, VE-cadherin, and vascular endothelial cell growth factor receptor 2 (VEGFR2).ConclusionsTriptonide effectively suppressed TNBC cell tumorigenesis, vasculogenic mimicry, and strongly inhibited the metastasis of TNBC via degradation of Twist1 and Notch1 oncoproteins, downregulation of metastatic and angiogenic gene expression, and reduction of NF-κB signaling pathway. Our findings provide a new strategy for treating highly lethal TNBC and offer a potential new drug candidate for combatting this aggressive disease.

Silencing of α-N-acetylgalactosaminidase in the gastric cancer cells amplified cell death and attenuated migration, while the multidrug resistance remained unchanged.

Although the elevated level of the α-N-acetylgalactosaminidase enzyme (encoded by the NAGA gene) is a well-recognized feature of cancer cells; little research works have been undertaken on the cancer malignancy mechanisms. The effects of NAGA gene downregulation on cancer cells' features such as drug resistance, impaired programmed cell death, and migration were analyzed in this study. The cells grew exponentially with a doubling time of 30 h in an optimal condition. Toxicity of daunorubicin chemotherapy drug on NAGA-transfected EPG85.257RDB cells was evaluated in comparison to control cells and no significant change was recorded. Quantitative transcript analyses and protein levels revealed that the MDR1 pump almost remained unchanged during the study. Moreover, the NAGA gene downregulation enhanced the late apoptosis rate in EPG85.257RDB cells at 24 h posttransfection. The investigated expression level of genes and proteins involved in the TNFR2 signaling pathway, related to cancer cell apoptosis, showed considerable alterations after NAGA silencing as well. MAP3K14 and CASP3 genes were downregulated while IL6, RELA, and TRAF2 experienced an upregulation. Also, NAGA silencing generally diminished the migration ability of EPG85.257RDB cells and the MMP1 gene (as a critical gene in metastasis) expression decreased significantly. The expression of the p-FAK protein, which is located in the downstream of the α2 β1 integrin signaling pathway, was reduced likewise. It could be concluded that despite drug resistance, NAGA silencing resulted in augmentative and regressive effects on cell death and migration.

A heme-regulatable chemodynamic nanodrug harnessing transcription factor Bach1 against lung cancer metastasis

Non-small cell lung cancer (NSCLC) is a type of cancer dominated by metastasis-induced death. The transcription factor BTB and CNC homology 1 (Bach1) regulates almost all metastasis steps by activating the transcription of critical metastatic genes. It is urgent to engineer a nanodrug enabling regulation of Bach1 against tumor metastasis. Herein, a minimalist nanodrug integrating chemodynamic therapy (CDT) and Bach1 degradation was reported to prevent metastasis of NSCLC. The nanodrug was achieved by self-assembly of ferrocene (Fc) and Tin protoporphyrin IX (TinPPIX). In our nanodrug, Fc not only triggers the production of highly cytotoxic ∙OH for tumor ablation via Fenton reaction, but also induces heme release from heme-containing proteins to stimulate Bach 1 degradation. Moreover, TinPPIX further augments the free heme level along with amplifies the CDT efficacy by disabling heme oxygenase-1 (HO-1)-mediated heme conversion into antioxidative bilirubin. The results showed that, compared with control group, TinPPIX/Fc nanodrug caused a four-fold increase in heme level, which triggered remarkable Bach1 degradation in Fbxo22-mediated manner and successfully inhibited Bach1-dominated metastasis. Therefore, this nanodrug could powerfully impeded NSCLC progression and metastasis, offering an innovative heme-regulatable chemodynamic therapeutic approach for lung cancer with strong metastasis capability.

Identification and validation of hub genes in prostate cancer progression based on weighted gene co-expression network analysis

To identify the key hub genes in prostate cancer metastasis based on weighted gene co-expression network analysis (WGCNA) and verify the identified genes. Whole-genome chip data GSE6919 of prostate cancer study were analyzed using principal component analysis (PCA), and the differentially expressed genes (DEGs) were analyzed using R software. WGCNA was performed to construct a gene co-expression network for screening the key genes. TCGA database was used to explore the expressions of the DEGs and their association with the prognosis. To validate the results, we designed siRNA fragments targeting the metastasis-related gene HNRNPA2B1, and observed its effect on growth, apoptosis, clone formation, migration and invasion of prostate cancer cell lines using MTT assay, flow cytometry, clone formation assay, and Transwell assay. PCA analysis showed obvious clustering of significant DEGs in metastatic cancer group. The modules obtained by WGCNA analysis in metastasis group involved stem cell differentiation, amino acid metabolism and immune response. Further screening of the genes identified 3 genes related with prostate cancer occurrence (BDH1, PAK4 and EXTL3) and another 3 with prostate cancer metastasis (NKTR, CTBP2 and HNRNPA2B1), which were shown to have differential expressions in TCGA database and were correlated with the patient's overall survival. In the cell experiment, PC3 and LNCap cells transfected with the siRNA fragment targeting HNRNPA2B1 showed obvious growth inhibition with increased cell apoptosis, lowered clone formation ability, and suppressed capacities for migration and invasion. We identified 3 hub genes related with the occurrence (BDH1, PAK4 and EXTL3) and another 3 with metastasis of prostate cancer (NKTR, CTBP2 and HNRNPA2B1) using WGCNA, which provides a new approach for studying the regulatory mechanisms of prostate cancer.

