Cancer Biomarkers

N6-methyladenosine (m6A) is a common RNA modification on eukaryotic mRNA and some of the m6A regulatory proteins play a crucial role in breast cancer. However, the copy number variations for m6A regulatory proteins and their role in clinicopathological characteristics and survival in breast cancer remain unclear.

In this study, we screened the m6A related genes alterations in breast cancer by analyzing the Molecular Taxonomy of Breast Cancer International Consortium and The Cancer Genome Atlas database, and further analyzed the clinical prognostic value of YTHDF1 amplification.

The YTH domain family (YTHDF3 and YTHDF1) amplification exhibited higher alteration rates among 10 m6A regulatory genes. YTHDF1 and YTHDF3 amplification resulted in higher mRNA expression ( P < 0.0001). Protein expression of YTHDF1 and YTHDF3 were higher in breast cancer ( P < 0.0001). YTHDF1 amplification presented a high correlation with worse clinicopathological characteristics and overall survival in patients with breast cancer. Cox regression analysis showed that YTHDF1 amplification was an independent risk factor for 10-year overall survival in breast cancer (Hazard ratio: 1.663; 95% confidence interval: 1.298–2.131; P < 0.001). Gene set enrichment analysis revealed that the downstream target of YTHDF1 may be related to MYC signaling regulation and T cell differentiation. Moreover, YTHDF1 amplification and high expression resulted in lower immune cell infiltration. YTHDF1 knockdown retrained proliferation, migration and invasion in breast cancer cells in vitro.

We found significant worse clinical characteristics and lower immune infiltrates in patients with YTHDF1 amplification. The findings indicate that YTHDF1 amplification may be a potential target for the treatment of breast cancer.

Topical cidofovir and imiquimod can effectively treat approximately 55% of patients with vulval intraepithelial neoplasia (VIN), thus avoiding the need for surgery. Human papillomavirus (HPV) E ⁢ 2 gene methylation predicts response to treatment but a methylation measurement is only obtainable in approximately 50% of patients.

This work aimed to determine if the applicability and predictive power of the E ⁢ 2 methylation assay could be improved by combining it with the components of a host and viral DNA methylation panel (S5) that has been found to predict disease progression in patients with cervical intraepithelial neoplasia.

HPV E2 methylation and S5 classifier score were measured in fresh tissue samples collected pre-treatment from 132 patients with biopsy-proven VIN grade 3 who participated in a multicentre clinical trial and were randomised to treatment with cidofovir or imiquimod.

Combining HPV16 E ⁢ 2 and HPV16 L ⁢ 1 methylation provides a biomarker that is both predictive of response to topical treatment and that can produce a clinically applicable result for all patients. Patients with HPV 16 L ⁢ 1 ℎ𝑖𝑔ℎ and HPV 16 E ⁢ 2 ℎ𝑖𝑔ℎ (36/132 (27.3%)) were more likely to respond to treatment with cidofovir (12/15 (80.0%)) than imiquimod (9/21 (42.9%)) ( p = 0.026). Patients with HPV 16 L ⁢ 1 𝑙𝑜𝑤 or HPV 16 E ⁢ 2 𝑙𝑜𝑤 (including those with no HPV/unassessable methylation) were more likely to respond to imiquimod: 23/50 (46.0%) vs 31/46 (67.4%) ( p = 0.035).

Combined HPV E ⁢ 2 and L ⁢ 1 methylation is a potential predictive marker in treatment for all patients with VIN. These findings justify validation in a prospective trial.

The prognostic role of annexin A5 (ANXA5) in stomach adenocarcinoma (STAD) has not been studied, and its relationship with immune infiltration is still unclear.

This investigation aimed at exploring the role of ANXA5 in STAD using an integrated bioinformatics analysis.

The expression of ANXA5 in STAD and the correlations between the effect of ANXA5 and survival of STAD patients were investigated using database. The clusterProfiler package in R software was used to perform enrichment analysis on the top 100 co-expressed genes of ANXA5 from the COXPRESdb online database. Correlations between ANXA5 and immune cell infiltrates were analyzed using the TIMER database.

In STAD, ANXA5 expression was significantly upregulated and increased ANXA5 expression was significantly correlated with poor overall survival ( P < 0.05). In multivariate analysis, upregulated ANXA5 expression was an independent predictive factors of poor prognosis ( P < 0.05). The co-expressed genes were involved in extracellular matrix (ECM)-related processes. In STAD, ANXA5 expression was significantly correlated with various infiltrating immune cells ( P < 0.05).

