Pan-Cancer Molecular Biomarkers: A Paradigm Shift in Diagnostic Pathology

Multi-Institutional Evaluation of Interrater Agreement of Biomarker-Drug Pair Rankings Based on the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) and Sources of Discordance

BACKGROUND

The widespread use of next-generation sequencing in clinical practice has contributed to the accumulation of a large number of genomic findings associated with targeted therapy; therefore, the problem of ranking the detected findings has become acute. The European Society for Medical Oncology Scale of Clinical Actionability of molecular Targets (ESCAT) system was designed by the European Society for Medical Oncology to rank biomarkers into levels of evidence that reflect their potency and clinical significance based on published clinical data. However, the ESCAT system remains imperfect, as it is based on a subjective assessment of the levels of evidence.

OBJECTIVE

The objective of this study was to determine whether the ranking of LOE for biomarker-drug pairs based on the ESCAT system is dependent on the human factor, and to uncover potential issues associated with the use of the framework.

METHODS

To evaluate the inter-rater agreement, we created a dataset of a total of 154 biomarker-drug pairs for 18 unique tumor types. We aimed to include biomarker-drug pairs that could be considered standard of care as well as less common and under investigated pairs. Fourteen precision oncology experts were invited to assign an ESCAT level of evidence for biomarker-drug pairs. Statistical analysis was carried out using Cohen's kappa and the Kolmogorov-Smirnov test.

RESULTS

The inter-rater agreement was low with some exceptions, and significant deviations from the consensus level of evidence were observed. For biomarker-drug associations, the deviations from the consensus were observed for more than 50% of the contributors' rankings. The most agreement between the contributors was observed for lung adenocarcinoma (p < 0.005), while the most disagreement was observed for esophageal cancer (p < 0.01) biomarker-drug pairs in our dataset.

CONCLUSIONS

This study demonstrates noteworthy discordances between the precision oncology experts and may provide the directions for future developments in modifying the ESCAT framework and the overall applicability of the results of genomic profiling into clinical practice.

Comprehensive analysis of ALG3 in pan-cancer and validation of ALG3 as an onco-immunological biomarker in breast cancer

ALG3 has significant modulatory function in the process of tumor development. Yet how ALG3 involves in the advancement of different malignancies isn't fully understood. We performed a pan-cancer assessment on ALG3 utilizing datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) to examine its tumor-related roles across malignancies and its link to particular molecules and cells in the tumor microenvironment (TME). Furthermore, we focused on breast cancer to examine the influence of ALG3-mediated signaling pathways and intercellular interactions in the advancement of tumors. The biological effects of ALG3 were verified by breast cancer cells. Enhanced ALG3 expression was discovered to be substantially linked to patients' grim prognoses in a number of malignancies. Furthermore, the expression of ALG3 in the TME was linked to the infiltration of stromal and immune cells, and ALG3-related immune checkpoints, TMB, and MSI were also discovered. We also discovered that cancer patients having a high level of ALG3 exhibited a lower probability of benefiting from immunotherapy. Furthermore, our research found that KEGG enrichment, single-cell RNA and spatial sequencing analyses were effective in identifying key signaling pathways in ALG3-associated tumor growth. In vitro, knockdown of ALG3 could decrease the proliferation of breast cancer cells. In summary, our research offers a comprehensive insight into the advancement of tumors under the mediation of ALG3. ALG3 appears to be intimately associated with tumor development in the TME. ALG3 might be a viable treatment target for cancer therapy, particularly in the case of breast cancer.

TMX family genes and their association with prognosis, immune infiltration, and chemotherapy in human pan-cancer

BACKGROUND

The thioredoxin (TMX) system, an important redox system, plays crucial roles in several immune-related diseases. However, there is limited research on the correlation of TMX family gene expression with human pan-cancer prognosis, tumor microenvironment (TME), and immunotherapy.

METHODS

Based on the integration of several bioinformatics analysis methods, we explored the expression levels and prognostic value of TMX family members in pan-cancer and analyzed their association between TME, immune infiltration, stemness scores, and drug sensitivity. Using KEGG enrichment analysis, we explored the potential signaling pathways of their regulation. Additionally, we conducted a transwell assay to verify the relationship between TMX family gene expression and epithelial-mesenchymal transition (EMT) in liver cancer.

RESULTS

Expression of the TMX family genes was shown to have an obvious intratumoral heterogeneity. In some cancers, TMX family members expression was also been found to correlate with poor prognosis of patients. Furthermore, TMX family genes may serve important roles in TME. The expression of TMX family genes was found to have a strong correlation with the stromal scores, immune scores, DNAss and RNAss in pan-cancer. Specifically, the expression levels of TMX family genes have been found to be associated with immune subtypes of renal clear cell carcinoma and liver hepatocellular carcinoma. High TMX2 expression promote EMT in liver cancer.

CONCLUSIONS

The findings of this study may elucidate the biological roles of TMX family genes as potential targets for pan-cancer and also offer valuable insights for further investigating how these genes function in the development and spreading of cancer.

Mutational Signatures in Cancer: Laboratory Considerations and Emerging Applications

Patterns of somatic mutations have emerged from the broad sequencing of human cancer genomes. These mutational signatures reflect mechanisms of mutagenesis and DNA repair defects and represent an emerging class of cancer biomarkers. The appropriate interpretation of mutational signatures from sequencing assays holds implications in the reporting of molecular diagnostic results for patients with cancer. This brief review describes the scientific principles, laboratory considerations, and emerging clinical applications of mutational signature analysis from clinical cancer genomes.

Pan-cancer analysis of LINC02535 as a potential biomarker and its oncogenic role in lung adenocarcinoma

Background

LINC02535 has gained much attention for its oncogenicity across several cancers, but the systematic pan-cancer analysis of LINC02535 has not been carried out before.

Methods

Herein, we explored the expression level, prognostic value, and hallmark pathways of LINC02535 across multiple cancers using the Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) databases. Moreover, the expression and biological features of LINC02535 in lung adenocarcinoma (LUAD) were confirmed by qRT-PCR, in vitro and in vivo experiments.

Results

LINC02535 is differentially expressed in 10 of 17 human cancers and serves as a favorable or unfavorable biomarker in distinct cancer types. Gene set enrichment analysis (GSEA) indicated that key oncogenic pathways/phenotypes were remarkably activated in most cancers with intratumoral increased LINC02535, whereas these pathways/phenotypes were suppressed in other cancer types (colon adenocarcinoma, kidney renal clear cell carcinoma, rectal adenocarcinoma) with intratumoral decreased LINC02535. Of note, the epithelial-mesenchymal transition (EMT) phenotype was greatly enriched in LUAD patients with elevated LINC02535. Based on the TCGA and CCLE datasets, LINC02535 was positively correlated with the EMT-related gene CD73 (also named as NT5E, an immunosuppressive gene) in almost all cancer types (Spearman R > 0.5, P < 0.001) including LUAD. Most importantly, qRT-PCR confirmed that LINC02535 was upregulated in lung cancer cells or tissues as opposed to human bronchial epithelial cells or paratumor tissues. Knockdown of LINC02535 inhibited proliferation, migration of LUAD cells and retarded xenografted tumor growth. Moreover, silencing of LINC02535 induced apoptosis and cell cycle arrest at G1 phase.

Conclusions

The findings from our pan-cancer analysis provide a relatively comprehensive understanding of the potential value of LINC02535 across multiple cancers, and the oncogenic role of LINC02535 in LUAD has been confirmed.