Extracellular Vesicle Molecular Signatures Characterize Metastatic Dynamicity in Ovarian Cancer.

BackgroundLate-stage diagnosis of ovarian cancer, a disease that originates in the ovaries and spreads to the peritoneal cavity, lowers 5-year survival rate from 90% to 30%. Early screening tools that can: i) detect with high specificity and sensitivity before conventional tools such as transvaginal ultrasound and CA-125, ii) use non-invasive sampling methods and iii) longitudinally significantly increase survival rates in ovarian cancer are needed. Studies that employ blood-based screening tools using circulating tumor-cells, -DNA, and most recently tumor-derived small extracellular vesicles (sEVs) have shown promise in non-invasive detection of cancer before standard of care. Our findings in this study show the promise of a sEV-derived signature as a non-invasive longitudinal screening tool in ovarian cancer.MethodsHuman serum samples as well as plasma and ascites from a mouse model of ovarian cancer were collected at various disease stages. Small extracellular vesicles (sEVs) were extracted using a commercially available kit. RNA was isolated from lysed sEVs, and quantitative RT-PCR was performed to identify specific metastatic gene expression.ConclusionThis paper highlights the potential of sEVs in monitoring ovarian cancer progression and metastatic development. We identified a 7-gene panel in sEVs derived from plasma, serum, and ascites that overlapped with an established metastatic ovarian carcinoma signature. We found the 7-gene panel to be differentially expressed with tumor development and metastatic spread in a mouse model of ovarian cancer. The most notable finding was a significant change in the ascites-derived sEV gene signature that overlapped with that of the plasma-derived sEV signature at varying stages of disease progression. While there were quantifiable changes in genes from the 7-gene panel in serum-derived sEVs from ovarian cancer patients, we were unable to establish a definitive signature due to low sample number. Taken together our findings show that differential expression of metastatic genes derived from circulating sEVs present a minimally invasive screening tool for ovarian cancer detection and longitudinal monitoring of molecular changes associated with progression and metastatic spread.

Identification of Cancer Trait Genes and Association Analysis Under Pan-Cancer

Background: Different cancers have different sites of origin, cell types, and forms of genetic mutations that manifest different forms of cancers. Therefore, identifying genes associated with cancer traits and analyzing their functions in different cancers is important for understanding the mechanisms of cancer. Objective: The purpose of this paper is to make up for the shortcomings of single tumor analysis and realize the discovery and identification of genes related to each cancer trait at the level of multiple tumors, and their association analysis. Methods: In this paper, we use structural equation model to quantitatively identify genes associated with cancer traits for five cancers. We verify the correctness and effectiveness of the method through correlation analysis. Then we analyze the functions of genes and the biological processes involved through GO and KEGG pathways. Finally, we further analyze and verify the experimental results through protein interaction network and survival analysis. Results: Through five types of cancer data, we identify 44 genes related to cancer traits. We verify the combined effects of these genes and the biological processes they participate in. Moreover, we find key gene pathways and two significant gene functional modules. Conclusion: The results show that the structural equation model has unique advantages in quantifying the combined effects of genes. Many of the genes we have identified are tumor metastasis genes and are related to many cancers. There are strong potential commonalities among cancers. Four cancer genes are not only related to protein metabolism but also related to the regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism, which are of great significance for cancer treatment.

Investigating Differential Expression of mTOR1/UCA1 in Tumor Samples of Colorectal Cancer Compared with Tumor Marginal Samples

