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Challenges in identifying candidate amplification targets in human cancers: chromosome 8q21 as a case study
Jennifer A Byrne1, Yuyan Chen, Nancy Martin La Rotta
1Molecular Oncology Laboratory, Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Westmead, Australia ; The University of Sydney Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead, Westmead, Australia.
Abstract:
Detailed genomic characterization of cancer specimens is required to identify all genes whose dysregulation contributes to tumorigenesis and/or tumor progression. These include amplification target genes, whose oncogenic functions derive from their overexpression in response to increased gene copy number, and which increasingly serve as therapeutic targets and predictive markers. We propose that identifying novel amplification target genes is becoming more challenging, and may require the comparative analysis of multiple studies mapping gene copy number changes and/or defining associations between gene copy number and expression. We therefore reviewed the array comparative genomic hybridization and single nucleotide polymorphism profiling literature to identify copy number increases that were restricted to chromosome 8q21 in human cancers, which were reported most frequently in breast cancer. We determined the minimal regions of overlap between gained regions and then examined which chromosome 8q21 genes were most frequently overexpressed, or otherwise supported, in individual studies. As these combined approaches supported the previously proposed amplification targets TCEB1, TPD52, and WWP1, the comparison of multiple genomic studies may therefore effectively predict candidate gene amplification targets, and prioritize these for further study.
Insights
Identifying novel cancer-driving genes requires comparing multiple genomic studies. Analyzing chromosome 8q21 copy number changes and gene expression helps pinpoint amplification target genes for cancer research.
Area of Science:
- Genomics
- Cancer Biology
- Molecular Oncology
Background:
- Genomic characterization is crucial for identifying genes driving cancer development and progression.
- Amplification target genes, overexpressed due to increased copy number, are key therapeutic and predictive targets.
- Discovering new amplification target genes is increasingly complex, necessitating comparative analyses.
Purpose of the Study:
- To develop a method for identifying novel amplification target genes.
- To investigate copy number increases specifically on chromosome 8q21 in human cancers.
- To validate previously proposed amplification targets using comparative genomic approaches.
Main Methods:
- Reviewed array comparative genomic hybridization and single nucleotide polymorphism profiling literature.
- Identified copy number increases restricted to chromosome 8q21 across multiple cancer studies.
- Determined minimal overlapping regions of gain and analyzed gene overexpression patterns.
Main Results:
- Copy number increases on chromosome 8q21 were most frequently reported in breast cancer.
- Comparative analysis supported TCEB1, TPD52, and WWP1 as amplification targets.
- The methodology effectively predicted candidate gene amplification targets.
Conclusions:
- Comparative analysis of multiple genomic studies is an effective strategy for predicting novel amplification target genes.
- This approach aids in prioritizing candidate genes for further investigation in cancer research.
- Understanding gene amplification is vital for advancing cancer therapeutics and diagnostics.
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