A sequence polymorphism on 8q24 is associated with survival in hepatocellular carcinoma patients who received radiation therapy.

There is a growing consensus that genetic variation in candidate genes can influence cancer progression and treatment effects. In this study, we genotyped the rs9642880 G > T polymorphism using DNA isolated from blood samples of 271 hepatocellular carcinoma (HCC) patients who received radiotherapy treatment. We found that patients who carried the GT or TT genotypes had significantly shorter median survival times (MSTs) compared to patients with the GG genotype (14.6 vs.21.4 months). The multivariate P value was 0.027, the hazard ratio (HR) was 1.38, and the 95% confidence interval was 1.04-1.84. Further analysis revealed that patients with the variant genotypes had an increased risk of poor tumour response to radiotherapy (P = 0.036 and 0.002 for stable disease and progressive disease, respectively) and higher incidence of multiple intrahepatic lesions (P = 0.026) and BCLC C stage (P = 0.027). Moreover, further stratified survival analyses revealed that at least radioresponse and BCLC stage contributed to the association between the rs9642880 G > T polymorphism and survival of HCC patients in this study (P value, 0.017 vs 0.053 for BCLC C stage vs B stage; 0.011 vs 0.531 for radioresponse SD + PD vs CR + PR). These results illustrate the potential association between rs9642880 G > T and survival in HCC patients who received radiotherapy treatment.

Proliferation indices correlate with diagnosis and metastasis in diagnostically challenging melanocytic tumors.

The diagnosis of melanocytic lesions remains a formidable challenge in dermatopathology. For diagnostically challenging lesions, ancillary tests are available to inform the diagnosis, including immunohistochemistry and molecular testing (particularly fluorescence in situ hybridization [FISH]). However, the test result that most robustly informs the diagnosis remains controversial. Thirty-seven diagnostically challenging melanocytic lesions from our consultation service were reviewed. Histopathologic, immunohistochemical, and second-generation FISH results (NeoGenomics; probes 6p25, 8q24, 11q13, 9p21, and centromere 9) were correlated with the final consensus diagnosis and clinical follow-up using logistic regression and Fisher exact test. Based on histopathologic and immunohistochemical features, cases were designated as "favor benign" (n=19) or "favor malignant" (n=18) by a consensus group of up to 7 dermatopathologists. The sensitivity of FISH for the diagnosis of melanoma was 39%, and the specificity was 84%. Univariate logistic regression models for a final diagnosis of melanoma showed that only increased Ki-67-positive dermal tumor cells (≥5%; P=.01) significantly correlated with the diagnosis of melanoma. FISH result did not correlate with the final diagnosis (melanoma or nevus; P=.26). Follow-up (range, 8-29months) was available for 35 cases (19 diagnosed as nevus and 16 as melanoma), and metastases (restricted to sentinel lymph nodes) were detected from 5 melanomas (3 FISH negative and 2 FISH positive). Only increased dermal mitotic figures (>1/mm(2)) correlated with metastases to sentinel lymph nodes (P=.04). Thus, in the classification of diagnostically challenging melanocytic lesions, indices of proliferation emerge as the most informative diagnostic adjuncts-correlating with diagnosis and clinical behavior, respectively.

Cultivation and differentiation change nuclear localization of chromosome centromeres in human mesenchymal stem cells.

Chromosome arrangement in the interphase nucleus is not accidental. Strong evidences support that nuclear localization is an important mechanism of epigenetic regulation of gene expression. The purpose of this research was to identify differences in the localization of centromeres of chromosomes 6, 12, 18 and X in human mesenchymal stem cells depending on differentiation and cultivating time. We analyzed centromere positions in more than 4000 nuclei in 19 mesenchymal stem cell cultures before and after prolonged cultivation and after differentiation into osteogenic and adipogenic directions. We found a centromere reposition of HSAX at late passages and after differentiation in osteogenic direction as well as of HSA12 and HSA18 after adipogenic differentiation. The observed changes of the nuclear structure are new nuclear characteristics of the studied cells which may reflect regulatory changes of gene expression during the studied processes.

Relaxin receptors 1 and 2 and nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) mRNAs are expressed in oral components of developing mice.

