Cancer Genetics and Cytogenetics

Editorial Board

2010-10-01

Development of a multiplex MethyLight assay for the detection of multigene methylation in human colorectal cancer

2010-10-01

Abstract: In peripheral blood, cell-free methylated DNA has been reported to be a useful biomarker of noninvasive blood screening for the detection of colorectal cancer (CRC), including the genes ALX homeobox 4 (ALX4), septin 9 (SEPT9), or transmembrane protein with EGF-like, and two follistatin-like domains 2 (TMEFF2). Here we report a multiplex MethyLight polymerase chain reaction (PCR) assay that simultaneously detected the methylation status of ALX4, SEPT9, and TMEFF2, as well as quantifying methylation level of these genes in a total of 127 fresh tissue samples and 182 peripheral blood samples from CRC patients. Using the multiplex MethyLight assay, methylated ALX4, SEPT9, and TMEFF2 occurred in 56, 78, and 75% of CRC tissue samples and in 48, 75, and 71% of peripheral blood samples from CRC patients. The sensitivities of the combined study using the three genes as biomarkers for the detection of CRC in primary tissues and peripheral blood samples were 84 and 81%, with specificities of 87 and 90%, respectively. Combining the specificity of real-time PCR, the high throughput of multiplex PCR, and the high sensitivity of multigene detection, this multiplex MethyLight PCR assay may allow for future screening programs with large-scale noninvasive blood testing for early-stage CRC.

Fusion of HMGA2 to COG5 in uterine leiomyoma

2010-10-01

Abstract: Uterine leiomyomas are smooth muscle tumors most commonly seen in middle-aged women. Approximately 10% of these tumors contain rearrangements of the chromatin-remodeling gene HMGA2 at the chromosome band 12q14.3. Herein, we report on a uterine leiomyoma with a novel HMGA2 fusion gene. A 44-year-old woman presented with a 20-cm mass uterine leiomyoma. From a histological standpoint, the tumor exhibited extensive hyalinization, very low mitotic activity (<1/10 HPH), and no cytologic atypia. Smooth muscle differentiation was confirmed by the expression of smooth muscle actin and desmin. Standard cytogenetic analysis showed the reciprocal translocation t(7;12)(q31.2;q14.3). Fluorescence in situ hybridization analysis confirmed a balanced rearrangement of the HMGA2 locus in 80% of the cells. 3'RACE reverse-transcription polymerase chain reaction identified the fusion of HMGA2 exon 4 to the COG5 locus on 7q31 (component of oligomeric golgi complex 5 isoform). The fusion sequence is predicted to encode a 96-amino acid chimeric protein that retains all three DNA-binding domains (AT hooks) of HMGA2, but that is shorter than the original HMGA2 protein. Since the general structure of the fusion gene is similar to other previously described HMGA2 fusions, its biologic activity is predicted to be likely similar.

Deep fibrous histiocytoma with a clonal karyotypic alteration: molecular cytogenetic characterization of a t(16;17)(p13.3;q21.3)

2010-10-01

Abstract: Deep fibrous histiocytoma, a rare lesion occuring in deep soft tissues, has recently been formally characterized as a diagnostically distinguishable variant of the benign fibrous histiocytoma spectrum with distinct morphological features. Nevertheless, because of the small number of cases published, information on their clinical behavior, including propensity for local recurrence and metastasis, is quite limited, and no molecular genetic or cytogenetic data are available. We report a 46,XY,t(16;17)(p13.3;q21.3) karyotype in a deep fibrous histiocytoma. Fluorescence in situ hybridization using bacterial artificial chromosome (BAC) clones refined the translocation breakpoints within 119.9 kb at 16p13.3 and 214 kb at 17q21.3. Moreover, to ascertain whether they may be nonrandomly involved in changes in this rare tumor type, we designed two dual-color break-apart probes with BAC clones, mapping proximally and distally to the two breakpoints, to be tested in additional archival cases by interphase fluorescence in situ hybridization. No break-apart signals were observed in the six additional cases studied, indicating either that the translocation is sporadic or that it is rare in deep fibrous histiocytoma. In conclusion, our data show that chromosome aberrations may be found in deep fibrous histiocytoma and that, as with cutaneous lesions, they may have clonal, at present nonrecurrent, chromosome changes.

