Array-CGH shows amplification of 8q including MYC as the sole aberration in a leiomyosarcoma of the female lower genital tract.

Leiomyosarcomas (LMS) are uncommon in the female genital tract, and the literature on LMS of the vagina consists mostly of case reports. We report the cytogenetic, FISH and array-CGH findings in a LMS of the vagina. Tumor microscopy showed a cellular spindle cell tumor composed of oval to spindly cells arranged in sheets or fascicles supported by a rich vascular network and stained positive for smooth muscle markers (SMA, HHF35). The majority of metaphase cells from the short-term cultures of tumor cells had 49 chromosomes including 3 copies of a derivative chromosome that consisted in most part of 8q material. The remaining cells had 4 copies of the derivative chromosome. FISH studies showed that each derivative chromosome consisted in its entirety of chromosome 8 material, had 2 copies of MYC and 8qter signals, lacked an 8pter signal, and was devoid of a centromeric alpha satellite or satellite III signal of any of the 24 chromosomes. Strong positive staining for MYC was demonstrated in tumor nuclei. Microarray-CGH study on DNA extracted from the tumor confirmed amplification of 8q12.1∼q22.2 and 8q24.13∼qter, and to a lesser extent 8q22.3∼q24.12, as the sole genetic abnormality in the tumor. The present report, to the best of our knowledge, is the first cytogenetically characterized primary LMS of the vagina, and our findings indicate that amplification of 8q including MYC is a primary genetic abnormality as well as a pathway of evolution in the tumor.

Loss of 17p is a major consequence of whole-arm chromosome translocations in hematologic malignancies.

To ascertain the distribution of whole-arm translocations (WATs) and their consequential imbalances in hematologic malignancies, we analyzed the imbalances related to chromosomes involved in clonal, acquired WATs in 140 consecutive tumors with WATs and near-diploid karyotypes. Tumors for analysis were obtained from a survey of the cytogenetic database in the Department of Medical Genetics, Henry Ford Health System, Detroit, MI. Of the 140 tumors, 9 had balanced WATs; the remaining 131 had WATs that rarely or never involved chromosome X, Y, 2, 3, 4, 6, 19, or 20. Chromosome arms were lost more often than they were gained, and short arms were lost more often than long arms, except for chromosomes 7 and 16 (more long arms lost than short) and chromosome 11 (both arms equally lost). The long arm of chromosome 1 was the only arm gained with substantial frequency, in 26% of tumors. Of WATs that resulted in gain of 1q, short arm of chromosome 7 and acrocentric long arms were involved in 47 and 24%, respectively. Acrocentric chromosomes were involved in acquired WATs in 45% of tumors (the D-group acrocentrics more than the G-group), and were more likely to be involved in non-Robertsonian than Robertsonian translocations (P < 0.001, normal test). Loss of 17p was the most common short-arm loss (23% of tumors) and often occurred as part of complex karyotypes suggestive of disease progression. The present findings show that acquired whole-arm chromosome translocations in hematologic malignancies are nonrandom, commonly involve acrocentric chromosomes, and often result in loss of 17p, which is often associated with advanced disease and poor prognosis in a wide spectrum of hematologic malignancies.

Isochromosome (X)(p10) in hematologic disorders: FISH study of 14 new cases show three types of centromere signal patterns.

Though X chromosome anomalies are uncommon in hematologic malignancies, isodicentric X chromosomes, idic(X)(q13), with break and fusion points at Xq13 are well known among older females with de novo myelodysplasia. In contrast, only 17 patients with X isochromosomes involving break and fusion points at the centromere i(X)(p10) have been published, to our knowledge. We present 14 new patients with i(X)(p10) identified by G-banding and further characterized by fluorescence in situ hybridization (FISH) using probes for the X p-arm, X alpha-satellite DNA (DXZ1), and the XIST gene (Xq13). These anomalies each had an X p-arm probe signal on either side of a single centromeric FISH signal, thus they are monocentric isochromosomes. On the basis of FISH, the following three centromeric patterns were identified: (1) centromere signal same size as normal X, (2) centromere signal larger than normal X, and (3) centromere signal smaller than normal X. These centromere patterns may be related to the mechanism of i(X)(p10) formation. In 9 (64%) of 14 patients, the i(X)(p10) was the sole anomaly, attesting to its pathogenic potential. Our series, when collated with information on previously reported cases of i(X)(p10), show that this anomaly is associated with females with a median age 74 years, though patients from 3.75 to 49 years, including a 17-year-old in the present cohort, have been described. i(X)(p10) is observed in a wide range of hematologic malignancies, including myeloid and lymphoid disorders, as well as a patient with therapy-related AML in the present series. i(X)(p10) has been reported in occasional males, indicating that this anomaly can arise from active X chromosomes. It is not known whether i(X)(p10) arises randomly from the active or inactive X chromosome in female patients.

