Cancer Biomarkers - Volume 38, issue 4

Authors: Vishwakarma, Gajendra K. | Bhattacharjee, Atanu | Tank, Fatih | Pashchenko, Alexander F.

Article Type: Research Article

Abstract: BACKGROUND: The initiation biomarker-driven trials have revolutionized oncology drug development by challenging the traditional phased approach and introducing basket studies. Notable successes in non-small cell lung cancer (NSCLC) with ALK, ALK/ROS1, and EGFR inhibitors have prompted the need to expand this approach to other cancer sites. OBJECTIVES: This study explores the use of dose response modeling and time-to-event algorithms on the biomarker molecular targeted agent (MTA). By simulating subgroup identification in MTA-related time-to-event data, the study aims to develop statistical methodology supporting biomarker-driven trials in oncology. METHODS: A total of n patients are …selected assigned for different doses. A dataset is prepared to mimic the situation on Subgroup Identification of MTA for time to event data analysis. The response is measured through MTA. The MTA value is also measured through ROC. The Markov Chain Monte Carlo (MCMC) techniques are prepared to perform the proposed algorithm. The analysis is carried out with a simulation study. The subset selection is performed through the Threshold Limit Value (TLV) by the Bayesian approach. RESULTS: The MTA is observed with range 12–16. It is expected that there is a marginal level shift of the MTA from pre to post-treatment. The Cox time-varying model can be adopted further as causal-effect relation to establishing the MTA on prolonging the survival duration. The proposed work in the statistical methodology to support the biomarker-driven trial for oncology research. CONCLUSION: This study extends the application of biomarker-driven trials beyond NSCLC, opening possibilities for implementation in other cancer sites. By demonstrating the feasibility and efficacy of utilizing MTA as a biomarker, the research lays the foundation for refining and validating biomarker use in clinical trials. These advancements aim to enhance the precision and effectiveness of cancer treatments, ultimately benefiting patients. Show more

Keywords: Bayesian algorithm, biomarker, personalized medicine

DOI: 10.3233/CBM-230181

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 413-424, 2023

Authors: Huang, Wen-Juan | Yuan, Jia-Rui | Zhang, Lei | Wang, Wen | Miao, Shi-Di | Wang, Xin | Wang, Rui-Tao

Article Type: Research Article

Abstract: BACKGROUND: The albumin-bilirubin (ALBI) score is a novel indicator of liver function. Some studies showed that the ALBI score was a predictive marker for the prognosis and efficacy of drug therapy in malignancies. We aimed to assess the predicted role of ALBI score in the sensitivity to therapy with trastuzumab in patients with human epidermal growth factor receptor 2 (HER2) positive breast cancer (BC). The clinical data of 226 HER2-positive BC patients at the Harbin Medical University Cancer Hospital from January 2017 and December 2018 were retrospectively collected. The ALBI score was calculated with serum albumin and …bilirubin before diagnosis. The associations between ALBI score and trastuzumab resistance were analyzed by logistic regression analyses. The patients with trastuzumab resistance had higher ALBI scores compared with the patients without trastuzumab resistance. Moreover, there were weak correlations between the ALBI score and lymph node status (P = 0.093). In addition, multivariate analysis revealed that the ALBI score was an independent prognostic factor for trastuzumab resistance in HER2-positive BC. High ALBI score is associated with trastuzumab resistance in HER2-positive BC. Future studies are needed. Show more

Keywords: Breast cancer, HER2-positive, albumin, bilirubin, trastuzumab resistance

DOI: 10.3233/CBM-230077

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 425-432, 2023

Authors: Ratnam, Sam | Jang, Dan | Alaghehbandan, Reza | Gilbert, Laura | Xu, Yunwen | Wang, Wei | Andrews, Phillip | Green, Ashley | Speicher, David J. | Chernesky, Max

