Primary Microcephaly Gene MCPH1 Shows Signatures of Tumor Suppressors and is Regulated by miR-27a in Oral Squamous Cell Carcinoma

Abstract

Autosomal recessive primary microcephaly (MCPH) is a congenital neurodevelopmental disorder characterised by a reduced occipital-frontal head circumference (OFC) of less than -3 SDs below the population mean for age and sex. It is a genetically heterogeneous disorder caused by mutations in one of the following 10 MCPH genes: MCPH1 (microcephalin 1), WDR62 (WD repeat domain 62), CDK5RAP2 (cyclin-dependent kinase 5 regulatory associated protein 2), CASC5 (cancer susceptibility candidate 5), CEP152 (centrosomal protein 152 kDa), ASPM (asp [abnormal spindle] homolog, microcephaly associated [Drosophila]), CENPJ (centromeric protein J), STIL (SCL/TAL1-interrupting locus), CEP135 (centrosomal protein 135 kDa) and CEP63 (centrosomal protein 135 kDa). The MCPH1 (microcephalin 1) gene is located on chromosome 8p23.1. Microsatellite analysis has previously shown LOH at the markers D8S518 and D8S277 flanking the MCPH1 locus in 1/21 oral tumors. Furthermore, LOH at the markers D8S1742 and D8S277 flanking the MCPH1 locus has also been observed in 2/32 hepatocellular carcinomas. MCPH1 has been found to be mutated in breast and endometrial cancers. Additionally, it was found to be downregulated at the transcript level in 19/30 ovarian cancer tissues and the protein level in 93/319 breast cancer tissues. Decreased MCPH1 protein levels are associated with triple negative breast cancers and a lower transcript level of MCPH1 correlates with lesser time for metastasis to occur in breast cancer patients. Interestingly, MCPH1 knockout mice in a null TP53 background show susceptibility to cancer.So far, studies have indicated that MCPH1 is a DNA repair protein. MCPH1 is required for the formation of DNA repair foci, chromatin relaxation, HR and NHEJ. It regulates G1/S and G2/M cell cycle checkpoints. Also, depletion of MCPH1 leads to genomic instability and centrosome amplification. Hence, the defect in the function of MCPH1 can lead to plethora of anomalies including cancer. Based on these observations, we hypothesized that MCPH1 may also function as a tumor suppressor (TS) gene, in addition to its role in the brain development. The purpose of this study was to test if MCPH1 also functions as a TS gene using different approaches in OSCC (oral squamous cell carcinoma). OSCC is the sixth most common type of cancer. It includes the cancer of the lips, anterior 2/3rd of the tongue, buccal mucosa, floor of the mouth, retromolar trigone and gingiva. Despite the advances in the treatment of oral cancer, the five-yr survival rate has not increased. Hence, the effective treatment of OSCC requires the identification of molecular targets to design appropriate therapeutic strategies. LOH, mutations and promoter methylation in tumors are the hallmarks of TS genes. In order to ascertain the TS roles of MCPH1, we carried out LOH analysis in 81 matched blood/normal and tumor oral tissues using D8S1819, D8S277 and D8S1798 markers flanking the MCPH1 locus. The results showed LOH at one or more markers in 14/71 (19.72%) informative samples across the tumor stages from T1 to T4. The entire coding region and the exon-intron junctions of the MCPH1 gene were sequenced for mutations in 15 OSCC samples and 5 cancer cell lines (viz., A549, HeLa, KB, SCC084 and SCC131). In total, three mutations namely c.1561G>T(p.Glu521X), c.321delA(p.Lys107fsX39) and c.1402delA(p.Thr468fsX32) were identified. The expression of MCPH1 was analysed at both the transcript and protein levels by real-time quantitative RT-PCR and immunohistochemistry, respectively, in OSCC samples. MCPH1 was downregulated in 51.22% (21/41) of OSCC samples at the transcript level. The MCPH1 protein was downregulated in 76% (19/25) of the OSCC samples. In order to elucidate if the MCPH1 promoter was methylated in OSCC tissues, we retrieved the MCPH1 promoter from the database TRED (Transcriptional Regulatory Element Database). The promoter was analysed for the presence of CpG islands using the CpG Plot/CpG Report program. Two CpG islands (CpGI and CpGII) were identified within the MCPH1 promoter. Both the CpG islands were analysed for methylation in 40 OSCC samples by COBRA (Combined Bisulfite Restriction Analysis). CpGI showed no methylation in 40 OSCC samples. However, CpGII showed methylation in 4/40 (10%) OSCC samples and the methylation was absent in their corresponding normal oral tissues. To analyse the methylation of the MCPH1 promoter in cancer cell lines, HeLa, KB, SCC084 and SCC131 cells were treated with 5’-2-deoxy azacytidine (AZA), a methyltrasferase inhibitor. HeLa and KB cells did not show any change in the MCPH1 transcript level after the AZA treatment. However, SCC084 and SCC131 cells showed upregulation of MCPH1 after the treatment, suggesting methylation of the MCPH1 promoter. To validate these observations, we examined the methylation status of both the CpG islands in these cell lines. We found methylation of CpGII only in SCC084 cells. HeLa, KB and SCC131 cells showed no methylation of CpGI and CpGII. The results obtained by COBRA in these cell lines were further confirmed by bisulfite sequencing of CpGI and CpGII islands. Further, the upregulation of MCPH1 after azacytidine treatment in SCC131 cells can be attributed to a promoter independent mechanism or due to methylation of the CpG sites not examined by us. To elucidate the biological effects of MCPH1 in a cancer cell line, we generated stable clones overexpressing MCPH1 in KB cells. The results showed that MCPH1 overexpression decreased cellular proliferation, cell invasion, anchorage-independent growth in soft-agar and tumor growth in nude mice. Further, MCPH1 overexpression lead to apoptosis. A low frequency of LOH, mutations and promoter methylation suggested that they might not be the major mechanisms of downregulation of MCPH1 in OSCC. We then speculated that MCPH1 could be regulated by miRNAs. We therefore used five miRNA target prediction softwares to identify miRNAs targeting MCPH1. The programs identified two binding sites for miR-27a within the 5.4 kb region of the 3’-UTR of MCPH1. The luciferase assay showed that both the seed regions of MCPH1 were binding to miR-27a. In addition, transient transfection of the premiR-27a construct in KB cells decreased the protein level of MCPH1. Additionally, in a small panel of 10 OSCC samples, there was a negative correlation between the levels of miR-27a and MCPH1. To the best of our knowledge, this is the first report showing any miRNA regulating the MCPH1 gene. It is important to note that tumor suppressors can serve as potential biomarkers with prognostic value. Hence, we analysed the correlation of the expression levels of MCPH1 with clinico-pathological parameters such as TNM, gender, age and site of the cancer by Fischer’s exact test. No statistical correlation was observed between the transcript or protein levels with any of the clinico-pathological parameters. In summary, the results of the present study have suggested that the primary microcephaly gene MCPH1 shows several hallmarks of TS genes and functions as a tumor suppressor in OSCC, in addition to its role in brain development. We have for the first time shown that miR-27a targets MCPH1 and regulates its level. It is interesting to note that none of the other 10 MCPH genes have been shown to be regulated by any miRNA yet. Our study will be useful in designing novel therapeutic methods for the treatment of OSCC either by overexpression of MCPH1 or reducing the level of miR-27a by an antagomir.