Frameshift mutation of candidate tumor suppressor genes QK1 and TMEFF2 in gastric and colorectal cancers

1. Introduction

QKI gene encodes an RNA-binding protein that regulates diverse mRNA functions such as splicing, export and stability of mRNA [1]. QKI regulates target mRNAs such as p27, beta-catenin and c-fos that are related to cancer development [2, 3, 4]. Aberrant expression of QKI has been reported in many tumors [5, 6, 7]. For example, QKI gene is silenced in gastric (GC) and colorectal (CRC) cancers [3, 7]. QKI overexpression inhibits proliferation of GC and CRC cells [3, 7]. These reports suggest that QKI has tumor suppressor gene (TSG) activity in multiple cancers. TMEFF2, also known as HPP1, encodes the tomoregulin family of transmembrane proteins [8]. Loss of TMEFF2 expression by promoter hypermethylation has been reported in many tumors, including GC, CRC and breast cancers [8, 9, 10]. TMEFF2 expression promotes apoptosis and induces cell cycle arrest [11, 12], indicating that TMEFF2 gene is a candidate TSG as well.

About one third of GC and CRC are classified as high microsatellite instability (MSI-H) cancers [13]. Many TSGs harbor frameshift mutations at monocleotide repeats in MSI-H cancers [13]. In the human genome database, we observed that both QKI and TMEFF2 genes possess nucleotide repeats in coding sequences that might be mutated in MSI-H cancers. Intratumoral heterogeneity (ITH) is a common phenomenon in cancers, which may result in cancer evolution and influence on clinical outcomes [14, 15, 16]. Thus, identification of genetic ITH is important in understanding biological and clinicopathologic features of the cancers. The current study aimed to find whether QKI and TMEFF2 frameshift mutations are common and harbor ITH in MSI-H GC and CRC.

3. Results

4. Discussion

Inactivation of a TSG by somatic mutations is known to lead the cell to cancer development in combination with other genetic changes. Earlier studies identified that both QKI and TMEFF2 possess TSG activities in cells [3, 7, 11, 12]. Both QKI and TMEFF2 are known to lose their activities by expression losses through promoter hypermethylation in GC and CRC [3, 7, 8, 9]. In the COSMIC database that encompasses overall mutation incidences to date, the QKI recurrently has hotspot p.K134 frameshift mutations in GC ( n = 5) and CRC ( n = 23). The TMEFF2 has the hotspot p.K303 frameshift mutation in CRC ( n = 3), but none in GC. Such validation in the public data may indicate that the recurrent frameshift mutations of QKI and TMEFF2 may be present irrespective of regions and ethnicities of the cancer patients. QKI are recurrently A8 of PLA2R1 and the A7 of SRPK1 harbored deletion mutations in 3 (one GC, one CRC and one melanoma) and one (one CRC) cases, respectively. However, there has been no report on inactivating mutations of QKI and TMEFF2 TSGs in GC and CRC. This study by us identified that both MSI-H GC and CRC exhibited QKI (17.6% of GC and 12.7% of CRC) and TMEFF2 (6.3% of CRC) frameshift mutations. These results indicate that QKI and TMEFF2 TSGs are altered not only by protein losses as shown previously [3, 7, 8, 9] but also by frameshift mutations identified in this study and suggest that QKI and TMEFF2 inactivating mutations might inhibit their TSG functions in MSI-H GC/CRC as well. Thus, QKI and TMEFF2 frameshift mutations might play a role in the pathogenesis of MSI-H GC/CRC by inhibiting their TSG activities.

Two opposite activities (TSG and oncogenic) of TMEFF2 have been identified [8, 9, 21]. In prostate cancers, TMEFF2 promotes cell proliferation in an ADAM17-depencdent manner [22]. By contrast, in GC and CRC, TMEFF2 expression is decreased compared to the normal cells [8, 9]. In addition, loss of TMEFF2 expression is related to the tumor stages and poor clinical outcomes of GC patients [22]. TMEFF2-mediated tumor suppression requires activation of STAT1/2 pathways that induces G0/G1 phase cell cycle arrest [11, 12]. These earlier data may indicate that TMEFF2 function either oncogenic or TSG is context- and cell type-dependent. Together, TMEFF2 may behave as a TSG that is frequently altered by frameshift mutations as well as expression loss in GC and CRC. The QKI and TMEFF2 frameshift mutations may truncate and disable QKI and TMEFF2 proteins and hence be considered loss-of-function mutations. Expression of QKI increases the enterocyte differentiation markers in CRC cells along with p27 protein level and beta-catenin, and inhibits cell proliferation [3]. The truncated mutants of QKI predicted by our data may possibly inactivate their TSG function (maintenance of cell differentiation and inhibition of proliferation), but the cellular consequences as well as clinical implications remain to be further clarified.

In this study, we identified mutational ITH of QKI or TMEFF2 in 3 of 16 CRCs (19%), which is consistent with previous studies that had reported frequent mutational ITH in CRCs with MSI-H [23]. It is well known that cancer ITH of driver mutations could result in poor clinical outcomes in patients. For instance, single or a group of mutations with a metastasis potential might redirect clinical outcomes since such rare clones may accomplish dominance during tumor progression [14, 15, 16]. Based on the TSG properties of QKI and TMEFF2 in CRC, our results suggest that loss of the TSG properties may have regional heterogeneity that could be further selected and influence the clinical outcomes. However, it should be further studied how the ITH change during the progression and the ITH play a causal role in tumor pathogenesis.

TMEFF2 has EGF-like domain that is known to bind with ERBB4 [24]. Given the importance of oncogenic erbB proteins in cancer therapies, further understanding of TMEFF2 alterations in our data (mutational inactivation in MSI-H GC and CRC) here may provide useful information for its potential clinical application. In these points, our data may reveal information on biological mechanisms as well as therapeutic strategies in cancer cells.