OBJECTIVE: Relaxin is a pleiotropic hormone of the insulin-like peptide hormone family that plays an important role in reproductive physiology as well as in fibrosis, angiogenesis, and bone remodelling. It binds to the relaxin family peptide receptors 1 and 2 (Rxfp1 and Rxfp2) and can, in addition and independently, bind and activate the glucocorticoid receptor Nr3c1. Despite the wide-ranging effect of relaxin, the expression patterns of Rxfp1 and 2 during facial development have not been examined. In this study, we aimed to identify the mRNA expression patterns of Rxfp1, Rxfp2, and Nr3c1 in oral tissues during late mouse facial development in order to pinpoint the structures that could be sensitive to relaxin signalling during this period. DESIGN: Rxfp1, Rxfp2, and Nr3c1 mRNAs were identified by in situ hybridization using digoxigenin-labelled riboprobes on coronal sections of mouse heads from embryonic days 13.5 to 18.5. RESULTS: We found that Rxfp1, Rxfp2, and Nr3c1 mRNAs were expressed on the developing maxilla and mandible, Meckel's cartilage, tongue, and tooth primordia between embryonic days 13.5-18.5. CONCLUSIONS: Receptors that bind relaxin were present in developing oral tissues of mice. This finding suggests that relaxin may be involved in the prenatal development of the face.

[Acute myeloid leukemia possibly originating from the same clone of testicular germ cell tumor].

This report describes a 30-year-old man with a testicular germ cell tumor, which later developed into acute myeloid leukemia (AML) with a common chromosomal abnormality. Testicular germ cell tumors had developed at the age of 26. He was successfully treated with surgery followed by chemotherapy.Four years after the onset of the germ cell tumor, he developed pancytopenia with elevated serum LDH. More than 95% of the bone marrow was occupied by blastic cells. These cells were CD13+, CD34+ but CD45- and MPO-. Amplification of the short arm of chromosome 12 was recognized by fluorescence in situ hybridization using the blastic cells in the bone marrow and the previous testicular tumor specimen. Because testicular germ cell tumor recurrence and other malignant tumors could be ruled out pathologically, he was diagnosed as having AML.Allogeneic stem cell transplantation from a HLA-matched sibling donor was performed after chemotherapy. As of 19 months after the transplantation, recurrence of neither AML nor testicular tumors has been observed. Because the same genetic abnormality was observed in the testicular germ cell tumor and AML in this case, the possibility of AML having a common origin with the testicular germ cell tumor is indicated.

Tertiary trisomy of 10p15.pter and 14pter.ql3 due to maternal translocation t(10;14)(p15;q13).

Double partial trisomy resulting from 3:1 segregation of the respective chromosomal segments of the chromosomes involved in a balanced translocation in meiosis is rarely reported in the literature. We present here a first patient with multiple congenital malformations associated with double partial trisomy of 10pter-p15 and 14pter-q13 resulting from 3:1 segregation of maternal balanced translocation t(10;14)(p15;q13). Proximal partial trisomy of chromosome 14 and subterminal trisomy of the short arm of the chromosome 10 are rare. The present case is the first case with double partial trisomy of these segments resulting from 3:1 segregation of a maternal balanced translocation.

Double partial trisomy of 6p23-pter and 9pter-q21.2 in a neonate resulting from 4:2 meiotic segregation of a maternal complex t(6;7;9)(p23;p15;q21.2) translocation.

We report, a newborn presenting multiple congenital abnormalities with karyotype; 47,XY,der(7)t(6;7)(pter-p23::p15-->qter),+der(9)t(7;9)(pter-->p15::q21.2--> pter)t(6;7;9)(p23;p15;q21.2)mat[20]. The mother and her phenotypically normal daughter were carriers of a complex chromosomal rearrangement with karyotypes; 46,XX,t(6;7;9)(p23;p15;q21.2)[20]. Paternal chromosomes were normal. In our case the extra derivative chromosome was the result of a 4:2 segregation of the chromosomes involved in translocation during oogenesis. Double partial trisomy in newborns resulting from 4:2 segregation is a rare event, and double partial trisomies of the 6p23-pter and trisomy 9pter-q22 regions have not reported to date.