Together with our findings, ANXA5 could serve as a potential biomarker to assess prognosis and immune infiltration level in STAD.

Bladder Cancer (BCa) is the tenth most incident malignancy worldwide. BCa is mostly attributed to environmental exposure and lifestyle, particularly tobacco smoking. The Aryl Hydrocarbon Receptor Repressor (AhRR) participates in the induction of many enzymes involved in metabolizing carcinogens, including tobacco smoke components. Additionally, studies have shown that smoking demethylates the (AhRR) gene in blood, suggesting AhRR demethylation as a specific serum smoking biomarker.

This study aimed to validate AhRR demethylation as a smoking biomarker in the target tissue and investigate its contribution to bladder carcinogenesis.

AhRR percent methylation was tested for its association with patient smoking status and oncogenic outcome indicators, particularly p53, RB1, and FGFR3 activating mutations, muscle-invasiveness, and tumor grade, in 180 BCa tissue-based DNA.

Results showed significantly higher AhRR percent methylation in muscle-invasive compared to non-muscle invasive tumors (42.86% vs. 33.98%; p = 0.011), while lower AhRR methylation was significantly associated with FGFR3 Codon 248 mutant genotype compared to wild-type (28.11% ± 9.44 vs. 37.87% ± 22.53; p = 0.036). All other tested associations were non-statistically significant.

Although AhRR methylation did not predict smoking status in BCa tumors, it may be a contributor to carcinogenesis and disease progression. Our findings constitute the basis for further research.

Nodal peripheral T-cell lymphomas [nPTCL] constitute a heterogeneous group of rare malignancies with aggressive biological behavior and poor prognosis. Epigenetic phenomena involving genes that control DNA-methylation and histone deacetylation play a central role in their pathogenesis. However, the mutational landscape involving epigenetic regulators has never been reported in Latin American patients and their prognostic impact remains controversial.

From 2000 to 2019, 59-Brazilian patients with nPTCL were eligible for screening mutations in the IDH-1, IDH-2, RHOA, TET-2 and DNMT3A genes by Sanger sequencing at Formalin-Fixed Paraffin-Embedded samples [FFPE] of diagnosis. We reported the frequency, distribution and potential prognosis of these mutations.

With a median follow-up of 3.70 years, estimate 2-year OS and PFS were 57.1% and 49.2%, respectively. Mutations in the IDH-1 gene were not found, mutations in the IDH-2 occurred in 3.4% (2/59), RHOA in 23.7% (14/59), TET-2 in 50.8% (30/59) and DNMT3A in 62.7% (37/59). RHOA gene mutations were more frequent in PTCL, NOS and AITL ( p = 0.06). Almost half of the patients had more than one mutation in concomitance, particularly RHOA-mut and TET-2-mut. Mutations in RHOA ( p = 0.030) and TET-2 ( p = 0.046) were associated with high-tumor burden. In the non-ALCL subgroup (PTCL, NOS and AITL) TET-2 mutations were associated with decreased 2-year PFS [HR: 2.22, p = 0.048]. Likewise with lower overall response rate [ORR] ( p = 0.048) and unfavorable clinical features, as bulky disease ( p = 0.012), ECOG ⩾ 2 ( p = 0.032), B-symptoms ( p = 0.012), ⩾ 2 extranodal sites compromised ( p = 0.022) and high-risk Prognostic Index for T-cell lymphoma ( p = 0.005).

Mutations in RHOA, TET-2 and DNMT3A were frequent in Brazilian patients with nPTCL. TET-2 mutations were associated with lower ORR for CHOP-like chemotherapy, decreased PFS and unfavorable clinical-biological characteristics in non-ALCL (PTCL, NOS and AITL). Further studies using a larger cohort may validate our findings.

The clinicopathological significance of spatial tumor-infiltrating lymphocytes (TILs) subpopulations is not well studied due to lack of high-throughput scalable methodology for studies with large human sample sizes.

Establishing a cyclic fluorescent multiplex immunohistochemistry (mIHC/IF) method coupled with computer-assisted high-throughput quantitative analysis to evaluate associations of six TIL markers (CD3, CD8, CD20, CD56, FOXP3, and PD-L1) with clinicopathological factors of breast cancer.

Our 5-plex mIHC/IF staining was shown to be reliable and highly sensitive for labeling three biomarkers per tissue section. Through repetitive cycles of 5-plex mIHC/IF staining, more than 12 biomarkers could be detected per single tissue section. Using open-source software CellProfiler, the measurement pipelines were successfully developed for high-throughput multiplex evaluation of intratumoral and stromal TILs.