Activated mitogen-activated protein kinase expression during human breast tumorigenesis and breast cancer progression.

PURPOSE: The purpose of this study is to address the hypothesis that activatedmitogen-activated protein kinase (MAPK; extracellular signal-regulated kinases 1 and 2) has a role in breast tumorigenesis, breast cancer progression, and the development of tamoxifen resistance. EXPERIMENTAL DESIGN: H-score analysis and a specific antibody for the immunohistochemical detection of activated MAPK in formalin-fixed, paraffin-embedded tissue sections were used to compare expression in: (a) human breast tumors and their matched adjacent normal breast tissue; (b) primary human breast tumors and their matched lymph node metastases; and (c) primary breast tumors from patients who later proved to be sensitive or resistant to tamoxifen treatment. RESULTS: Active MAPK expression was detected in 48% of primary human breast tumors and was significantly increased in tumors compared with adjacent normal breast (Wilcoxon test, P = 0.027). A significant positive association (chi(2), P = 0.02; n = 55) was obtained between active MAPK and the presence of lymph node metastases. Moreover, increased active MAPK (Wilcoxon test, P = 0.0098) was found in concurrent lymph node metastases compared with primary breast tumors. No significant difference in active MAPK was found in primary tumors of patients who later responded to tamoxifen or did not respond to tamoxifen. CONCLUSIONS: These data suggest that active MAPK is a marker of breast cancer metastasis and has a role in the metastatic process. However, active MAPK is unlikely to be a marker of endocrine sensitivity or involved in de novo tamoxifen resistance.

Phospho-serine-118 estrogen receptor-alpha detection in human breast tumors in vivo.

PURPOSE: To determine whether estrogen receptor (ER)-alpha specifically phosphorylated at Ser(118) is detectable in multiple human breast cancer biopsy samples. To gain insight into possible roles for P-Ser(118)-ERalpha in human breast cancer in vivo. EXPERIMENTAL DESIGN: A specific antibody for P-Ser(118)-ERalpha was validated for immunohistochemistry (IHC), and Western blot analysis confirmed IHC results. IHC was used to determine the relationship of P-Ser(118)-ERalpha to known prognostic markers and active mitogen-activated protein kinase (MAPK; erk1/2) expression. RESULTS: P-Ser(118)-ERalpha was significantly correlated with the expression of total ER, determined by ligand binding assay (r = 0.442, P = 0.002), but not with progesterone receptor expression or nodal status. P-Ser(118)-ERalpha was inversely correlated with histological grade (r = -0.34, P = 0.023), reflecting a similar trend for total ER (r = -0.287, P = 0.056). Categorical contingency analysis confirmed that P-Ser(118)-ERalpha was more frequently associated with lower than higher grade breast tumors (P = 0.038). In addition P-Ser(118)-ERalpha was significantly associated with detection of active MAPK (Erk1/2; Spearman r = 0.649, P < 0.0001; Fisher's exact test, P = 0.0004). CONCLUSIONS: P-Ser(118)-ERalpha detection is associated with a more differentiated phenotype and other markers of good prognosis in human breast cancer. P-Ser(118)-ERalpha is correlated with active MAPK in human breast tumor biopsies, suggesting the possibility that active MAPK either directly or indirectly has a role in the regulation of P-Ser(118)-ERalpha expression in vivo. These data provide evidence for a role of P-Ser(118)-ERalpha in human breast cancer in vivo.

Analysis of gene expression in ductal carcinoma in situ of the breast.

PURPOSE: The risk of recurrence and progression of ductal carcinoma in situ (DCIS) of the breast is best designated by morphological indicators, including the presence of necrosis. Our purpose was to identify molecular alterations underlying progression of DCIS. EXPERIMENTAL DESIGN: We have compared gene expression within a cohort of six cases of DCIS with necrosis (DCIS(necrosis+)) and four cases without necrosis (DCIS(necrosis-)) using microdissection and cDNA microarray. RESULTS: A set of 69 cDNAs from a group of 1,181 was identified that were consistently differentially expressed. Among this set, the mRNA for angio-associated migratory cell protein and a serine threonine protein kinase, nuclear Dbf2 related, were consistently higher in DCIS(necrosis+) and were also found to be overexpressed in the T47D breast cancer cell line subjected to hypoxia. Further study of angio-associated migratory cell protein by quantitative reverse transcriptase-PCR and in situ hybridization analysis of 37 cases of DCIS confirmed higher mRNA expression in DCIS(necrosis+) (P = 0.0095). CONCLUSIONS: This study shows that although levels of gene expression are mostly similar between morphologically different DCIS, consistent differences in expression of a subset of genes can be identified between DCIS with and without necrosis.