HPV type-related chromosomal profiles in high-grade cervical intraepithelial neoplasia.

BACKGROUND: The development of cervical cancer and its high-grade precursor lesions (Cervical Intraepithelial Neoplasia grade 2/3 [CIN2/3]) result from a persistent infection with high-risk human papillomavirus (hrHPV) types and the accumulation of (epi)genetic host cell aberrations. Epidemiological studies have demonstrated variable CIN2/3 and cancer risks between different hrHPV types. Recent genomic profiling studies revealed substantial heterogeneity in the chromosomal aberrations detected in morphologically indistinguishable CIN2/3 suggestive of varying cancer risk. The current study aimed to investigate whether CIN2/3 with different hrHPV types vary with respect to their chromosomal profiles, both in terms of the number of aberrations and chromosomal loci affected. METHODS: Chromosomal profiles were determined of 43 p16INK4a-immunopositive CIN2/3 of women with long-term hrHPV infection (≥ 5 years). Sixteen lesions harboured HPV16, 3 HPV18, 14 HPV31, 1 HPV33, 4 HPV45, 1 HPV51, 2 HPV52 and 2 HPV58. RESULTS: Unsupervised hierarchical clustering analysis of the chromosomal profiles revealed two major clusters, characterised by either few or multiple chromosomal aberrations, respectively. A majority of 87.5% of lesions with HPV16 were in the cluster with relatively few aberrations, whereas no such unbalanced distribution was seen for lesions harbouring other hrHPV types. Analysis of the two most prevalent types (HPV16 and HPV31) in this data set revealed a three-fold increase in the number of losses in lesions with HPV31 compared to HPV16-positive lesions. In particular, losses at chromosomes 2q, 4p, 4q, 6p, 6q, 8q & 17p and gain at 1p & 1q were significantly more frequent in HPV31-positive lesions (FDR < 0.2). CONCLUSIONS: Chromosomal aberrations in CIN2/3 are at least in part related to the hrHPV type present. The relatively low number of chromosomal aberrations observed in HPV16-positive CIN2/3 suggests that the development of these lesions is less dependent on genetic insult than those caused by other types like HPV31.

Bilateral renal tumors; conventional clear cell carcinoma and contralateral t(6;11)/t(X;17)-like tumor Histomorphologic, immunohistochemical, ultrastructural and molecular genetic studies including the report of a novel mutation in the VHL gene.

A 34-year-old pregnant woman with bilateral kidney tumors 9.5 and 2.5 cm in maximum diameter is presented. The larger tumor was clear renal cell carcinoma. The smaller contralateral tumor was focally HMB45 positive and had unusual histomorphology, including features resembling clear renal cell carcinoma with features of both t(6;11)- and t(X;17)/ASPL-TFE3 carcinomas. This tumor displayed a complex karyotype. A novel germ line mutation in the VHL gene (c.439A>G/p.I147V) was also identified in this patient.

Genetic alterations in children and adolescents with acute myeloid leukaemia.

Acute Myeloid Leukemia is a clinically and genetically heterogeneous disease, in which cytogenetic aberrations are the most important factors to determine biological behavior and prognosis. More than 20 different chromosomal abnormalities have been identified in a high percentage of children (70-85%) with the novo AML. We reviewed the most frequently found and the impact of these aberrations on prognosis. Differences according to the age of patients and mainly in relation to adult population have been enhanced, although the low incidence of AML in children and the high number of abnormalities make difficult to accurately define the prognosis significance of these aberrations.

The prognostic value of Ki-67, p53, epidermal growth factor receptor, 1p36, 9p21, 10q23, and 17p13 in skull base chordomas.

