GPRC5A is a family member of the GPCRs, which is one of the largest and most various group of membrane protein family in the human genome. Previous studies have been reported that transcription of the GPRC5A can be induced through retinoic acid response element in the 5' UTR region (Allenby et al. 1993; Ye et al. 2009). In addition, GPRC5A transcription has been reported to be regulated by cAMP (cyclic adenosine monophosphate), TP53 (Tumor Protein P53), BRCA1 (Breast Cancer Gene 1), and hypoxia-inducible factors (HIFs) (Wu et al. 2005; Hirano et al. 2006; Sokolenko et al. 2014; Greenhough et al. 2018b). Expression of GPRC5A differs in various human cancers, its dual role in tumorigenesis makes it intriguing. GPRC5A has tumor suppressor activity in lung cancer. It has been reported by Tao et al. that knockout of the Gprc5a results in development of lung cancers in mice (Tao et al. 2007). Deng et al. have demonstrated that knockout of Gprc5a leads to activation of NF-κB (Nuclear Factor kappa B) in lung epithelial cells in mice, resulting in increased inflammatory microenvironment, and have suggested that this may promote tumorigenesis (Deng et al. 2010). Moreover, deletion of Gprc5a leads to activation of signal transducer and activator of transcription 3 (Stat3) that was important for lung cancer cell survival and transformation (Chen et al. 2010). Furthermore, it has also been reported that GPRC5A has a potential role in inhibition of epidermal growth factor receptor (EGFR) expression and activation. It is thought that GPRC5A deficiency may contribute to the initiation of lung tumorigenesis by leading to dysregulated EGFR (Zhong et al. 2015). However, GPRC5A display oncogenic properties in other cancer types such as breast, stomach, pancreatic, liver, and colon cancers. For example, Greenhough et al. showed that upregulation of GPRC5A during hypoxia activates the Hippo pathway effector YAP and protects colorectal tumor cells from apoptosis; HIFs directly induce the GPRC5A expression (Greenhough et al. 2018b). In gastric cancer, GPRC5A expression levels are high compared with normal tissues (Cheng et al. 2012). Knockdown of GPRC5A has been reported that lead to decreased proliferation, migration, and cell growth in pancreatic cancer cell lines via STAT3 inactivation (Jahny et al. 2017). rs1640875 in GPRC5A is thought to have a pleiotropic effect on both nevus and melanoma (Duffy et al. 2018). In a study by Sokolenko et al. it was revealed that GPRC5A c.183delG (p.Arg61fs ) allele affects the disease susceptibility in carriers of BRCA1 mutation in breast cancer. They also found that this allele was marginally overrepresented in lung cancer patients who smoke relative to healthy inividuals (Sokolenko et al. 2014). This information indicates that variants in GPRC5A gene may play important roles in many different types of cancer in human.
In this study, the putative effects of GPRC5A variants on protein function, gene regulation and post-translational mechanisms were investigated. In recent years, several prediction tools which have specific computational algorithms were developed for pathogenicity assessment of variants of the genome (Cline and Karchin 2011). Since different scoring algorithms were used, the are not always consistent, it is very important to carefully evaluate the estimated results (Ghosh et al. 2017). In the current study, the functional consequences of GPRC5A missense variants were investigated. For this reason, the PP2, MT2 and MutPred2 tools were used. These tools are the most common predictors for amino acid substitutions in in-silico analyses. 76 missense variants were categorized as pathogenic based on combined scores of these three algorithms from 391 missense variants, 210 have the same score using three different algorithms. The results of this study show that the three in-silico tools frequently give the same results even though they used different algorithms.
Proteins are vital to life, and understanding their structure is important to understanding their functions (Lee et al. 2007). AlphaFold is an AI system that predicts the 3D protein structure, developed by DeepMind(Varadi et al. 2022) (https://alphafold.ebi.ac.uk). The AlphaFold model of the GPRC5A protein and the position of six variants (p.Tyr350His, p.Tyr350Cys, p.Tyr347Cys, p.Ser336Tyr, p.Gly38Arg, and p.Cys9Phe) on GPRC5A that have the potential of being functional importance in terms of pathogenicity are shown in Fig. 5a. Additionally, VarSite predictions of these variants, as a schematic diagram of the variant and as histogram of the disease propensity are shown in Fig. 5b. According to MutPred2 p.Tyr347Cys variant have a g-score of 0.576 and was predicted to alter the transmembrane protein with a p-value of 3.1e-04. Two different variants on the same location (p.Tyr350Cys and p.Tyr350His (g = 0,65; p = 1.6e-03)) were predicted to the loss of phosphorylation on this amino acid.There is a disulfide bond between Cys9 and Cys21; p.Cys9Phe in GPRC5A has been predicted tocause loss of disulfide linkage at C9 (g = 0,810; p = 8.3e-05). p.Cys9Phe has also been predicted to cause alterations in the metal binding ability (p = 3.8e-03). p.Gly38Arg was the only variant with a RegulomeDB score < 3, which may have a regulatory effect among the variants that was classified as pathogenic. p.Ser336Tyr is the only PTM-related pathogenic variant as well as predicted to alter transmembrane protein (g = 0,578; p = 3.5e-04) by MutPred2.
