Abstract
High-grade serous ovarian cancer (HGSC) is among the most lethal forms of cancer in women. By analyzing the mRNA-seq reads from The Cancer Genome Atlas (TCGA), we uncovered a novel cancer-enriched chimeric RNA as the result of splicing between MUC1, a highly glycosylated transmembrane mucin, TRIM46, a tripartite motif containing protein, and KRTCAP2, a keratinocyte associated protein. Experimental analyses by RT-PCR (reverse transcription PCR) and Sanger sequencing using an in-house cohort of 59 HGSC patient tumors revealed a total of six MUC1-TRIM46-KRTCAP2 isoforms joined by different annotated splice sites between these genes. These chimeric isoforms are not detected in non-cancerous ovaries, yet are present in three out of every four HGSC patient tumors, a significant frequency given the exceedingly heterogeneous nature of this disease. Transfection of the cDNA of MUC1-TRIM46-KRTCAP2 isoforms in mammalian cells led to the translation of mutant MUC1 fusion proteins that are unglycosylated and cytoplasmically localized as opposed to the cell membrane, a feature resembling the tumor-associated MUC1. Because the parental MUC1 is overexpressed in 90% of HGSC tumors and has been proposed as a clinical biomarker and therapeutic target, the chimeric MUC1-TRIM46-KRTCAP2 isoforms identified in this report could represent significantly better MUC1 variants for the same clinical utilities.
Highlights
High-grade serous ovarian cancer (HGSC) is the most lethal gynecological malignancy and the fifth most common cause of cancer-related deaths in women in the USA [1]
By RT-PCR screening of three serous type cancer cell lines (ES2, OV-90 and OVCAR8), we found that isoforms of MUC1-TRIM46-KRTCAP2 are expressed in all three cell lines are detected in the 24 non-cancerous ovary samples (Figure 3B)
We are not able to confirm the presence of endogenous MUC1-TRIM46-KRTCAP2 isoforms expressed in tumor tissue and in cancer cell lines because (1) most of the commercially available antibodies target the variable number of tandem repeats (VNTR) domain that is lacking in our fusion protein isoforms and (2) the sizes of these fusion protein isoforms are very similar to the various protein isoforms of parental MUC1, making it difficult to conclusively distinguish between the two groups
Summary
High-grade serous ovarian cancer (HGSC) is the most lethal gynecological malignancy and the fifth most common cause of cancer-related deaths in women in the USA [1]. We took advantage of The Cancer Genome Atlas (TCGA) transcriptome sequencing data to identify MUC1-TRIM46-KRTCAP2 as a novel and cancer-enriched chimeric RNA in HGSC. MUC1 is typically found on the apical surface of epithelial cells lining various tissues, and is thought to provide hydration, lubrication, protection from proteases and defense against pathogens to the underlying epithelia It is overexpressed in about 90% of HGSC tumors patients [9], possibly disrupting cell–cell and cell–matrix adhesions [10,11], thereby facilitating invasive growth and metastasis. We utilized the TCGA high-throughput transcriptome sequencing data to identify MUC1-TRIM46-KRTCAP2 as a novel, cancer-enriched chimeric RNA in HGSC. This aberrant RNA has six splicing isoforms and they are expressed in three of every four HGSC tumors. Unlike parental MUC1 that is present in both normal ovary and cancer cells, MUC1-TRIM46-KRTCAP2 chimeric RNAs are detected primarily in tumors, and may represent significantly better MUC1 variants for cancer detection using local biomaterials such as biopsy tissues
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