CONTEXT: Skull base chordomas are rare, locally aggressive, notochord-derived neoplasms for which prognostically relevant biomarkers are not well established. OBJECTIVE: To evaluate whether newly discovered molecular alterations in chordomas have prognostic significance similar to what has been described regarding Ki-67 proliferation index. DESIGN: We conducted a retrospective study of 28 cases of primary clival chordomas. RESULTS: Ki-67 proliferation index 5% or more, p53 accumulation, and epidermal growth factor receptor expression were seen in 32%, 44%, and 8% of chordomas, respectively. 1p loss of heterozygosity (LOH) and/or 1p36 hemizygous deletion was seen in 30% of tumors, while 9p LOH and/or 9p21 homozygous deletion was seen in 21% of cases. Loss of heterozygosity at 10q23 and 17p13 were identified in 57% and 52% of cases, respectively. Ki-67 proliferation index 5% or more and 9p LOH were significantly associated with a shorter overall survival, while homozygous deletion at 9p21 via fluorescence in situ hybridization approached significance. No correlation with survival was found for p53 or epidermal growth factor receptor expression, 1p36 hemizygous deletion, or LOH at 1p, 10q23, or 17p13. CONCLUSIONS: Chordomas with elevated Ki-67 proliferation index or deletion at 9p21 may be at risk for a more aggressive clinical course and shorter survival. These biomarkers may thus be used to improve therapeutic stratification.

Association of three genetic loci with uric acid concentration and risk of gout: a genome-wide association study.

BACKGROUND: Hyperuricaemia, a highly heritable trait, is a key risk factor for gout. We aimed to identify novel genes associated with serum uric acid concentration and gout. METHODS: Genome-wide association studies were done for serum uric acid in 7699 participants in the Framingham cohort and in 4148 participants in the Rotterdam cohort. Genome-wide significant single nucleotide polymorphisms (SNPs) were replicated in white (n=11 024) and black (n=3843) individuals who took part in the study of Atherosclerosis Risk in Communities (ARIC). The SNPs that reached genome-wide significant association with uric acid in either the Framingham cohort (p<5.0 x 10(-8)) or the Rotterdam cohort (p<1.0 x 10(-7)) were evaluated with gout. The results obtained in white participants were combined using meta-analysis. FINDINGS: Three loci in the Framingham cohort and two in the Rotterdam cohort showed genome-wide association with uric acid. Top SNPs in each locus were: missense rs16890979 in SLC2A9 (p=7.0 x 10(-168) and 2.9 x 10(-18) for white and black participants, respectively); missense rs2231142 in ABCG2 (p=2.5 x 10(-60) and 9.8 x 10(-4)), and rs1165205 in SLC17A3 (p=3.3 x 10(-26) and 0.33). All SNPs were direction-consistent with gout in white participants: rs16890979 (OR 0.59 per T allele, 95% CI 0.52-0.68, p=7.0 x 10(-14)), rs2231142 (1.74, 1.51-1.99, p=3.3 x 10(-15)), and rs1165205 (0.85, 0.77-0.94, p=0.002). In black participants of the ARIC study, rs2231142 was direction-consistent with gout (1.71, 1.06-2.77, p=0.028). An additive genetic risk score of high-risk alleles at the three loci showed graded associations with uric acid (272-351 mumol/L in the Framingham cohort, 269-386 mumol/L in the Rotterdam cohort, and 303-426 mumol/L in white participants of the ARIC study) and gout (frequency 2-13% in the Framingham cohort, 2-8% in the Rotterdam cohort, and 1-18% in white participants in the ARIC study). INTERPRETATION: We identified three genetic loci associated with uric acid concentration and gout. A score based on genes with a putative role in renal urate handling showed a substantial risk for gout.

Integrative analysis of genomic aberrations associated with prostate cancer progression.

Integrative analysis of genomic aberrations in the context of trancriptomic alterations will lead to a more comprehensive perspective on prostate cancer progression. Genome-wide copy number changes were monitored using array comparative genomic hybridization of laser-capture microdissected prostate cancer samples spanning stages of prostate cancer progression, including precursor lesions, clinically localized disease, and metastatic disease. A total of 62 specific cell populations from 38 patients were profiled. Minimal common regions (MCR) of alterations were defined for each sample type, and metastatic samples displayed the most number of alterations. Clinically localized prostate cancer samples with high Gleason grade resembled metastatic samples with respect to the size of altered regions and number of affected genes. A total of 9 out of 13 MCRs in the putative precursor lesion, high-grade prostatic intraepithelial neoplasia (PIN), showed an overlap with prostate cancer cases (amplifications in 3q29, 5q31.3-q32, 6q27, and 8q24.3 and deletions in 6q22.31, 16p12.2, 17q21.2, and 17q21.31), whereas postatrophic hyperplasia (PAH) did not exhibit this overlap. Interestingly, prostate cancers that do not overexpress ETS family members (i.e., gene fusion-negative prostate cancers) harbor differential aberrations in 1q23, 6q16, 6q21, 10q23, and 10q24. Integrative analysis with matched mRNA profiles identified genetic alterations in several proposed candidate genes implicated in prostate cancer progression.

