Elevation of the TP53 isoform Δ133p53β in glioblastomas: an alternative to mutant p53 in promoting tumor development

As tumor protein 53 (p53) isoforms have tumor‐promoting, migration, and inflammatory properties, this study investigated whether p53 isoforms contributed to glioblastoma progression. The expression levels of full‐length TP53α (TAp53α) and six TP53 isoforms were quantitated by RT‐qPCR in 89 glioblastomas and correlated with TP53 mutation status, tumor‐associated macrophage content, and various immune cell markers. Elevated levels of Δ133p53β mRNA characterised glioblastomas with increased CD163‐positive macrophages and wild‐type TP53. In situ‐based analyses found Δ133p53β expression localised to malignant cells in areas with increased hypoxia, and in cells with the monocyte chemoattractant protein C‐C motif chemokine ligand 2 (CCL2) expressed. Tumors with increased Δ133p53β had increased numbers of cells positive for macrophage colony‐stimulating factor 1 receptor (CSF1R) and programmed death ligand 1 (PDL1). In addition, cells expressing a murine ‘mimic’ of Δ133p53 (Δ122p53) were resistant to temozolomide treatment and oxidative stress. Our findings suggest that elevated Δ133p53β is an alternative pathway to TP53 mutation in glioblastoma that aids tumor progression by promoting an immunosuppressive and chemoresistant environment. Adding Δ133p53β to a TP53 signature along with TP53 mutation status will better predict treatment resistance in glioblastoma. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.     

Detailed haplotype analysis at the TP53 locus in p.R337H mutation carriers in the population of Southern Brazil: evidence for a founder effect

Due to patterns of migration, selection, and population expansion, founder effects are common among humans. In Southern Brazil, a recurrent TP53 mutation, p.R337H, is detected in families with cancer predisposition. We have used whole locus resequencing and high‐density single nucleotide polymorphism (SNP) genotyping to refine TP53 locus haplotype definitions. Haplotyping of 12 unrelated p.R337H carriers using a set of 29 tag SNPs, revealed that all subjects carried the same haplotype, and presence of the mutation on this haplotype was confirmed by allele‐specific PCR. The probability that this haplotype occurs independently in all index cases was of 3.1×10^?9, demonstrating a founder effect. Analysis of the patterns of 103 tumors diagnosed in 12 families showed that the presence of p.R337H is associated with multiple cancers of the Li‐Fraumeni Syndrome (LFS) spectrum, with relatively low penetrance before the age of 30 but a lifetime risk comparable to classical LFS. The p.R337H families are mostly distributed along a road axis historically known as the main route used by merchants of Portuguese origin in the XVIII and XIX century. This historical circumstance and the relatively low penetrance before the age of 30 may have contributed to the maintenance of this pathogenic mutation in a large, open population. Hum Mutat 30:1–8, 2009. © 2009 Wiley‐Liss, Inc.     

TP53 mutation and haplotype analysis of two large African American families

Two large apparently unrelated African American families with a high incidence of breast cancer and other tumors characteristic of Li‐Fraumeni breast sarcoma cancer family syndrome were studied. Mutation screening revealed that in both families the affected members carried a germline mutation of the TP53 gene at codon 133 (ATG→ ACG, M133T). In order to determine whether an ancestral haplotype was shared by these two families, polymorphic markers within and flanking the TP53 gene were studied. Haplotype analysis using five markers revealed an identical haplotype shared by the two families. Loss of heterozygosity at the TP53 locus in the probands' tumor tissues from each family was observed; in each case, the retained allele carried the common haplotype. The frequency of this haplotype in the general African American population is <0.003. This unique haplotype, combined with the rare TP53 mutation, suggests that these African American families share a common ancestry. This finding suggests that other African Americans may be carriers of this mutation and thus may be at risk of early‐onset breast cancer or other cancers characteristic of the Li‐Fraumeni breast sarcoma cancer family syndrome. The finding of recurring mutations in African Americans may facilitiate carrier screening and identification in this population. Hum Mutat 14:216–221, 1999. © 1999 Wiley‐Liss, Inc.     

p53: out of Africa

Somatic mutations in the tumor suppressor gene p53 occur in more than half of all human cancers. Rare germline mutations result in the Li-Fraumeni cancer family syndrome. In this issue of Genes & Development, Jennis and colleagues (pp. 918–930) use an elegant mouse model to examine the affect of a polymorphism, P47S (rs1800371), in the N terminus of p53 that is found in Africans as well as more than a million African Americans. Remarkably, the single nucleotide change causes the mice to be substantially tumor-prone compared with littermates, suggesting that this allele causes an increased risk of developing cancer. The defect in p53 function is traced to a restriction in downstream gene regulation that reduces cell death in response to stress.     