Article Type: Research Article

Abstract: BACKGROUND AND OBJECTIVE: CINtec PLUS and cobas HPV tests (Roche) were previously ascertained for triaging an LSIL referral population [1 ]. As part of this study, genotype-specific distribution and attributable risk of high-risk (HR)-HPV in cervical intraepithelial neoplasia (CIN) were determined. METHODS: Archived cervical specimens in ThinPrep PreservCyt (Hologic Inc) from the LSIL referral population (n = 533) were genotyped using the Anyplex II HPV HR test (Anyplex, Seegene Inc). Since the study specimens had been in storage in ambient temperature for 31–47 months since collection, Anyplex results were compared with that …of the initial cobas testing of fresh specimens to validate the suitability and stability of specimens for the present study. RESULTS: Overall, Anyplex test was positive in 63% (336/533) vs. 55.7% (297/533) for cobas test. Anyplex test performed identical to cobas test identifying 93.2% (82/88) of ⩾ CIN2/adenocarcinoma in situ (AIS). Anyplex test detected genotypes 16/18 in 15.7% (36/230) ⩽ CIN1 vs. 45.5% (40/88) ⩾ CIN2/AIS; the corresponding figures were 13.5% (31/230) and 45.5% (40/48) for the cobas test. Genotype 16 showed increasing attribution, 13.2% in CIN1, 27.1% in CIN2 and 40% in CIN3/AIS. Of the 12 other high-risk (OHR) types collectively identified by cobas, Anyplex test specifically detected, in decreasing order, genotypes 51, 31, 35, 56, 39, and 45 as the most frequent types, often in multiple-type infections, in 64.8% ⩾ CIN2. Regardless, estimated attribution was evident for each of the 12 OHR types in ⩾ CIN2. Multiple-type infections were more frequent than single-type infections in all CIN grades. CONCLUSIONS: Attributable risk of all HR-HPV genotypes targeted by both Anyplex and cobas tests was evident in ⩾ CIN2/AIS Testing for these genotypes in HPV primary cervical screening and cytology triage could identify those at increased risk of cervical cancer and also be beneficial in the management of LSIL referral populations. Show more

Keywords: HPV genotype-specific distribution in cervical intraepithelial neoplasia (CIN), HPV genotype-specific attributable risk in CIN, Anyplex II HPV HR test, cobas HPV test, ThinPrep PreservCyt stability for HPV DNA testing

DOI: 10.3233/CBM-220470

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 433-442, 2023

Authors: Li, Hua | Li, Chun | Yang, Lu-Zong | Liu, Ji

Article Type: Research Article

Abstract: The high incidence of mutations and the crucial roles of KAT2A in cancer development have received increased attention. Nevertheless, a systematic comparison of the heterogeneity and dynamics across different cancer types has not been conducted. Hence, a deep analysis using public databases was performed to clarify the contributions of KAT2A and its correlation with tumorigenesis. The raw data regarding KAT2A expression in cancer patients and healthy controls were obtained from The Cancer Genome Atlas (TCGA). Sexually dimorphic manner, genomic alterations, and expression pattern of KAT2A, as well as the association of the KAT2A with survival, were retrieved from UALCAN, cBioportal, …and TISIDB databases. Additionally, the Protein-Protein Interaction (PPI) analysis was conducted using the STRING database. The human protein atlas was used to obtain the staining results of protein levels in cancer and normal samples. The correlation between KAT2A and its potential target drugs was determined using TISIDB and HISTome2. Compared to the normal tissues, CHOL and TGCT tumors presented significantly high KAT2A expression, which was positively correlated with BLCA, BRCA, CESC, CHOL, COAD, ESCA, HNSC, KICH, KIRP, LIHC, LUAD, LUSC, READ, STAD, and THCA. However, no significant difference was detected between normal and tumor tissues for the sex difference pattern of KAT2A expression. The PPI analysis indicated that TADA3, CCDC101, TRRAP, SUPT3H, MYC, TADA2A, and USP22 levels were positively correlated with KAT2A expression, while TADA2B and ATXN7 were negatively correlated. A positive link of KAT2A with cancer isotypes and significant connections of the KAT2A expression to poor overall and disease-free survival were also observed. Further validation was conducted using immunohistochemistry (IHC) staining, qPCR, and Western blot. Some potential HAT inhibitory drugs of KAT2A were also determined, but more work and clinical trials are required before their application. Show more