Characteristics of patients with TEL-AML1-positive acute lymphoblastic leukemia with single or multiple fusions.

BACKGROUND: The TEL-AML1 fusion in precursor-B ALL is generated by a cryptic 12;21 translocation that is detectable by fluorescence in situ hybridization (FISH). It is generally considered a favorable prognostic indicator. Some TEL-AML1+ ALL patients present at diagnosis with extra copies of the fusion, enumerated by FISH. The aim of the study was to determine whether additional copies of TEL-AML1 have clinical significance. PROCEDURE: Charts of all TEL-AML1+ ALL patients at the UM and Children's Hospitals and Clinics of Minnesota between 1996 and 2004 were reviewed. RESULTS: Eight patients (7 males/1 female, mean age 46 months) with two or more TEL-AML1 fusion signals and 24 with single TEL-AML1 fusion signals (18 males/6 females, mean age 52 months) were identified. There was no statistically significant difference in age or gender between the two groups. Patients with double TEL-AML1+ had a higher frequency of myeloid markers CD13 (P = 0.04) or CD33 (P = 0.003) than single TEL-AML1+ patients. Single TEL-AML1+ patients had higher WBC (P = 0.04) than double TEL-AML1+ patients. A trend toward slower therapy response was seen in double TEL-AML1+ patients versus single, (1 of 7 [14%] <5% marrow blasts on Day 7 vs. 13 of 23 [56%], P = 0.09). Double TEL-AML1+ patients had a higher relapse rate (P = 0.09) than single TEL-AML1+ patients. CONCLUSIONS: Utilizing FISH to distinguish subgroups of TEL-AML1 fusion patients may have important prognostic implications. The presence of an extra fusion may portend poorer prognosis. A larger and longer-term follow-up study will be required to verify the possible clinical significance of the presence of multiple TEL-AML1 fusions.

Tumor suppressor gene alterations in respiratory epithelial adenomatoid hamartoma (REAH): comparison to sinonasal adenocarcinoma and inflamed sinonasal mucosa.

Respiratory epithelial adenomatoid hamartoma (REAH) is an unusual benign sinonasal glandular proliferation. REAH is not considered a neoplasm, although, no molecular evidence exists to support or refute this possibility. Microdissection of 10 cases of REAH, 9 cases of sinonasal adenocarcinoma (SNAC) and 10 cases of chronic sinusitis was performed. DNA was extracted and polymerase chain reaction performed using fluorescently labeled primers flanking known tumor suppressor genes on chromosomes 9p (CDKN2/p16), 11p (H-ras), 17p (p53), and 18q (DCC/DPC4). Polymerase chain reaction products were analyzed semiquantitatively by capillary electrophoresis. Allele ratios were calculated using the peak height from the shorter allele divided by the peak height from the longer allele. The loss of heterozygosity (LOH) ratio was calculated as the allele ratio from tumor tissue divided by the allele ratio from normal tissue. The fractional allelic loss (FAL) was calculated as the percentage of loci that harbored LOH divided by the number of loci that were informative. REAH demonstrated an intermediate FAL of 31% compared with SNAC (64%) and chronic sinusitis (2%). REAH and SNAC had the highest LOH for multiple loci located on 9p (p16) and 18q (DCC/DPC4). The molecular profile of REAH shows a mean FAL of 31%, which would be considered unusually high for a non-neoplastic entity. Appreciable allelic loss within REAH suggests the possibility that REAH may be a benign neoplasm rather than a hamartoma.