In analyses of 188 breast cancer samples from the Nashville Breast Health Study, high-grade tumors showed significantly increased intratumoral CD3 + CD8 + cytotoxic T lymphocyte density ( P = 0.0008, false discovery rate (FDR) adjusted P = 0.0168) and intratumoral PD-L1 expression ( P = 0.0061, FDR adjusted P = 0.0602) compared with low-grade tumors.

The high- and low-grade breast cancers exhibit differential immune responses which may have clinical significance. The multiplexed imaging quantification strategies established in this study are reliable, cost-efficient and applicable in regular laboratory settings for high-throughput tissue biomarker studies, especially retrospective and population-based studies using archived paraffin tissues.

CD133 is a transmembrane glycoprotein and is considered the most common cell surface marker to identify cancer stem cells in hematological and solid tumors, including breast cancer.

To evaluate the impact of immunohistochemical expression of CD133 on response rate and survival in metastatic breast cancer, as well as to correlate it with various demographics and clinicopathological characteristics.

One-hundred metastatic breast cancer patients were prospectively recruited at the Medical Oncology Department at South Egypt Cancer Institute during the period from January 2018 to January 2020.

There was a statistically significant correlation between CD133 positive patients with various adverse clinicopathological parameters such as high grade ( p = 0.013), higher tumor ( p = 0.001), and nodal staging ( p = 0.024) during a median follow-up time of 17 months. In addition, cases with CD133 positive expression had a significantly lower survival time than those with negative expression (3-years OS 37.4% versus 85.5%, p = 0.024). Regarding the response rate, CD133 positive patients had a lower response rate than negative patients (50% versus 54%, p = 0.012).

Positive CD133 is correlated with poor prognosis in metastatic breast cancer patients.

Endothelial activation and insult may contribute to the aggressive clinical course of small-cell lung cancer (SCLC); however, no predictive biomarker for this pathogenesis has been identified.

To evaluate the clinical impact of the endothelial activation and stress index (EASIX) in SCLC.

In this retrospective study, the EASIX was calculated from measurements of serum lactate dehydrogenase, creatinine, and platelet levels. A total of 264 patients with SCLC treated with platinum-based chemotherapy were stratified into high and low EASIX groups.

Complete and objective response rates in the limited-stage (LD) were 19.5% vs. 33.3% ( P = 0.050) and 85.4% vs. 97.9% ( P = 0.028) in the high and low EASIX groups, respectively. There was no significant difference in the response rate between the two groups in the extensive-stage (ED). The median overall survival was 9.8 vs. 40.5 months in LD ( P < 0.001) and 7.2 vs. 11.9 months in ED ( P < 0.001) in the high and low EASIX groups, respectively. In multivariate analyses, a high EASIX level was an independent prognostic factor for worse progression-free and overall survival irrespective of stage.

EASIX may be a potential predictive biomarker of SCLC.

Hepatocellular carcinoma (HCC) is one of the most common liver malignancies in the world. With highly invasive biological characteristics and a lack of obvious clinical manifestations, hepatocellular carcinoma usually has a poor prognosis and ranks fourth in cancer mortality. The etiology and exact molecular mechanism of primary hepatocellular carcinoma are still unclear.

This work aims to help identify biomarkers of early HCC diagnosis or prognosis based on weighted gene co-expression network analysis (WGCNA).

Expression data and clinical information of HTSeq-Counts were downloaded from The Cancer Genome Atlas (TCGA) database, and gene expression map GSE121248 was downloaded from Gene Expression Omnibus (GEO). By differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA) searched for modules in the two databases that had the same effect on the biological characteristics of HCC, and extracted the module genes with the highest positive correlation with HCC from two databases, and finally obtained overlapping genes. Then, we performed functional enrichment analysis on the overlapping genes to understand their potential biological functions. The top ten hub genes were screened according to MCC through the string database and Cytoscape software and then subjected to survival analysis.

High expression of CDK1, CCNA2, CDC20, KIF11, DLGAP5, KIF20A, ASPM, CEP55, and TPX2 was associated with poorer overall survival (OS) of HCC patients. The DFS curve was plotted using the online website GEPIA2. Finally, based on the enrichment of these genes in the KEGG pathway, real hub genes were screened out, which were CDK1, CCNA2, and CDC20 respectively.

High expression of these three genes was negatively correlated with survival time in HCC, and the expression of CDK1, CCNA2, and CDC20 were significantly higher in tumor tissues of HCC patients than in normal liver tissues as verified again by the HPA database. All in all, this provides a new feasible target for early and accurate diagnosis of HCC, clinical diagnosis, treatment, and prognosis.