ETV6–ARNT fusion in a patient with childhood T lymphoblastic leukemia

2010-10-01

Abstract: The ETS variant gene 6 (ETV6) gene is located at 12p13, and is frequently involved in translocations in various human neoplasms, resulting in the expression of fusion proteins consisting of the amino-terminal part of ETV6 and unrelated transcription factors or protein tyrosine kinases. Leukemia with t(1;12)(q21;p13) was previously described in a 5-year-old boy with acute myeloblastic leukemia (AML-M2) who exhibited a novel ETV6-aryl hydrocarbon receptor nuclear translocator (ARNT) fusion protein. We herein report the case of a 2-year-old boy with T-cell lymphoblastic leukemia (T-ALL) harboring t(1;12)(q21;p13). Fluorescence in situ hybridization (FISH) with a ETV6 dual-color DNA probe revealed that the split signals of the ETV6 gene in 96.7% of bone marrow cells, indicating rearrangement of the ETV6 gene. Therefore, we performed a FISH analysis with bacterial artificial chromosome (BAC) probes containing the ARNT, BCL9, and MLLT11 genes located at 1q21, and these results indicated that the ARNT gene might be involved in the t(1;12)(q21;p13). Reverse transcriptase–polymerase chain reaction analysis disclosed the existence of a ETV6–ARNT fusion gene. To our knowledge, the current report is novel in its report of the ETV6–ARNT fusion in childhood T-ALL. The ETV6–ARNT fusion is associated not only with AML but also with T-ALL.

Novel BRCA1/2 mutations in Serbian breast and breast–ovarian cancer patients with hereditary predisposition

Jelena Dobričić, Mirjana Branković-Magić, Slađana Filipović, Siniša Radulović — 2010-10-01

Abstract: Mutations in breast cancer susceptibility (BRCA) genes lead to defects in DNA repair processes resulting in elevated genome instability and predisposing to breast and ovarian cancer. The study was designed to detect mutational spectra of BRCA1/2 genes in a Serbian population. Using automated DNA sequencing, we tested individuals for BRCA mutations, based on positive family history of either breast or ovarian cancer or both. Two novel mutations (c.4765_4784del in BRCA1 exon 15 and c.4367_4368dupTT in BRCA2 exon 11) were detected, in three probands from two different families. These mutations have not been reported previously in the BIC or LOVD databases. Protein products of these mutated alleles lack domains necessary for their DNA repair functions, an indicator that these are deleterious mutations. Neither mutation was found in any proband from 50 other families with hereditary predisposition, so the two mutations are likely family-specific rather than population-specific. Although BRCA1-associated tumors are typically negative for estrogen receptor (ER), progesterone receptor (PR), and ERBB2, the novel BRCA1 mutation identified in this study was detected in a proband with ER- and PR-positive breast cancer. Steroid receptor–positive BRCA-related breast cancer in this proband supports the idea of characteristic pathological features and older age of onset among BRCA1-mutated ER-positive breast cancers.

Amplification of the RARA gene in acute myeloid leukemia: significant finding or coincidental observation?

Anna D. Asleson, Vickie Morgan, Stephen Smith, Gopalrao V.N. Velagaleti — 2010-10-01

Abstract: Oncogene amplification resulting in aberrant expression, although common in solid tumors, is rare in acute myeloid leukemia (AML) and is mostly associated with amplification of MYC, RUNX1, and MLL genes. Retinoic acid receptor α (RARA) and other target sequences at 17p11.2 often represent the amplicons expressed in breast cancer, not in AML. We present a unique case of a 59-year-old female with a history of breast cancer, now presenting with pancytopenia and bilateral infiltration with effusion in nodules of the right upper lobe of the lung. She was diagnosed with AML-M5. Chromosome analysis demonstrated a hypodiploid clone with complex numerical/structural abnormalities including 5q deletion, monosomy 7, as well as structurally rearranged chromosome 11 and several marker chromosomes. Fluorescence in situ hybridization (FISH) analysis showed amplification of RARA, loss of 7q, monosomy 7, loss of DEK (6p23), and additional copies of NUP214 (9q34) and MLL (11q23). Additional FISH studies showed both ERBB2 and TOP2A genes, which were co-amplified on one of the marker chromosomes. The follow-up bone marrow did not yield any metaphases, but FISH was normal for all probes, including RARA. After a short remission, the patient relapsed and showed clonal evolution. Additional case reports are necessary to assess whether RARA amplification in hematologic malignancies serves as an independent prognostic factor.

