Pseudogene Associated Recurrent Gene Fusion in Prostate Cancer

Abstract

We present the functional characterization of a pseudogene associated recurrent gene fusion in prostate cancer. The fusion gene KLK4-KLKP1 is formed by the fusion of the protein coding gene KLK4 with the noncoding pseudogene KLKP1 . Screening of a cohort of 659 patients (380 Caucasian American; 250 African American, and 29 patients from other races) revealed that the KLK4-KLKP1 is expressed in about 32% of prostate cancer patients. Correlative analysis with other ETS gene fusions and SPINK1 revealed a concomitant expression pattern of KLK4-KLKP1 with ERG and a mutually exclusive expression pattern with SPINK1, ETV1, ETV4, and ETV5. Development of an antibody specific to KLK4-KLKP1 fusion protein confirmed the expression of the full-length KLK4-KLKP1 protein in prostate tissues. The in vitro and in vivo functional assays to study the oncogenic properties of KLK4-KLKP1 confirmed its role in cell proliferation, cell invasion, intravasation, and tumor formation. Presence of strong ERG and AR binding sites located at the fusion junction in KLK4-KLKP1 suggests that the fusion gene is regulated by ERG and AR . Correlative analysis of clinical data showed an association of KLK4-KLKP1 with lower preoperative PSA values and in young men (<50 years) with prostate cancer. Screening of patient urine samples showed that KLK4-KLKP1 can be detected noninvasively in urine. Taken together, we present KLK4-KLKP1 as a class of pseudogene associated fusion transcript in cancer with potential applications as a biomarker for routine screening of prostate cancer.

KLK4T2 Is a Hormonally Regulated Transcript from the KLK4 Locus

“…They suggest that the transcript is created by trans-splicing of KLK4 and KLKP1 transcripts, but without any supporting experimental data. In a more recent article by another group, it was described as a transcript generating a KLK4–KLKP1 fusion protein [ 26 ]. The amino acid sequence of the fusion protein is identical to that of the KLK4T2 protein product, but the transcript sequence (Genbank MN037411) includes the full sequence of exon 3 and is 32 bp longer than KLK4T2 described in this paper.…”

Androgen-Driven Fusion Genes and Chimeric Transcripts in Prostate Cancer

“…Recently, Chakravarthi and colleagues identified a fusion occurring in around 30% of primary prostate cancer cases and involving the AR target gene KLK4 as a 5′ partner and the non-coding pseudogene KLKP1 (Chakravarthi et al, 2019 ). Both KLK4 and KLKP1 belong to the kallikrein family of serine proteases, and their genes are located adjacent to each other in a cluster of 15 genes on chromosome 19 (q13.33–q13.41), containing also the well-known KLK3 (PSA).…”

“…The resulting chimeric sequence predicts a 164–amino acid protein, of which the latter third is derived from KLKP1, leading to a conversion of the non-coding pseudogene to a protein-coding gene. Utilizing cell culture and chicken chorioallantoic membrane (CAM) assay, the expression of KLK4-KLKP1 fusion transcript was shown to affect cell proliferation, cell invasion, intravasation, and tumor formation (Chakravarthi et al, 2019 ).…”

“…Recent evidence has shown that, in addition to fusions at the genetic level, also chimeric fusion transcripts may be relevant for prostate cancer. As mentioned already above, the KLK4-KLKP1 fusion, combining sequences of a protein-coding gene and a pseudogene, may potentially be formed by a trans-splicing mechanism (Chakravarthi et al, 2019 ). So far, the most studied one in prostate cancer is the one where SLC45A3 is involved in the generation of a chimeric transcript with ELK4 ( Figure 1 ).…”

“…As many AR target genes are also regulated by ERG (Yu et al, 2010 ; Zhang et al, 2019 ), the ERG fusion positive cancers may have correlating expression of the androgen-driven fusion transcripts due to overexpression of ERG . For example, correlative analysis with other ETS gene fusions showed that KLK4-KLKP1 expression is associated with ERG but not ETV1, ETV4, or ETV5 (Chakravarthi et al, 2019 ). This may be explained by the presence of a strong ERG binding site at the fusion junction, suggesting that the expression of the KLK4-KLKP1 fusion gene is regulated by ERG in addition to AR.…”