Background: Colorectal cancer (CRC) is the second and third most common cancer in men and women respectively, and the fourth cause of cancer death of individuals. Mutations in specific genes can lead to colorectal cancer. UCA1 is one of the oncogenic genes that have been shown to stimulate cell proliferation. mTOR1 is another gene that leads to the growth of cancer cells through anabolic processes and autophagy inhibition. Objectives: In this study, we evaluate the expression of these two genes in different phases of CRC, that helps the early detection of colorectal cancer which can increase the survival rate. Methods: First, we collected 25 colorectal cancer tumor tissues and 25 adjacent normal tissues as a control group. Then, RNA was extracted from tissue samples and cDNA synthesized. The UCA1 and mTOR1 expression was evaluated in CRC tissues compared to adjacent normal tissues by Real Time PCR. Results: Our results showed that the UCA1 and mTOR1 expression in the tumor tissues was significantly higher than in the adjacent normal tissues (P < 0.05). There was also a significant difference in Lynph inv and Vescu inv with mTOR1 expression (P < 0.05). Conclusions: Our results showed that UCA1/mTOR1 may be important genes involved in colorectal cancer. mTOR1 was also identified as one of the possible genes in metastasis of colorectal cancer. Thus, UCA1 and mTOR1 can probably be considered as biomarkers in CRC therapy and diagnosis.

A novel liquid biopsy (NETest) identifies paragangliomas and pheochromocytomas with high accuracy.

Pheochromocytomas and paragangliomas (PHEOs/PGLs) represent diagnostically challenging and complex neuroendocrine tumors (NETs). Current biomarker tests for PHEOs/PGLs are technically complex or limited. We assessed the diagnostic utility of a NET-specific 51-marker gene blood assay (NETest) in patients with PHEOs/PGLs (n = 81), including ten pediatric patients, and age-/gender-matched controls (n = 142) using a prospective case:control (1:2) analysis. mRNA was measured (qPCR), and results were scaled from 0 to 100 (upper limit of normal < 20). Receiver operating curve (ROC) and non-parametric (Mann-Whitney) tests were used for analyses (two-tailed). All data are presented as mean ± s.e.m. NETest accuracy for PHEO/PGL diagnosis was 100%. PHEO/PGL scores were 70 ± 3 vs 8.5 ± 1 in controls (P < 0.0001), and ROC analysis was 0.99 ± 0.004 (P < 0.0001). Diagnostic metrics were 94% accurate, 100% sensitive, and 92% specific. Imaging correlation with 68Ga-PET-SSA was 100%. NETest levels in PHEOs (n = 26) were significantly (P < 0.0001) elevated (83 ± 4) vs 66 ± 4 in PGLs (n = 40) and mixed PHEOs/PGLs (n = 5: 37 ± 3). Adrenal-derived tumors (n = 30) exhibited higher scores (76 ± 5) than extra-adrenal-derived tumors (66 ± 4, P < 0.05). Cluster 2 tumors exhibited significantly (P = 0.034) elevated NETest levels (n = 4: 92 ± 2) vs cluster 1 tumors (n = 35: 69 ± 4). Regulatory pathway analysis identified elevated RAS-RAF, metastatic, pluripotential, neural and secretory gene cluster levels (P < 0.05) in PHEOs compared to PGLs. Cluster 2 PPGLs exhibited elevated (P = 0.046) levels of growth factor signaling genes compared to cluster 1. The PHEOs/PGLs in the pediatric cohort (n = 10) were all NETest-positive (81 ± 8) and exhibited a gene expression profile spectrum analogous to adults. Circulating NET transcript analysis identifies PHEOs/PGLs with 100% efficacy and is likely to have clinical utility in the diagnosis and management of PHEO/PGL patients.

New approach of prediction of recurrence in thyroid cancer patients using machine learning.

Although papillary thyroid cancers are known to have a relatively low risk of recurrence, several factors are associated with a higher risk of recurrence, such as extrathyroidal extension, nodal metastasis, and BRAF gene mutation. However, predicting disease recurrence and prognosis in patients undergoing thyroidectomy is clinically difficult. To detect new algorithms that predict recurrence, inductive logic programming was used in this study.A total of 785 thyroid cancer patients who underwent bilateral total thyroidectomy and were treated with radioiodine were selected for our study. Of those, 624 (79.5%) cases were used to create algorithms that would detect recurrence. Furthermore, 161 (20.5%) cases were analyzed to validate the created rules. DELMIA Process Rules Discovery was used to conduct the analysis.Of the 624 cases, 43 (6.9%) cases experienced recurrence. Three rules that could predict recurrence were identified, with postoperative thyroglobulin level being the most powerful variable that correlated with recurrence. The rules identified in our study, when applied to the 161 cases for validation, were able to predict 71.4% (10 of 14) of the recurrences.Our study highlights that inductive logic programming could have a useful application in predicting recurrence among thyroid patients.

Differences in and verification of genetic alterations in chemotherapy and immunotherapy for metastatic melanoma.