A case of angioimmunoblastic T-cell non-Hodgkin lymphoma with a neocentric inv dup(1)

Eric Blom, Fenna H. Heyning, Wilma G.M. Kroes — 2010-10-01

Abstract: Neocentromeres are rare epigenetic phenomena in which functional centromeres are formed onto novel chromosomal locations without any α-satellite DNA. To date, constitutional human neocentromeres have been reported in at least 90 cases. In cancer, however, the knowledge is much more limited. Acquired neocentromeres have been described in a particular class of lipomatous tumors (atypical lipomas and well-differentiated liposarcomas; ALP-WDLPS), three cases of acute myeloid leukemia (AML), one case of non-Hodgkin lymphoma (NHL), and one case of lung carcinoma. Here, we report on a 66-year-old male with angioimmunoblastic T-cell NHL. Cytogenetic analysis of his bone marrow showed multiple aberrations, including the presence of a supernumerary chromosome. Using the fluorescence in situ hybridization technique, the supernumerary chromosome was demonstrated to be entirely composed of material derived from chromosome 1. It represented an inverted duplication of the segments between 1q21 and 1qter with a neocentromere in band 1q31. To our knowledge, this is the second reported case of NHL (both T-cell) with the presence of a neocentromere. The occurrence of neocentromeres in tumor cells, however, may be underestimated because of technical limitations during the routine diagnostic chromosomal analysis. The prognostic impact is therefore currently unknown.

Acute myeloid leukemia associated with t(10;17)(p13-15;q12-21) and phagocytic activity by leukemic blasts: a clinical study and review of the literature

2010-10-01

Abstract: Translocation (10;17)(p13-15;q12-21) in acute leukemia is rarely reported in the literature. Here, we present both a novel t(10;17) case study and a review of relevant literature on t(10;17) in acute leukemia (10 cases). In summary, we came to the following preliminary conclusions: t(10;17) is associated with poorly differentiated acute leukemia subtype [90%; eight cases of acute myeloid leukemia (AML M0, M1) and one case of acute undifferentiated leukemia], phagocytic activity by blasts occurs (30%), and the survival time was short in three of the seven t(10;17) cases for whom follow-up data were available (median, 8 months). More clinical studies concerning the prognosis, treatment response, and survival of patients with t(10;17) are necessary.

Characterization of FRA7B, a human common fragile site mapped at the 7p chromosome terminal region

Nazario Bosco, Franca Pelliccia, Angela Rocchi — 2010-10-01

Abstract: Common fragile sites (CFS) are specific regions of the mammalian chromosomes that are particularly prone to gaps and breaks. They are a cause of genome instability, and the location of many CFS correlates with breakpoints of aberrations recurrent in some cancers. The molecular characterization of some CFS has not clarified the causes of their fragility. In this work, by using fluorescence in situ hybridization analysis with BAC and PAC clones, we determined the DNA sequence of the CFS FRA7B. The FRA7B sequence was then analyzed to identify coding sequences and some structural features possibly involved in fragility. FRA7B spans about 12.2 megabases, and is therefore one of the largest CFS analyzed. It maps at the 7p21.3-22.3 chromosome bands, therefore at the interface of G- and R-band regions that are probably difficult to replicate. A 90-kilobase long sequence that presents very high flexibility values was identified at the very beginning of the more fragile CFS region. Three large genes (THSD7A, SDK1, and MAD1L1) and two miRNA genes (MIRN589 and MIRN339) map in the fragile region. The chromosome band 7p22 is a recurrent breakpoint in chromosome abnormalities in different types of neoplasm. FRA7B is the first characterized CFS located in a chromosome terminal region.