Age‐related macular degeneration and functional promoter and coding variants of the apolipoprotein E gene

Age‐related macular degeneration (AMD) is a frequent, multifactorial disease of the central retina and a major cause of irreversible vision loss in industrialized countries. Apolipoprotein E (APOE) has been consistently associated with AMD, particularly its two functional isoforms E2 (predisposing) and E4 (protective). The biological correlate of this association, however, is still unclear. In this study, we have defined an extended haplotype block encompassing the entire APOE gene locus, including known coding as well as cis‐regulatory promoter variants. Of the five extended APOE haplotypes common in the general population, two were found to be significantly associated with AMD, namely G‐G‐G‐G‐ε2 (odds ratio [OR], 1.59; 95% confidence interval [CI], 1.19–2.12) and T‐G‐A‐G‐ε4 (OR, 0.76; 95% CI, 0.58–0.99). When analyzing common extended haplotype combinations, T‐C‐G‐G‐ε3/T‐G‐A‐G‐ε4 exhibited the most prominent effect (OR, 0.32; 95% CI, 0.20–0.51). Intriguingly, we also found one extended ε3‐haplotype, G‐G‐G‐A‐ε3, to be protective in the homozygous state (OR, 0.65; 95% CI, 0.49–0.87). Since single nucleotide polymorphism (SNP) rs405509:G>T is a constituent of the extended ε‐haplotype block and is known to significantly influence APOE promoter activity, we hypothesize that both the relative rate of APOE isoform expression in conjunction with established functional differences of the respective isoforms may be crucial in mediating AMD pathology. This would also imply that genotyping of the core ε‐haplotypes alone is not sufficient to estimate AMD risk, but that determination of extended haplotype combinations, including the functional promoter SNP rs405509, is required instead. Hum Mutat 0:1–6, 2009. © 2009 Wiley‐Liss, Inc.     

Highly sensitive mutation screening by REF with low concentrations of urea: A blinded analysis of a 2‐kb region of the p53 gene reveals two common haplotypes

Restriction endonuclease fingerprinting (REF), a hybrid modification of single‐strand conformation polymorphism (SSCP) and restriction endonuclease digestion, has been used previously to detect mutations in 1‐ to 2‐kb segments of DNA. This paper demonstrates that fragment resolution, and thus sensitivity of REF, can be markedly improved by electrophoresis under partially denaturing, rather than nondenaturing, conditions, for genes with a high G+C content. A 2.1‐kb segment of the p53 tumor suppressor gene (54.5% G+C) containing exons 5–9, including the intervening introns, was screened in a blinded analysis of 48 samples from human breast tumors containing known wild‐type or mutant p53 genes. In gels containing 0.5 M urea, 97% of the mutant samples were detected correctly, and more than 80% of the mutations were localized within a 200‐bp region. In the process of this methodological analysis, it was discovered that: (1) there are two common and four uncommon haplotypes; (2) the two common haplotypes occurred in the three races examined, suggesting an ancient origin; and (3) haplotype II is of substantially higher frequency in the Chinese relative to Japanese (P = 0.023) and Caucasians (P = 0.005). Two other improvements in the REF procedure included (1) the selection of an optimal set of restriction endonucleases by new software (REF Select) developed recently in our laboratory; and (2) the addition of an oligonucleotide “tail,” containing two recognition sequences for restriction endonucleases, to the PCR primers to prevent coterminal fragments at the end of amplified products. These modifications facilitate the use of REF for efficient and sensitive mutation screening in p53 and other genes with a high G+C content. Hum Mutat 14:175–180, 1999. © 1999 Wiley‐Liss, Inc.     

