A pan-cancer analysis of ABI3BP: a potential biomarker for prognosis and immunoinfiltration

Our plain-English summary of A pan-cancer analysis of ABI3BP: a potential biomarker for prognosis and immunoinfiltration, by Y. Feng, F. Tao, H. Qiao, et al (Frontiers in Oncology, 2023).

The study

• Authors: Y. Feng, F. Tao, H. Qiao, H. Tang
• Journal: Frontiers in Oncology
• Published: 2023;13:1159725
• Cited by: 8 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Objective: ABI Family Member 3 Binding Protein (ABI3BP) is an extracellular matrix protein that affects the carcinogenesis of lung and esophageal cancer. However, the relevance of ABI3BP in different forms of cancer is uncertain.

Methods: ABI3BP expression was interpreted using the Cancer Genome Atlas (TCGA) database, the Genotype Tissue Expression Atlas (GTEx) database, the Human Protein Atlas (HPA) database, the Cancer Cell Line Encyclopedia (CCLE) database, and immunohistochemistry. The R programming language was used to analyze the association between ABI3BP expression and patient prognosis and evaluate the relationship between ABI3BP and the immune characteristics of tumors. Using the GDSC and CTRP databases, a drug sensitivity analysis of ABI3BP was conducted.

Results: ABI3BP mRNA expression was shown by differential analysis to be down-regulated in 16 tumor types relative to normal tissues, corresponding with its protein expression level as determined by immunohistochemistry. Abnormal expression of ABI3BP accurately predicts the prognosis of patients with renal chromophobe carcinoma (KICH), mesothelioma (MESO), and pancreatic adenocarcinoma (PAAD). Meanwhile, aberrant expression of ABI3BP was associated with immune checkpoints, TMB, MSI, tumor purity, HRD, LOH, and drug sensitivity. A correlation between ABI3BP expression and the amount of infiltration of several immune-related cells in pan-cancer was determined by Immune Score, Stromal Score, and Estimated Score.

Conclusion: Our results show that ABI3BP might be employed as a molecular biomarker to predict prognosis, treatment susceptibility, and immunological response in patients with pan-cancer.

Copyright © 2023 Feng, Tao, Qiao and Tang.

In plain English

This was a computer-based analysis of a gene called ABI3BP across many cancer types. It did not study asbestos or any other occupational or environmental exposure. The authors analyzed gene and protein data from public databases (TCGA, GTEx, HPA and CCLE) and stained 8 pairs of tumor and nearby normal tissue from patients at Qingdao Municipal Hospital, China. In TCGA data, ABI3BP levels were lower in tumors than in normal tissue for 16 listed cancer types, not including mesothelioma. In CCLE, a mesothelioma cell line had the highest ABI3BP levels. In mesothelioma patients, high ABI3BP expression was associated with an unfavorable outcome for overall survival. In a time-dependent analysis, the authors reported an AUC of 0.758 for predicting 5-year survival in mesothelioma patients. ABI3BP expression in mesothelioma correlated significantly with microsatellite instability, a genetic marker. The article does not say how many mesothelioma patients were analyzed or which type of mesothelioma. The authors concluded that ABI3BP might be used as a biomarker to predict prognosis, treatment susceptibility and immune response. They said further experiments are needed.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Bioinformatics (computer) analysis of public gene and protein databases, plus immunohistochemistry staining of hospital tissue samples
• Who was studied: Tumor and normal tissue data from the TCGA, GTEx, HPA and CCLE databases covering many cancer types, including mesothelioma (MESO), plus 8 pairs of cancer and adjacent normal tissue from patients at Qingdao Municipal Hospital, China. The number of mesothelioma cases is not given.
• Exposure: No asbestos or other occupational or environmental exposure was studied. The main variable was the level of the ABI3BP gene and protein. A separate analysis correlated ABI3BP expression with drug sensitivity in cancer cell lines, using the GDSC and CTRP databases.
• Main results:
  • In TCGA data, ABI3BP expression was higher in normal tissue than in tumor tissue for 16 cancer types (BLCA, BRCA, CESC, COAD, ESCA, HNSC, KICH, LIHC, LUAD, LUSC, PCPG, PRAD, READ, STAD, THCA, UCEC). Mesothelioma is not in this list.
  • Among 32 tumor cell lines in the CCLE database, the mesothelioma (MESO) cell line had the highest ABI3BP expression.
  • For overall survival, high ABI3BP expression was associated with an unfavorable outcome in KICH, MESO (mesothelioma) and BLCA patients.
  • A time-dependent ROC analysis gave AUC values for predicting 5-year survival of 0.800 in KICH, 0.758 in MESO (mesothelioma) and 0.754 in PAAD patients. The authors described this as superior predictive power for 5-year survival.
  • ABI3BP expression correlated significantly with microsatellite instability (MSI) in CHOL, DLBC, ESCA, HNSC, LUSC, SKCM, STAD and MESO.
  • Immunohistochemistry showed reduced ABI3BP protein in BRCA, LUSC, LUAD, LIHC, KICH, THCA, PRAD and UCEC tumors. Mesothelioma was not among the stained tumors.
• The authors' conclusion: The authors concluded that ABI3BP might be used as a molecular biomarker to predict prognosis, treatment susceptibility and immunological response across cancers.
• Limitations the authors state:
  • Further basic experimental study is needed to understand how ABI3BP works in tumor growth.
  • Only abnormal expression of ABI3BP-related genes was studied. The resulting changes in gene-protein signaling pathways were not fully investigated.

Topics

Medical terms in this study, explained in our Lexicon: Biomarker, Prognosis, Carcinogenesis, Esophageal Cancer, Immunohistochemistry, Carcinoma, Mesothelioma, Adenocarcinoma.

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