Keywords: KAT2A, pan-cancer, database, prognosis

DOI: 10.3233/CBM-220464

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 443-463, 2023

Authors: Alotaibi, Amal | Gadekar, Veerendra P. | Gundla, Pranav Swaroop | Mandarthi, Sumana | Ravi, Subramanyeshwari | Mallya, Dhyeya | Tungekar, Asna | Lavanya, B.V. | Bhagavath, Ashok Kumar | Cordero, MaryAnne Wong | Pitkaniemi, Janne | Seetharam, Raviraja N. | Bepari, Asmatanzeem | Hebbar, Prashantha

Article Type: Research Article

Abstract: AIM: Esophageal Squamous Cell Carcinoma (ESCC) is a histological subtype of esophageal cancer that begins in the squamous cells in the esophagus. In only 19% of the ESCC-diagnosed patients, a five-year survival rate has been seen. This necessitates the identification of high-confidence biomarkers for early diagnosis, prognosis, and potential therapeutic targets for the mitigation of ESCC. METHOD: We performed a meta-analysis of 10 mRNA datasets and identified consistently perturbed genes across the studies. Then, integrated with ESCC ATLAS to segregate ‘core’ genes to identify consequences of primary gene perturbation events leading to gene-gene interactions and dysregulated …molecular signaling pathways. Further, by integrating with toxicogenomics data, inferences were drawn for gene interaction with environmental exposures, trace elements, chemical carcinogens, and drug chemicals. We also deduce the clinical outcomes of candidate genes based on survival analysis using the ESCC related dataset in The Cancer Genome Atlas. RESULT: We identified 237 known and 18 novel perturbed candidate genes. Desmoglein 1 (DSG1) is one such gene that we found significantly downregulated (Fold Change = - 1.89, p -value = 8.2e-06) in ESCC across six different datasets. Further, we identified 31 ‘core’ genes (that either harbor genetic variants or are regulated by epigenetic modifications) and found regulating key biological pathways via adjoining genes in gene-gene interaction networks. Functional enrichment analysis showed dysregulated biological processes and pathways including “Extracellular matrix”, “Collagen trimmer” and “HPV infection” are significantly overrepresented in our candidate genes. Based on the toxicogenomic inferences from Comparative Toxicogenomics Database we report the key genes that interacted with risk factors such as tobacco smoking, zinc, nitroso benzylmethylamine, and drug chemicals such as cisplatin, Fluorouracil, and Mitomycin in relation to ESCC. We also point to the STC2 gene that shows a high risk for mortality in ESCC patients. CONCLUSION: We identified novel perturbed genes in relation to ESCC and explored their interaction network. DSG1 is one such gene, its association with microbiota and a clinical presentation seen commonly with ESCC hints that it is a good candidate for early diagnostic marker. Besides, in this study we highlight candidate genes and their molecular connections to risk factors, biological pathways, drug chemicals, and the survival probability of ESCC patients. Show more

Keywords: Esophagus cancer, ESCC, desmogleins, toxicogenomics, krüppel-like factor, stanniocalcin

DOI: 10.3233/CBM-230145

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 465-487, 2023

Authors: Hou, Shuang | Gu, Tianqi | Shi, Ying | Huang, Yushan | Yao, Jiarong | Luo, Peng | Cao, Manming | Zhang, Jian | Lin, Anqi | Zhu, Weiliang