Clinical and cytogenetic analyses in uveal melanoma.

PURPOSE: Uveal melanoma is one of the most frequently occurring primary intraocular malignancies in the Western world. Cytogenetically these tumors are characterized by typical chromosomal losses and gains, such as loss of 1p, 3, and 6q and gain of 6p and 8q. Whereas most studies focus on known aberrations, in this one, cytogenetic changes were characterized and correlated with clinical and histopathologic parameters. METHODS: Karyotypes of 74 primary uveal melanomas were analyzed with respect to the presence or absence of chromosomal gains and losses. In the analysis, classic clinical and histopathologic parameters were analyzed together with the chromosomal aberrations. RESULTS: At a median follow-up of 43 months, 34 patients had died or had metastatic disease. Clonal chromosomal abnormalities were present in 59 tumors. The most frequent chromosomal abnormalities involved chromosome 8 (53%); loss of chromosome 3, p-arm (41%) and q-arm (42%); partial loss of chromosome 1, p-arm (24%); and abnormalities in chromosome 6 that resulted in gain of 6p (18%) and/or loss of 6q (28%). Less-frequent aberrations were abnormalities in chromosome 16, in particular loss of chromosome 16 q-arm (16%). In the univariate analysis, loss of chromosome 3, largest tumor diameter, gain in 8q, and mixed/epithelioid cell type in the tumor compared with tumors without these chromosomal changes or with a spindle cell type was associated with decreased disease-free survival. When corrected for confounding variables, significance of gain of 8q and cell type was decreased, whereas the significance of loss of chromosome 3p or 3q and largest tumor diameter remained the same. CONCLUSIONS: Monosomy 3 and largest tumor diameter are the most significant in determining survival of patients with uveal melanoma. Abnormalities in the q-arm of chromosome 16 are relatively common in uveal melanoma, but are not associated with survival or other cytogenetic or histopathologic parameters.

Malignant glioma: the involvement of loss of allelic heterozygosity and PTEN mutations in a group of Malay patients.

Frequent loss of heterozygosity (LOH) and mutations of the tumor suppressor gene PTEN (phosphatase and tensin homologue deleted from chromosome 10) have been found in sporadic gliomas. The most documented regions of allelic losses include 9p21, 10q23-25 and 17p1 3 whereas PTEN aberrations are preferentially found in glioblastoma multiformes. This research aimed to detect the incidence of allelic losses on chromosomes 10q, 9p, 17p and 13q and mutations on exons 5, 6 and 8 of PTEN in malignant gliomas. Malignant glioma specimens obtained were classified histopathologically according to the WHO criteria. Each tumor was then subjected to polymerase chain reaction (PCR)-LOH analysis using microsatellite markers and single-stranded conformational polymorphism (SSCP) analysis. Twelve of 23 (52%) malignant glioma cases showed allelic losses whereas 7 of 23 (30%) samples showed aberrant band patterns and mutations of PTEN. Four of these cases showed LOH in 10q23 and mutations of PTEN. The data on LOH indicated the involvement of different genes in the genesis of glioma whereas mutations of PTEN indicated the role of PTEN tumor suppressor gene in the progression of glioma in Malay population.

Renal metanephric adenoma with previously unreported cytogenetic abnormalities: case report and review of the literature.

We report a case of a renal metanephric adenoma in a 10-year-old boy, in which cytogenetic analysis showed a balanced translocation, t(9;15)(p24;q24) and a balanced paracentric inversion of chromosome 12, inv(12)(q13q15). Immunohistochemically, the tumor showed diffuse reactivity for cytokeratin AE1/AE3, CAM5.2, CD57, and WT1; patchy reactivity for CD56; and focal reactivity for cytokeratin 7, epithelial membrane antigen, and CD10. Tumor cells were entirely nonreactive for alpha-methyl acyl coenzyme A racemase. Published cytogenetic data for metanephric adenomas are limited, and this is the first report of these cytogenetic abnormalities. The involvement of the chromosome region 9p24 is particularly interesting because of the recent identification of a tumor suppressor gene, KANK (kidney ankyrin repeat-containing protein), at this locus.