Polymorphisms in TP53 are associated with risk and survival of osteosarcoma in a Chinese population

Osteosarcoma (OS) is the most frequent histological form of primary bone cancer in adolescence. TP53 is a tumor suppressor gene which is essential for regulating cell division and preventing tumor formation. The purpose of this study is to examine whether genetic mutations in the TP53 gene are associated with OS risk and survival in a Chinese population. Five polymorphisms in the TP53 gene were selected in a case-control study, including 210 OS patients and 420 cancer-free controls. We found that subjects carrying rs12951053 CC genotype and rs1042522 GG genotype were significantly associated with risk of OS [odds ratio (OR) = 1.68, 95% confidence intervals (CI): 1.05-2.68; OR = 1.89, 95% CI: 1.16-3.07] compared with subjects carrying the common genotypes. Results of haplotype analysis also showed that A-G-G-A-C haplotype (rs12951053, rs1042522, rs8064946, rs9895829 and rs12602273) conferred significant decreased risk of OS (OR = 0.37, 95% CI: 0.19-0.72) compared with A-C-G-A-C haplotype. Besides, rs1042522 was an independent prognostic factor for OS with hazard radio (HR) = 1.94 (95% CI: 1.03-3.65) in GG genotype than in CC genotype. Our data suggest that genetic mutations in the TP53 gene are associated with risk and survival of OS in Chinese population.     

-1227C>T polymorphism in the pleiotrophin gene promoter influences bone mineral density in postmenopausal women

Our gene expression microarray data of primary cultures of osteoblasts revealed that the expression of the pleiotrophin (PTN) gene is decreased in osteoporosis. PTN is involved in osteoblasts' proliferation and differentiation, response to mechanical stimuli and cross-talk with Wnt signaling. On the basis of these findings, we studied the PTN gene as a candidate gene for genetic susceptibility to osteoporosis. The aim of the study was to evaluate the association of two PTN gene promoter polymorphisms with osteoporotic phenotype in postmenopausal women. 530 postmenopausal women, 480 without and 50 with hip fracture, were genotyped for the presence of PTN gene promoter polymorphisms -1734C>T (rs161335) and -1227C>T (rs321198). Three common haplotypes, CC (14.2%), CT (42.8%) and TC (42.9%), were inferred. Bone mineral densities (BMDs) at lumbar spine and (contralateral) hip were measured. In non-osteoporotic postmenopausal women without hip fracture, the association of -1227C>T and CT haplotype with lumbar spine BMD was shown (p=0.014 and 0.014). No other significant association of the studied genotypes and haplotypes in the PTN gene promoter with BMDs was found. Comparing age-matched postmenopausal women with and without hip fractures, no differences in frequency distributions of the studied genotypes and haplotypes was shown. For the first time we have shown that, in postmenopausal women, the PTN gene promoter polymorphism -1227C>T and CT haplotype could contribute to the genetic background of osteoporosis, but these findings need further functional and clinical confirmation.     

基于家系的Tim-3基因多态性与儿童变应性哮喘的关联研究

目的 以家系资料为基础,利用遗传不平衡原理探讨染色体5q33.2区Tim-3基因启动子两个多态性位点rs10053538和rs10515746与中国湖北地区汉族儿童变应性哮喘的关系.方法 应用限制性片段长度多态性技术结合测序方法,分析了118个儿童变应性哮喘核心家系Tim-3基因rs10053538和rs10515746的基因型;采用基于家系的关联分析方法,包括单体型相对风险分析(HRR)和传递不平衡检验(TDT),分析基因分型数据;应用Transmit软件构建单体型并进行单体型关联分析.结果 118个核心家庭HRR分析显示Tim-3基因启动子区两个多态性位点rs10053538和rs10515746不使病人具有更高的发病风险(X2=2.430,P>0.05;x2=1.368,P>0.05).118个满足经典TDT分析的核心家庭中,杂合子父母传递给患病子代的等位基因频率不比预期值高(x2=2.042,P>O.05;x2=0.750,P>O.05).Transmit双位点单体型分析也未见父母传递给子女各个单体型的观察值和期望值有明显差异(P>O.05).结论 中国湖北地区汉族人群中,Tim-3基因启动子区两个多态性位点rs10053538和rs10515746与儿童变应性哮喘不具有相关性.     