Due to the effects of PTM-associated SNVs on human diseases, particularly cancer, the PTM sites of GPRC5A were analysed using PhosphositePlus. Lin et al. have shown that GPRC5A undergoes EGFR-mediated phosphorylation at double tyrosine motifs (Y317/Y320 and Y347/Y350). Importantly, they showed by immunohistochemical analysis that GPRC5A, which is non-phosphorylated in normal lung tissues, was highly tyrosine-phosphorylated in NSCLC tissues (Lin et al. 2014). In the current study, among these 4 tyrosine motif containing locations, three variants (p.Tyr347Cys (rs759993863), p.Tyr350His (rs770022212) and p.Tyr350Cys (rs372263202)) were classified as pathogenic and two other (p.Tyr347His (rs757980943) and p,Tyr317Cys (rs146929355) variants were classified as VUS according to PP2, MT2 and MutPred results.
A single variant had MAF > 0.01 according to GnomAD results. This information indicates that variants of this gene are rare in the human populations.
miRNAs are molecules with key regulatory roles in the cell in both normal and pathological conditions. Polymorphisms in miRNA target sites have been associated with a wide range of diseases including cancers (Ryan et al. 2010). There are various algorithms that could predict possible miRNA-binding sites. PolymiRTS is a database including that naturally occurring DNA variations in putative miRNA target sites (Bhattacharya et al. 2014). The 16 miRNA target sites identified for two variants (rs144308510 and rs144308510) were found in the 3'UTR region of the GPRC5A gene using the PolymiRTS database (Table 4). Some of these miRNA target sites have been associated with various cancers (Darvishi et al. 2020; Ghanbari et al. 2021; Li et al. 2021; Dastmalchi et al. 2022). miR-195 inhibits gastric cancer cell proliferation and metastasis by targeting GPRC5A (Liang et al. 2019). DNA methyltransferase 1 (DNMT1) mediates the miR-497/GPRC5A axis in breast cancer, leading to increased chemotherapy resistance and metastasis (Liu et al. 2022).
Cellular function depends on functional interactions among the proteins. STRING database anaylsis showed that GPRC5A strongly interacts with proteins of GRM2 (Glutamate metabotropic receptor 2) and EIF4A1 (Eukaryotic initiation factor 4A-I). GRM2 - a GPCR family member protein- is activated by glutamate and modulates the activity of down-stream effectors, such as adenylate cyclase via G proteins and is widely expressed in brain (González-Maeso et al. 2008). It may mediate suppression of neurotransmission or participate in the modulation of synaptic transmission and neuronal excitability (Joo et al. 2001; Niswender and Conn 2010). Fukuda et al., suggested that in humans the GRM2 gene product may regulate the metastatic phenotype of some colorectal cancers (Fukuda et al. 1997). Bidkhori et al., in their study used a "genome-scale co-expression network" approach, and identified a number of genes, including GMR2, that play a role in lung adenocarcinoma (Bidkhori et al. 2013). EIF4A1, an ATP-dependent RNA helicase, is required for mRNA to attach to the ribosome (Jeong et al. 2009). EIF4A1 has been found to be overexpressed in various malignancies such as hepatocellular carcinoma, NSCLC, endometrial cancer, cervical cancer, and breast cancer (Raza et al. 2015). Furthermore, high expression level of EIF4A1 has been associated with poor prognosis in breast and cervical cancer patients and metastasis in NSCLC patients. In addition to all this, EIF4A1 is known to play a role in many cancers (Xue et al. 2021).
In conclusion, the potential pathogenic consequences of GPRC5A coding variants resulting amino acid substitutions have been investigated comprehensively and their putative roles in gene regulation and PTMs evaluated by in-silico analysis. The results highlight the functional consequences of variants in GPRC5A. The results of this study may have important impact to future studies for further understanding the pathogenecity of GPRC5A-associated cancer types by unraveling the roles of putative functional variants.