Article Type: Research Article

Abstract: BACKGROUND: There is a lack of effective biomarkers that predict immunotherapy efficacy in clear cell renal cell carcinoma(KIRC). OBJECTIVE: We aimed to identify biomarkers that would predict the efficacy of KIRC treatment with immune checkpoint inhibitors (ICIs). METHODS: Cohort data of KIRC patients with somatic mutations, mRNA expression and survival data from The Cancer Genome Atlas (TCGA) database and immunotherapy cohort and Genomics of Drug Sensitivity in Cancer (GDSC) database were analyzed and divided into interleukin 3 (IL3) pathway-related genes high expression (IL3-High) and IL3 pathway-related genes low expression (IL3-Low) groups according to …pathway expression status to assess the relationship between the IL3 pathway-related genes activation status and the prognosis of KIRC patients treated with ICIs. The data were validated by immunohistochemistry experiments, and possible mechanisms of action were explored at the level of gene mutation landscape, immune microenvironment characteristics, transcriptome and copy number variation(CNV) characteristics RESULTS: The IL3 pathway-related genes was an independent predictor of the efficacy of ICIs in KIRC patients, and the IL3-High group had a longer overall survival (OS); KIRC patients in the IL3-High group had increased levels of chemokines, cytolysis, immune checkpoint gene expression and abundant immunity. The IL3-Low group had poor immune cell infiltration and significant downregulation of complement activation, cytophagy, B-cell activation, and humoral immune response pathways. The high group was more sensitive to targeted drugs of some signaling pathways, and its efficacy in combining these drugs with immunity has been predicted in the published literature. CONCLUSION: The IL3 pathway-related genes can be used as a predictor of the efficacy of ICIs in KIRC. The IL3 pathway-related genes may affect the therapeutic efficacy of ICIs by affecting the expression of immune-related molecules, immune cell infiltration, and the level of immune response pathways. Show more

Keywords: IL3 pathway-related genes, renal clear cell carcinoma, immune checkpoint inhibitors, immune microenvironment, immunotherapy

DOI: 10.3233/CBM-230226

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 489-504, 2023

Authors: Song, Zihan | Zhao, Zijun | Zhu, Siyu | Jin, Qianxu | Shi, Yunpeng | Zhang, Shiyang | Wang, Zairan | Wang, Yizheng | Zhao, Zongmao

Article Type: Research Article

Abstract: BACKGROUND: STEAP3 is a metal reductase located on the plasma membrane close to the nucleus and vesicles. Despite numerous studies indicating the involvement of STEAP3 in tumor advancement, the prognostic value of STEAP3 in glioma and the related mechanisms have not been fully investigated. METHODS: Initially, we examined the correlation between STEAP3 expression and the survival rate in various glioma datasets. To assess the prognostic capability of STEAP3 for one-year, three-year, and five-year survival, we created receiver operating characteristic (ROC) curves and nomograms. Additionally, an investigation was carried out to examine the mechanisms that contribute to …the involvement of STEAP3 in gliomas, including immune and enrichment analysis. To confirm the expression of STEAP3 in LGG and GBM, tumor tissue samples were gathered, and cell experiments were conducted to explore the impacts of STEAP3. The function of STEAP3 in the tumor immune microenvironment was assessed using the M2 macrophage infiltration assay. RESULTS: We found that STEAP3 expressed differently in group with different age, tumor grade IDH and 1p19q status. The analysis of survival illustrated that glioma patients with high level of STEAP3 experienced shorter survival durations, especially for IDH-mutant astrocytoma. Cox analysis demonstrated that STEAP3 had potential to act as an independent prognostic factor for glioma. The predictive value of STEAP3 for glioma prognosis was demonstrated by ROC curves and nomogram. Immune analysis showed that STEAP3 may lead to a suppressive immune microenvironment through the control of immunosuppressive cell infiltration and Cancer-Immunity Cycle. Combining enrichment analysis and cell experiments, we discovered that STEAP3 can promote glioma progression through regulation of PI3K-AKT pathway and M2 macrophage infiltration. CONCLUSION: STEAP3 plays significant roles in the advancement of glioma by regulating immune microenvironment and PI3K-AKT pathway. It has the potential to serve as a therapy target for glioma. Show more

Keywords: Glioma, STEAP3, prognosis, M2 macrophages, immunotherapy

DOI: 10.3233/CBM-230217

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 505-522, 2023

Authors: Jia, Xiongjie | Zhang, Tao | Lv, Xinze | Du, Haiwei | Sun, Yongkun | Guan, Yin