A haplotype containing the p53 polymorphisms Ins16bp and Arg72Pro modifies cancer risk in BRCA2 mutation carriers

Germline mutations in the BRCA1 and BRCA2 genes confer a high lifetime risk of developing breast and other cancers; however, remarkable differences exist regarding disease manifestation in mutation carriers. It has been suggested that other genetic and/or environmental factors modify not only the appearance but also the age of onset and type of tumor in BRCA1/2-associated cases. The aim of the present study was to investigate the role of two p53 polymorphisms (c.97-147ins16bp and c.215c>g, p.Arg72Pro) as potential modifiers. For this purpose we investigated the possible association between the two polymorphisms and disease status in 447 BRCA1/2 mutation carriers belonging to 170 Spanish breast and/or ovarian cancer families. Genotype and haplotype analyses revealed that the presence of a specific haplotype carrying the allele without the 16-bp insertion and the variant allele for the Arg72Pro (No Ins-72Pro haplotype) was associated with an earlier age of onset in BRCA2 mutation carriers. We found an increased risk of developing a first primary tumor (breast or ovarian) before 35 years of age for individuals who carried at least one No Ins-72Pro haplotype (OR: 2.69; 95% CI: 1.15-6.29; P=0.022). We confirmed these data by a functional study in which we compared different p53 genotypes in relation to their apoptotic response after cell treatment with a cytotoxic drug (AraC). Our results revealed a decrease in p53 apoptotic rate associated with the No Ins-72Pro haplotype.     

Absence of p53 gene mutation and infrequent overexpression of p53 protein in hepatoblastoma

Ten cases of hepatoblastoma were studies for overexpression of p53 protein by immunohistochemistry and for possible p53 gene mutation by single strand conformation polymorphism (SSCP) analysis and direct DNA sequencing of the polymerase chain reaction products. Only one case of the macrotrabecular type at stage IV showed overexpression of p53 protein. No DNA mobility shift was found in any of the cases studies by SSCP analysis. DNA sequencing performed on the case showing overexpression of p53 protein revealed no mutation within exons 5 to 8. The associated adrenal cortical carcinoma of the same case also showed overexpression of p53 protein, but no mutation of the p53 gene. These results indicate that mutation of the p53 gene is infrequent in hepatoblastoma. This observation supports the view that mutation of the p53 gene is not as important in the oncogenesis of childhood neoplasms as in adult cancers.     

MUT‐TP53 2.0: a novel versatile matrix for statistical analysis of TP53 mutations in human cancera

Analysis of the literature reporting p53 mutations shows that 8% of report display typographical mistakes with a notable increase in recent years. These errors are sometimes isolated, but in some cases, they concern several or even all mutations described in a single article. Furthermore, some works report unusual profile of p53 mutations whose accuracy is difficult to assess. To handle these problems we have developed MUT‐TP53 2.0, an accurate and powerful tool that will automatically handle p53 mutations and generate tables ready for publication that will lower the risk of typographical errors. Furthermore, using functional and statistical information issued from the UMD p53 database, it allows to assess the biological activity and the likelihood of every p53 mutant. Hum Mutat 31:1020–1025, 2010. © 2010 Wiley‐Liss, Inc.     

TP53 polymorphisms in gliomas from Indian patients: Study of codon 72 genotype, rs1642785, rs1800370 and 16 base pair insertion in intron-3

