Computational detection, analysis and interpretations of genomic variants in human diseases associated GENEMDM 2

Most of the mutations described in human MDM2 are tolerated without significantly disrupting the corresponding structural or molecular function. However, some of them are associated with a variety of human diseases, including cancer. Numerous computational methods have been developed to predict the effects of missense single nucleotide variants (SNVs). The non-synonymous single nucleotide polymorphisms affect the function of XRCC1, which impairs the ability to repair DNA and therefore increases the risk of diseases such as cancer. In this study, sequence and structure-based computational tools were used to screen the total listed coding SNPs of the MDM2 gene in order to recognize and describe them. The potential 6 ns SNP of MDM2 were identified from 29 ns SNP by consistent analysis using computational tools PolyPhen 2, SIFT, PANTHER and cSNP. The computational methods were used to systematically classify functional mutations in the regulatory and coding regions that modify the expression and function of the MDM2 enzyme. The HOPE project also made it possible to elaborate the structural effects of the substitutions of amino acids. In silico analysis predicted that rs759244097 is harmful. This study concluded that identifying this SNP will help to determine an individual's cancer susceptibility, prognosis and further treatment. Furthermore, current high-throughput sequencing efforts and the need for extensive interpretation of protein sequence variants requires more efficient and accurate computational methods in the coming years.

MDM2 (T309G) Gene Polymorphism Determines the Susceptibility of Hepatocellular Carcinoma in Bangladesh

Background: Hepatocellular carcinoma (HCC) is one of the fatal cancer types worldwide, and a variety of genetic factors are considered to be associated with this incidence. MDM2 gene plays a pivotal role in various pathways, which are essential to combat tumor formation. The study aimed to find out the associations of MDM2 (T309G, rs2279744) gene polymorphism with the development of HCC in the Bangladeshi population. Methods: A case-control study on 100 HCC patients and 110 control subjects was conducted. The genotyping of the MDM2 (T309G) gene was done using PCR-RFLP methods. Results: The percentage of TT and GG genotypes were significantly different (p<0.01) among the study subjects. There were four genotyping groups, while the subjects with TT genotypes were considered the reference group. Patients with GG genotypes were at high risk of developing HCC (OR, 3.6; 95 % CI, 1.64–7.80; p<0.01) compared to the control. On the other hand, the association of TG genotypes with HCC was not statistically significant (OR, 1.8; 95 % CI, 0.91–3.40, p>0.05). In addition, patients having either GG or TG genotypes showed higher risk for HCC compared to control group (OR = 2.20; 95% CI = 1.21–4.14; P < 0.05). Conclusion: Our study suggested that the MDM2 gene may have a strong association with the development of HCC, and the GG allele could serve as an essential determinant to identify the higher risk of HCC in the Bangladeshi population.

Dedifferentiated liposarcoma with abrupt transition of low-grade and high-grade dedifferentiated components: A case report

BackgroundDedifferentiated liposarcoma (DDLPS) is a unique subtype of liposarcoma, which has obvious histological heterogeneity. In affected patients, the condition typically manifests as the dedifferentiation of high-grade histological morphology, but it may also manifest as the dedifferentiation of low-grade histological morphology. In some cases, unique histological or immunophenotypic characteristics are observed. We describe, herein, a rare case of dedifferentiated liposarcoma, in which the high-grade and low-grade dedifferentiated components coexisted with a relatively sharp transition in pathology.Case presentationA 69-year-old woman with severe abdominal pain lasting for 1 hour presented to our hospital. Physical examination revealed a mobile large left abdominal mass, Magnetic resonance imaging (MRI) scan showed a huge mass with typical fat components and the non-fatty nodule in the left retroperitoneal cavity. After laparotomy, histologic analysis of the specimens could find the atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDLPS) and DDLPS components. Fluorescence in situ hybridization (FISH) analysis suggested the presence of MDM2 gene amplification. These findings supported a diagnosis of DDLPS.ConclusionIn our case, the high-grade and low-grade dedifferentiated components coexisted with a relatively sharp transition in pathology. We hypothesize that low-grade dedifferentiation may be a precursor to high-grade dedifferentiation. MRI images cannot distinguish the two components.

Association between TP53 and MDM2 Gene Polymorphisms and Risk of Hepatocellular Carcinoma in Hepatitis C Virus among Egyptian Populations

Background: The Murine double minute 2 (MDM2) gene is overexpressed in several human tumors. The oncogenic potential of MDM2 is partially explained by inhibition of the activity of the tumor suppressor protein P53 (negative regulator of the P53 tumor suppressor protein). A single nucleotide polymorphism (SNP) in the promoter region of MDM2 gene (T to G exchange at nucleotide 309) and TP53 gene (codon 72 exon 4, rs1042522 encoding either C or G) have been independently associated with increased risk of several cancer types. Few studies have analyzed the role of these polymorphisms in the development of hepatocellular carcinoma among Egyptian patients with chronic hepatitis C virus infection. Methods: The study consisted in the comparison of the genotype distribution of TP53 and MDM2 SNP309 in 100 viral hepatitis C-related hepatocellular carcinomas (HCC) cases and 100 controls without HCC matched for age, gender and ethnicity. PCR-RFLP (restriction fragment length polymorphism) and real time PCR methods were used to determine the genotype at the MDM2 SNP309T>G locus and TP53 rs1042522. Results: Overall, our results indicate that frequencies of TP53 alleles (C and G) were not significant different between HCC cases and healthy controls (p=0.093) (Odds Ratio, OR=1.361,95% Confidence Interval, 95% CI=0.949 – 1.951). A significant increase of MDM2 SNP309 G/G and T/G genotypes were observed among HCC cases (Odds Ratio, OR=4.868, 95% Confidence Interval, 95% CI= 2.873 – 8.251). Conclusions: Our finding suggest that people who have G allele increase the risk by 4.868 folds for developing HCC among Egyptian patients, consequently the MDM2 309T>G polymorphism is an important modulator of hepatocellular carcinoma development in Egyptian patients.