Article Type: Research Article

Abstract: BACKGROUND: Colon adenocarcinoma (COAD) is a globally prevalent cancer, with hormone secretion playing a crucial role in its progression. Despite this, there is limited understanding of the impact of hormone secretion on COAD prognosis. This study aimed to establish a prognostic signature based on hormone secretion-related genes and to elucidate the potential functional mechanisms of these genes in COAD. METHODS: Using data from The Cancer Genome Atlas COAD cohort (TCGA-COAD), six hormone secretion-related genes were identified (CYP19A1, FOXD1, GRP, INHBB, SPP1, and UCN). These genes were used to develop a Hormone secretion score (HSS), which was …then evaluated using the Kaplan-Meier curve and multivariable Cox analysis. The HSS model was further validated with external GEO cohorts (GSE41258, GSE39582, and GSE87211). Functional enrichment analyses were performed, and the CIBERSORT and TIDE algorithms were used to assess tumor infiltration. RESULTS: The study developed a prognostic signature, dividing patients into HSS-high and HSS-low groups. The HSS-high group showed a notably worse prognosis within the TCGA-COAD dataset and in three independent datasets: GSE41258, GSE39582, and GSE87211. Moreover, the HSS-high group predicted a shorter overall survival rate in patients maintaining microsatellite stability (MSS). The functional analysis associated HSS-high with the hypoxic, epithelial-mesenchymal transition (EMT), and TGF-β signaling pathways and correlated with distant and lymph node metastases. The tumor immune microenvironment analysis revealed an elevated CIBERSORT score in the HSS-high group, suggesting an association with tumor metastasis. Further, the HSS-high group showed a higher TIDE score, indicating that patients with high HSS scores are less likely to benefit from Immune Checkpoint Inhibitor (ICI) therapy. CONCLUSIONS: This study demonstrated the prognostic significance of a HSS signature based on six hormone secretion-related genes in COAD. The findings suggest that this gene signature may serve as a reliable biomarker for predicting survival outcomes in COAD patients. Show more

Keywords: Colon adenocarcinoma, hormone secretion, prognosis, hypoxia pathway, tumor microenvironment

DOI: 10.3233/CBM-230126

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 523-535, 2023

Authors: Wang, Kang | Ma, Lulu | Chen, Liying | Jiang, Yatong | Liu, Ningquan | Cai, Jianchun | Zhang, Yiyao

Article Type: Research Article

Abstract: BACKGROUND: The accurate Tumor-Node-Metastasis (TNM) staging of colorectal cancer (CRC) is of great guiding significance for the judgment of tumor progression and prognosis, and the formulation of treatment strategies. OBJECTIVE: The aim of this study was to construct a recurrence risk scoring (RRS) system and prognostic prediction model to improve the accuracy of staging, prognosis prediction, and clinical decision making in resectable CRC. METHODS: CRC patients who underwent radical resection were retrospectively enrolled into study. Multivariable Cox regression model was applied to screen for independent prognostic factors. The RRS system is composed of …independent prognostic factors which was awarded 1point each. A prognostic model composed of RRS and TNM staging system (RRS-TNM model) was applied to predict postoperative recurrence. RESULTS: TNM stage, tumor differentiation, preoperative elevated Carcinoembryonic Antigen, Carbohydrate Antigen 199, Prothrombin Time and Fibrinogen were the independent prognostic biomarkers. 173 of 540 patients had recurrence. The 5-year cumulative recurrence rate (5-y CRR) and disease-free survival (DFS) of postoperative p-TNM stage I, II, and III were 12.7% and 104.8 months, 26.5% and 89.3 months, and 55.5% and 57.3 months, respectively. The 5-y CRR and DFS of preoperative Low-risk (RRS 0-1score), Middle-risk (RRS 2-3scores), and High-risk (RRS 4-5scores) groups were 13.9% and 101.1 months, 40.9% and 75.5 months, and 70.2% and 41.1 months. The AUC (area under ROC curve) of RRS system was not inferior to that of TNM staging system (0.713 vs. 0.666; P = 0.093). The AUC (0.770) and C-index value (0.721) of RRS-TNM model were significantly better than both RRS and TNM staging system (P < 0.001). CONCLUSIONS: The RRS system accurately identifies CRC patients with high-risk recurrence preoperatively. Constructing a nomogram using the RRS system and TNM staging significantly improves the accuracy of staging and prognosis prediction, which is of great clinical significance for individualized clinical treatment and follow-up of CRC. Show more