Cell culture and senescence in uterine fibroids

2010-10-01

Abstract: The in vitro growth of cells from uterine fibroids is characterized by an early onset of senescence. Often, an even lower growth potential than that of matching myometrial cells is noted. Also, the tremendous differences in the expression of the high mobility group protein HMGA2 seen when comparing fibroids of different genetic subtypes are surprisingly not reflected by significant differences in their growth potential in vitro. We aimed to evaluate possible changes of the HMGA2 expression level between the native tissue and cell cultures, so we performed quantitative real-time polymerase chain reaction studies that revealed a marked decrease of the HMGA2 mRNA in culture in those cases with overexpression of HMGA2. In the two cases initially showing the highest expression, it decreased by approximately 97%. Associated with the decrease of HMGA2 was a clearly increased expression of the senescence-associated p19Arf. Together, these findings explain the similar behavior of cell cultures from fibroids of different genetic subgroups and may also offer an explanation for the early onset of in vitro senescence in these cell cultures.

Array comparative genomic hybridization in the detection of chromosomal abnormalities in T-cell prolymphocytic leukemia

2010-10-01

T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive disease derived from mature T cells . In T-PLL, the karyotype is usually complex and characterized by the presence of multiple chromosomal changes. Chromosome aberrations involving the T-cell receptor α and δ locus genes (TRA@ and TRD@; hereafter referred to as TCRα/δ) on chromosome subband 14q11.2; are primary oncogenic events in this disorder. These aberrations lead to deregulated transcription of targeted oncogenes by their juxtaposition with the TCRα/δ regulatory sequences. Recurring chromosomal lesions include inversion or translocation involving the TCL1A locus (alias TCL1) , that is, inv(14)(q11.2q32.3) or t(14;14)(q11.2;q32.3).

MYC in gastric carcinoma and intestinal metaplasia of young adults

2010-10-01

MYC has a key role in gastric carcinogenesis. We evaluated MYC copy number and protein expression in non-neoplasic, intestinal metaplasia, and gastric cancer samples from five young adults. We observed a significant increase of MYC amplification with the evolution of carcinogenesis process. MYC overexpression was observed in intestinal metaplasia and neoplastic tissue from all patients with intestinal-type gastric cancer and from no patients with diffuse type. MYC copy number and expression can be biomarkers of gastric malignance.

Analysis of the frequency of GNAS codon 201 mutations in advanced colorectal cancer

S. Idziaszczyk, C.H. Wilson, C.G. Smith, D.J. Adams, J.P. Cheadle — 2010-10-01

With the advancement of massively parallel sequencing technologies and the advent of the International Cancer Genome Consortium (ICGC), we are poised to see an exponential growth of sequencing data for numerous types of cancers. These data will allow identification of countless somatic mutations that cause cancers and will be a significant driver for cancer research, thus enabling the identification of new targets for therapy.

2010-10-01

Cancer Genetics and Cytogenetics

Editorial Board

Development of a multiplex MethyLight assay for the detection of multigene methylation in human colorectal cancer

Fusion of HMGA2 to COG5 in uterine leiomyoma

Deep fibrous histiocytoma with a clonal karyotypic alteration: molecular cytogenetic characterization of a t(16;17)(p13.3;q21.3)

ETV6–ARNT fusion in a patient with childhood T lymphoblastic leukemia

Novel BRCA1/2 mutations in Serbian breast and breast–ovarian cancer patients with hereditary predisposition

Amplification of the RARA gene in acute myeloid leukemia: significant finding or coincidental observation?

A case of angioimmunoblastic T-cell non-Hodgkin lymphoma with a neocentric inv dup(1)

Acute myeloid leukemia associated with t(10;17)(p13-15;q12-21) and phagocytic activity by leukemic blasts: a clinical study and review of the literature

Characterization of FRA7B, a human common fragile site mapped at the 7p chromosome terminal region

Cell culture and senescence in uterine fibroids

Array comparative genomic hybridization in the detection of chromosomal abnormalities in T-cell prolymphocytic leukemia

MYC in gastric carcinoma and intestinal metaplasia of young adults

Analysis of the frequency of GNAS codon 201 mutations in advanced colorectal cancer

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