Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers

Abstract

Pyruvate kinase muscle type (PKM) is a key enzyme in glycolysis and plays an important oncological role in cancer. However, the association of PKM expression and the survival outcome of patients with different cancers is controversial. We employed systems biology methods to reveal prognostic value and potential biological functions of PKM transcripts in different human cancers. Protein products of transcripts were shown and detected by western blot and mass spectrometry analysis. We focused on different transcripts of PKM and investigated the associations between their mRNA expression and the clinical survival of the patients in 25 different cancers. We find that the transcripts encoding PKM2 and three previously unstudied transcripts, namely ENST00000389093, ENST00000568883, and ENST00000561609, exhibited opposite prognostic indications in different cancers. Moreover, we validated the prognostic effect of these transcripts in an independent kidney cancer cohort. Finally, we revealed that ENST00000389093 and ENST00000568883 possess pyruvate kinase enzymatic activity and may have functional roles in metabolism, cell invasion, and hypoxia response in cancer cells. Our study provided a potential explanation to the controversial prognostic indication of PKM, and could invoke future studies focusing on revealing the biological and oncological roles of these alternative spliced variants of PKM.

Classification of clear cell renal cell carcinoma based on PKM alternative splicing

“…Interestingly, we also found four different isoforms of PKM play a very important role in controlling metabolism of ccRCC (Li et al, 2019b). We have observed that the expression level of four protein-coding transcripts of PKM, including ENST00000335181, which is encoding PKM2 and the most studied isoform of PKM, as well as ENST00000561609, ENST00000389093 and ENST00000568883 are highly associated with patients' prognoses (Li et al, 2019b). Among them, high expression of ENST00000335181 and ENST00000561609 indicated a favorable survival while high expression of ENST00000389093 and ENST00000568883 indicated an unfavorable survival.…”

“…The results suggested the molecular subtypes identified by our analysis also have consistent biological differences. Moreover, these 55 GO terms included all 27 GO terms that we recently reported to be associated with the four different prognostic transcripts in pan cancer analysis (Li et al, 2019b). We also identified three GO terms that are significantly enriched with downregulated genes in the high-risk group for both cohorts, and two of them, which are the histone modification and covalent chromatin modification pathways, are common in both groups.…”

“…In a previous study, PKM isoform switch mediated by PTBP1 was found in ccRCC (Jiang et al, 2017). Interestingly, we also found four different isoforms of PKM play a very important role in controlling metabolism of ccRCC (Li et al, 2019b). We have observed that the expression level of four protein-coding transcripts of PKM, including ENST00000335181, which is encoding PKM2 and the most studied isoform of PKM, as well as ENST00000561609, ENST00000389093 and ENST00000568883 are highly associated with patients' prognoses (Li et al, 2019b).…”

“…In a recent study, we have found that there are molecular subtypes that could be characterized by the expression of the four different prognostic PKM transcripts (Li et al, 2019b). In order to develop a REOs-based biomarker, we identified a signature gene set associated with these four transcripts based on the gene expression profiles of TCGA ccRCC samples.…”

The Correlation Between Novel Survival-related Alternative Splicing Signature and Prognostic Prediction and Immune Microenvironment in Clear Cell Renal Cell Carcinoma

“…Recently, increasing number of researchers pay attention to and lucubrate the AS events, as an essential regulatory mechanism, for which even have developed the effective targeted drugs in the eld of tumors, such as ovarian cancer [18] and prostate cancer [19]. In RCC, it has been reported that some AS events, such as PKM and HnRNPL, can promote the occurrence or development of tumors [20,21] and even resistance to chemotherapy drugs [22], however, mainly are focused on as the novel prognostic factors [23][24][25]. Besides, AS events are closely related to the immune microenvironment, meanwhile the feasibility and safety of splicing isoforms produced by AS as potential tumor immunotherapy targets are in-depth discussed, of which the clinical challenges are in-detail analysed [26].…”