Keywords: Carcinoembryonic antigen, carbohydrate antigen 199, prothrombin time, fibrinogen, colorectal cancer

DOI: 10.3233/CBM-230116

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 537-549, 2023

Authors: Zou, Renrui | Liu, Yaqian | Qiu, Sangsang | Lu, Ya | Chen, Yan | Yu, Hui | Zhu, Hangju | Zhu, Wenbo | Zhu, Longbiao | Feng, Jifeng | Han, Jing

Article Type: Research Article

Abstract: BACKGROUND: Hepatocellular carcinoma (HCC) has a high degree of malignancy and poor prognosis. N6-methyladenosine (m6A) modifications and microRNAs (miRNAs) play pivotal roles in tumorigenesis and development. However, the role of m6A-related miRNAs in HCC has not been clarified yet. This study aimed to identify the role of m6A-miRNAs in HCC prognosis through bioinformatics analysis. METHODS: The clinicopathological information and RNA sequencing data of 369 HCC tumor tissues and 49 tumor-adjacent tissues were downloaded from the TCGA database. A total of 23 m6A regulators were extracted to evaluated the m6A-related miRNAs using Pearson’s correlation analysis. Then, …we selected prognosis-related m6A-miRNAs using a univariate Cox regression model and used the consensus cluster analysis to explore the characteristics of the m6A-miRNAs. The coefficient of the least absolute shrinkage and selection operator (LASSO) Cox regression was applied to construct a prognostic risk score model. The receiver operated characteristic (ROC) analysis was applied to evaluate the prognostic value of the signature. The biological functions of targeted genes were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Then, to validate the potential predictive value for prognosis, the miRNA expression profiles from the GSE76903 and GSE6857 were used. Single sample Gene Set Enrichment Analysis (ssGSEA) and Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) were applied to assess the immune microenvironment of HCC. Additionally, a meta-analysis was used to verify the prognostic value of the m6A-microRNAs. RT-PCR was applied to validated the expression of miRNAs in HCC tissues. Cell viability, transwell assay and RNA m6A dot blot assays of HCC cells was applied to access the function of miR-17-5p. RESULTS: The expression of 48 m6A-related miRNAs was identified and 17 prognostic m6A-miRNAs was discovered. The expression profile of those 17 miRNAs was divided into three clusters, and these clusters were associated with the tumor microenvironment (TME) and prognosis. The nine m6A-related miRNA signature was associated with the prognosis of HCC, the AUC of the ROC was 0.771(TCGA dataset), 0.788(GSE76903) and 0.646(GSE6857). The TME and the expression of immune checkpoint molecules were associated with the risk score. The meta-analysis also validated the prognostic value of the m6A-related miRNAs (miR182-5p (HR:1.58, 95%CI:1.04-2.40) and miR-17-5p (HR:1.58, 95%CI: 1.04–2.40)). The expression of miR-17-5p was upregulated in HCC tissues and miR-17-5p showed an oncogenic role in HCC cells. CONCLUSION: The clinical innovation is the use of m6A-miRNAs as biomarkers for predicting prognosis regarding immunotherapy response in HCC patients. Show more

Keywords: Hepatocellular carcinoma, m6A related miRNAs, prognosis, tumor microenvironment, immune checkpoint

DOI: 10.3233/CBM-230263

Citation: Cancer Biomarkers, vol. 38, no. 4, pp. 551-566, 2023