Several single nucleotide polymorphisms of the TP53 gene have been reported, amongst which polymorphism in codon 72 (rs1042522) has received significant attention and shown to be associated with disease susceptibility in different cancer types. However, there are variable reports on this polymorphism in gliomas from worldwide with inconsistent results. In addition, the implications of other polymorphic loci are not much explored in gliomas. Hence, in the present study the TP53 sequence was analyzed for all polymorphism and mutations in a total of 84 gliomas of different types and grades from patients of Indian origin. The complete sequence of all coding exons (2 to 11) and introns 2, 3, 5 and 8 of TP53 gene were studied while for introns 1, 4, 6, 7, 9 and 10, only exon flanking regions could be studied. The polymorphic loci were compared with control population. In addition to the well known codon 72 polymorphism (rs1042522), three other polymorphisms rs1642785, rs1800370 and a 16 base pair insertion in intron-3 were found. At codon 72, our study showed higher Arg/Arg genotype in gliomas compared to normal population (38% versus 13%). The Arg allele frequency in glioma patients was comparatively higher than controls (0.55 versus 0.45; P = 0.037). The Arg allele frequency was also high in adult glioblastomas compared to paediatric counterparts (0.55 versus 0.36). However, there was no significant association of TP53 mutations with any genotype of codon 72. At rs1642785, the G allele frequency was significantly higher in gliomas than in control population (0.55 versus 0.36, P = 0.005). The genotype at a 16 base pair insertion in intron-3 was almost similar in case and control. However, the polymorphism at rs1800370 was exclusive to gliomas. This is the first report of TP53 gene polymorphism in glioma patients from India. Our study also delineates the frequency of four polymorphisms in gliomas for the first time. The codon 72 variant (rs1042522) and rs1642785 polymorphisms possibly poses risk to glioma development in Indian population. However, the functional significance of these polymorphism needs further elucidation.     

Lack of association of p53 polymorphisms and haplotypes in high and normal tension open angle glaucoma

Background: The final common pathway for open angle glaucoma (OAG) is retinal ganglion cell apoptosis. Polymorphisms in p53, a major regulator of apoptosis, affect the efficiency of cell death induction. Association studies of p53 haplotypes and OAG have had conflicting results. Objective: To examine the association between p53 haplotypes and OAG in a larger white population than in previous reports, and extend the analysis to normal tension glaucoma. Methods: 345 unrelated people with OAG were recruited (283 subjects with high tension glaucoma and 62 with normal tension glaucoma) and compared with 178 age matched controls. Genomic DNA was analysed for the p53 codon 72 Arg/Pro polymorphism as well as for the presence or absence of a 16 bp intron 3 insertion. Results: In this white cohort no association was found between glaucoma (high or normal tension) and either sequence variant or haplotype. Conclusions: The p53 codon 72 Arg/Pro polymorphism is not associated with age of onset or severity of glaucoma.     

白介素-23受体基因多态性与乙肝相关肝细胞癌的易感性研究

目的:探讨白介素-23受体(IL-23R)基因多态性与广西壮族人群乙肝相关肝细胞癌(HCC)易感性的关系。方法:采用聚合酶链反应-限制性片段长度多态性(PCR-RFLP)对84例乙肝表面抗原(HBSAg)阳性HCC患者(病例组)和94例HbsAg阳性体检者(对照组)IL-23R基因rs10889677、rs1884444、rs114658173个位点的单核苷酸多态性进行检测及其部分标本进行直接测序鉴定。采用SHEsis软件构建IL-23R基因3个位点的单体型。Logistic回归分析IL-23R基因多态性和单体型与HCC遗传易感性的关系。结果:IL-23Rrs10889677、rs11465817位点的AA、AC、CC3种基因型和A、C两种等位基因在HCC组与对照组之间的分布差异无统计学意义(P>0.05)。rs1884444位点的TT、TG、GG三种基因型及T、G两种等位基因在病例组和对照组的频率分布差异均有统计学意义(P均<0.05),Logistic回归分析发现携带TG基因型的个体发生HCC的风险较携带TT基因型的个体增加(校正OR=2.20,95%CI=1.11～4.37)。单体型构建发现CGC、AGC、CTC、ATC、CGA、AGA、CTA、ATA等8种单倍体,病例组和对照组的AGC单倍体分布差异有统计学意义(P<0.05),AGC单倍体携带者发生HCC的风险明显增加(校正OR=2.71,95%CI=1.06～6.93)。结论:IL-23R基因rs1884444位点TG基因型可能是HCC发病的危险因子;乙肝背景下AGC单倍体携带者患HCC的风险增加2.71倍,可能是乙肝相关肝癌发病的危险因素。