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Updated: Mar 14, 2026
Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Identification of Claudin 1 Transcript Variants in Human Invasive Breast Cancer
Anne A Blanchard1,2, Teresa Zelinski3,4, Jiuyong Xie2
1Department of Pathology, University of Manitoba, Winnipeg, Manitoba, Canada.
Background:
The claudin 1 tight junction protein, solely responsible for the barrier function of epithelial cells, is frequently down regulated in invasive human breast cancer. The underlying mechanism is largely unknown, and no obvious mutations in the claudin 1 gene (CLDN1) have been identified to date in breast cancer. Since many genes have been shown to undergo deregulation through splicing and mis-splicing events in cancer, the current study was undertaken to investigate the occurrence of transcript variants for CLDN1 in human invasive breast cancer.
Methods:
RT-PCR analysis of CLDN1 transcripts was conducted on RNA isolated from 12 human invasive breast tumors. The PCR products from each tumor were resolved by agarose gel electrophoresis, cloned and sequenced. Genomic DNA was also isolated from each of the 12 tumors and amplified using PCR CLDN1 specific primers. Sanger sequencing and single nucleotide polymorphism (SNP) analyses were conducted.
Results:
A number of CLDN1 transcript variants were identified in these breast tumors. All variants were shorter than the classical CLDN1 transcript. Sequence analysis of the PCR products revealed several splice variants, primarily in exon 1 of CLDN1; resulting in truncated proteins. One variant, V1, resulted in a premature stop codon and thus likely led to nonsense mediated decay. Interestingly, another transcript variant, V2, was not detected in normal breast tissue samples. Further, sequence analysis of the tumor genomic DNA revealed SNPs in 3 of the 4 coding exons, including a rare missense SNP (rs140846629) in exon 2 which represents an Ala124Thr substitution. To our knowledge this is the first report of CLDN1 transcript variants in human invasive breast cancer. These studies suggest that alternate splicing may also be a mechanism by which claudin 1 is down regulated at both the mRNA and protein levels in invasive breast cancer and may provide novel insights into how CLDN1 is reduced or silenced in human breast cancer.
Insights
Claudin 1 (CLDN1) transcript variants, including splice variants and SNPs, were identified in invasive breast cancer. These alterations may explain reduced CLDN1 levels, offering new insights into breast cancer progression.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Claudin 1 (CLDN1) is crucial for epithelial barrier function and is often downregulated in invasive breast cancer.
- The mechanisms behind CLDN1 downregulation, particularly genetic mutations, remain largely unclear.
- Splicing deregulation is a known factor in cancer, prompting investigation into CLDN1 transcript variants.
Purpose of the Study:
- To investigate the occurrence of CLDN1 transcript variants in human invasive breast cancer.
- To identify potential mechanisms contributing to CLDN1 downregulation in breast cancer.
Main Methods:
- RT-PCR analysis of CLDN1 transcripts in 12 invasive breast tumors.
- Sequencing of PCR products to identify splice variants.
- Genomic DNA analysis including SNP detection.
Main Results:
- Multiple CLDN1 transcript variants, all shorter than the classical form, were found in breast tumors.
- Splice variants, mainly in exon 1, led to truncated CLDN1 proteins, with one variant (V1) causing premature stop codons.
- Single nucleotide polymorphisms (SNPs) were identified in coding exons, including a rare missense SNP (rs140846629) in exon 2.
Conclusions:
- Alternate splicing is a significant mechanism contributing to CLDN1 downregulation at mRNA and protein levels in invasive breast cancer.
- Identified CLDN1 variants and SNPs provide novel insights into CLDN1 silencing in human breast cancer.
- These findings may open new avenues for understanding and potentially targeting CLDN1 in breast cancer therapy.