Synchronous Renal Dedifferentiated Liposarcoma and Retroperitoneal Well-Differentiated Liposarcoma: A Case Report With Literature Review

Liposarcoma is the most common soft tissue malignancy and usually occurs in the retroperitoneum or the extremities but rarely in the kidney. In this article, we report a case of a 71-year-old female patient who presented with abdominal lump and left flank pain for 1 month. An abdominal contrast-enhanced computed tomography scan demonstrated a 12 cm × 7 cm solid mass arising from the upper pole of left kidney and another 8 cm × 6 cm low-density retroperitoneal mass with fat density. Radical nephrectomy of the left kidney and resection of the retroperitoneal mass were performed. Surprisingly, pathological examination revealed a high-grade sarcoma (with minor lipomatous component) in the left kidney and a retroperitoneal well-differentiated liposarcoma. MDM2 gene amplification was identified by fluorescence in situ hybridization in both tumors, supporting final diagnosis of dedifferentiated liposarcoma of the kidney and well-differentiated liposarcoma of the retroperitoneum.

Dedifferentiated Liposarcoma with Abrupt Transition of Low-Grade and High-Grade Dedifferentiated Components ：A Case Report

Background: Dedifferentiated liposarcoma (DDLPS) is a unique subtype ofliposarcoma, which has obvious histological heterogeneity. In affected patients, the condition typically manifests as the dedifferentiation of high-grade histological morphology, but it may also manifest as the dedifferentiation of low-grade histological morphology. In some cases, unique histological or immunophenotypic characteristics are observed. We describe, herein, a rare case of dedifferentiated liposarcoma, in which the high-grade and low-grade dedifferentiated components coexisted with a relatively sharp transition in pathology.Case presentation: A 69-year-old woman with severe abdominal pain lasting for 1 hour presented to our hospital. Physical examination revealed a mobile large left abdominal mass, Magnetic resonance imaging (MRI) scan showed a huge mass with typical fat components and the non-fatty nodule in the left retroperitoneal cavity. After laparotomy, histologic analysis of the specimens could find the ALT/WDLPS and DDLPS components. Fluorescence in situ hybridization (FISH) analysis suggested the presence of MDM2 gene amplification. These findings supported a diagnosis of DDLPS.Conclusion: In our case, the high-grade and low-grade dedifferentiated components coexisted with a relatively sharp transition in pathology. We hypothesize that low-grade dedifferentiation may be a precursor to high-grade dedifferentiation. MRI images cannot distinguish the two components.

MDM2 gene amplification as selection tool for innovative targeted approaches in PD-L1 positive or negative muscle-invasive urothelial bladder carcinoma

AimsAccording to The Cancer Genome Atlas (TCGA), around 9% of bladder carcinomas usually show abnormalities of the murine double minute 2 (MDM2) gene, but a few studies have been investigated them. We profiled MDM2 gene amplification in a series of urothelial carcinomas (UC) considering the molecular subtypes and expression of programmed death ligand 1 (PD-L1).Methods117 patients with muscle-invasive UC (pT2-3) without (N0) or with (N+) lymph-node metastases were revised. Only cases with availability of in toto specimens and follow-up were studied. Tissue microarray was built. p53, ER, RB1, GATA-3, CK20, CK5/6, CD44 and PD-L1 (clone sp263) immunoexpression was evaluated. Fluorescent in situ hybridisation was assessed by using the HER-2/neu, FGFR-3, CDKN2A and MDM2 probes. True (ratio 12q/CEP12 >2) MDM2 gene amplification was distinguished from polyploidy/gains (ratio <2, absolute copy number of MDM-2 >2). MDM2 and PD-L1 values were correlated to the TCGA molecular phenotypes. Statistical analysis was performed.Results6/50 (12%) cases (5 N0 and 1 N+) were amplified for MDM2 without matching to molecular phenotypes. Of 50, 14 (37%) cases expressed PD-L1 at 1% cut-off; 3/50 (9%) at >50% cut-off; of these, 2 cases on side of neoplasia among inflammatory cells. Only one out of six (17%) cases amplified for MDM2 showed expression (>50% cut-off) of PD-L1. MDM2 amplification was independent to all documented profiles (k test=0.3) and was prevalent in recurrent UC.ConclusionMDM2 amplification has been seen in both PD-L1 positive and negative muscle-invasive bladder UC independently from the TCGA molecular phenotypes. MDM2 and PD-L1 might be assessed in order to predict a better response to combo/single targeted therapies.