Background: Metastatic melanoma has poor therapeutic response and may present resistance to chemotherapy or immunotherapy. Significant differences are observed in the survival time of patients with metastatic melanoma based on the administration of chemotherapy or immunotherapy; thus, we have explored the important role of specific differential genes between the two therapies in their effect on treatment response in melanoma.Methods: Metastatic melanoma gene expression data (RNAseq, mutation and methylation) and patient clinical information were downloaded from The Cancer Genome Atlas database and grouped according to chemotherapy or immunotherapy. The differentially expressed genes of the two groups were further screened for signature genes through a protein–protein interaction network and Lasso-Cox regression model. Then, differences in the treatment response, overall survival, mutation and methylation of characteristic genes were compared. Finally, western blot and real-time qPCR technology were used to detect the expression differences of the signature genes in metastatic melanoma tumor tissues in patients undergoing chemotherapy and immunotherapy.Results: The overall survival of the chemotherapy-based treatment group was significantly higher than that of the immunotherapy-based group. The immune infiltration level of immature dendritic cells (DCs) in the chemotherapy group was significantly higher than that in the immunotherapy group. Finally, seven signature genes were selected: CCKBR, KCNJ11, NMU, MMP13, ITGA10, IGFBP1 and CEACAM5. The results of these signature genes were significantly differentiated between the chemotherapy and immunotherapy groups in terms of overall survival and disease progression in response to treatment. In addition, differences in the expression of these genes were verified by western blot and real-time qPCR.Conclusion: In this study, significant differences in the expression of signature genes were verified. The findings indicate that immature DCs with potential application value should be considered and high mutation sites of signature genes should be identified to reduce the occurrence of treatment resistance.

Clinical and molecular feature-based nomogram model for predicting benefit from bevacizumab combined with first-generation EGFR-tyrosine kinase inhibitor (TKI) in EGFR-mutant advanced NSCLC

BackgroundThe combination of bevacizumab and epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) could prolong progression-free survival (PFS) in patients with EGFR-mutant advanced non-small-cell lung cancer (NSCLC). Our study investigated the clinical and molecular factors that affect the efficacy of first-generation EGFR-TKI with or without bevacizumab and identify the subset of patients who can benefit from combination therapy.MethodsOur study included 318 patients with EGFR-mutant locally advanced/advanced NSCLC treated with either first-generation EGFR-TKI combined with bevacizumab (A+T; n = 159) or EGFR-TKI monotherapy (T; n = 159). Two nomogram models to predict PFS and overall survival (OS), respectively, were constructed using two factors that impact EGFR-TKI efficacy: metastatic site and presence of concurrent mutations. The study cohort was stratified into 2 cohorts for training (n = 176) and validation (n = 142) of the nomogram model. Using the median score from the nomogram, the patients were stratified into two groups to analyze their survival outcome.ResultsThe A+T group had significantly longer PFS (14.0 vs. 10.5 months; p < 0.001) and OS (37.0 vs. 26.0 months; p = 0.042) than the T group. Among the patients with concurrent mutations in tumor suppressor genes, those in the A+T group had significantly longer PFS and OS than the T group (PFS 14.5 vs. 8.0 months, p < 0.001; OS 39.0 vs. 20.0 months, p = 0.003). The higher scores from the nomograms were associated with the presence of brain/liver/pleural metastasis or concomitant gene mutations, which indicated a higher likelihood of shorter PFS and OS. The validation of the nomogram revealed that patients with lower scores had significantly longer PFS for the T group than those with higher scores (15.0 vs. 9.0 months, p = 0.002), but not for the A+T group (15.9 vs. 13.9 months, p = 0.256).ConclusionsUsing a nomogram, our study demonstrated that the addition of bevacizumab may enhance the therapeutic effectiveness of EGFR-TKI by overcoming the negative impact of certain clinical and molecular factors on the efficacy of EGFR-TKI.

DNA methylation-based profiling reveals distinct clusters with survival heterogeneity in high-grade serous ovarian cancer

High-grade serous ovarian cancer (HGSOC) is the most common type of epigenetically heterogeneous ovarian cancer. Methylation typing has previously been used in many tumour types but not in HGSOC. Methylation typing in HGSOC may promote the development of personalized care. The present study used DNA methylation data from The Cancer Genome Atlas database and identified four unique methylation subtypes of HGSOC. With the poorest prognosis and high frequency of residual tumours, cluster 4 featured hypermethylation of a panel of genes, which indicates that demethylation agents may be tested in this group and that neoadjuvant chemotherapy may be used to reduce the possibility of residual lesions. Cluster 1 and cluster 2 were significantly associated with metastasis genes and metabolic disorders, respectively. Two feature CpG sites, cg24673765 and cg25574024, were obtained through Cox proportional hazards model analysis of the CpG sites. Based on the methylation level of the two CpG sites, the samples were classified into high- and low-risk groups to identify the prognostic information. Similar results were obtained in the validation set. Taken together, these results explain the epigenetic heterogeneity of HGSOC and provide guidance to clinicians for the prognosis of HGSOC based on DNA methylation sites.