Comparative cytogenetic and DNA flow cytometric analysis of 242 primary breast carcinomas.

The cytogenetic and DNA flow cytometric findings in 242 breast carcinomas were compared. The combined use of both techniques improved the detection of abnormal cell populations from 65% by cytogenetic analysis alone and 59% by DNA flow cytometric analysis alone to 84%. Informative and comparable cytogenetic and flow cytometric data were obtained for 155 tumors. Among these 155 tumors, there was good concordance (64%) between the estimates of genomic changes by the two methods. Most discrepancies were among the DNA-diploid cases, where cytogenetic analysis detected small genomic changes. There were, however, also some exceptions in which large genomic changes detected by one method were missed by the other. Of the specific breast cancer-associated cytogenetic aberrations subjected to separate correlation analysis, polysomy for chromosome 20 was significantly associated with a high S-phase fraction, whereas loss of the long arm of chromosome 16 and/or the presence of a der(1;16) were significantly associated with a low S-phase fraction. Our data show that cytogenetic and DNA flow cytometric analyses of breast carcinomas give largely comparable results, and that combining data from both methods significantly improves the information obtained by either technique used alone on the genetic abnormalities in these tumors.

Cytogenetics of chronic myeloproliferative disorders and related myelodysplastic syndromes.

The only MPD associated with any specific chromosome anomaly is CML, which is linked with t(9;22)(q34;q11.2) or a variant of this anomaly. An association exists for del(13)(q12q14) and CIMF; t(5;12)(q33;p13) and CEL; and del(20q11), +8, and +9 and PV, but these anomalies can be seen in various hematologic malignancies. The most common chromosomal anomalies among MPD in order of frequency are t(9;22)(q34;q11.2), -Y, +8, +9, -7, del(20) (q11q13), del(13)(q12q14), del(5)(q13q33), and del(12)(p12). FISH techniques are useful for MPD to study inadequate bone marrow or blood specimens and to monitor disease status among patients with known chromosome anomalies, but they are not more sensitive than conventional chromosome studies.

Marker chromosomes are a significant mechanism of high-level RUNX1 gene amplification in hematologic malignancies.

To understand the cytogenetic mechanisms responsible for multiple RUNX1 gene copy numbers in hematologic malignancies, we analyzed the chromosomal and molecular cytogenetic findings in bone marrow or peripheral blood samples of individuals who were diagnosed with acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), or acute lymphoblastic leukemia (ALL). Included in the analysis were 113 consecutive samples received in our laboratory between January 2005 and June 2007. Bone marrow and/or peripheral blood samples were characterized using conventional G-banding techniques and fluorescent in situ hybridization (FISH) techniques with commercially available RUNX1/RUNX1T1 or ETV6/RUNX1 dual-color fusion probes. Eighty-one (72%) of the 113 samples showed an abnormal karyotype and/or abnormal FISH results. Eight of these had, by interphase FISH, RUNX1/RUNX1T1 or RUNX1/ETV6 fusion, and 19 had three or more RUNX1 signals not related to fusion with RUNX1T1 or ETV6 gene. Of the 19 cases with multiple RUNX1 gene signals, 5 had high-level RUNX1 amplification--defined as 5 or more RUNX1 signals in interphase cells--whereas the remaining 14 had 3-4 RUNX1 signals. Four of the five tumors with high-level RUNX1 amplification were myeloid disorders--three cases of AML and one case of MDS. The karyotypes of tumors with high-level amplification of RUNX1 were significantly characterized by the presence of marker chromosomes that harbored extra copies of the RUNX1 gene compared with tumors that had three to four RUNX1 gene signals (P=0.026, Fisher's exact test). Our findings show that high-level RUNX1 amplification, especially in myeloid disorders, often results from marker chromosomes harboring extra copies of the RUNX1 gene . This suggests that amplification of RUNX1 in these tumors may be secondary to a previous rearrangement of 21q22, which later evolved into a complex marker chromosome as part of tumor progression.

Subtelomere deletions and translocations are frequently familial.

In recent years, strategies have been developed to investigate the possible role of chromosomal subtelomere regions in genetic disorders. The present study was to determine the incidence of familial subtelomeric abnormalities among individuals with developmental delay, idiopathic mental retardation, or non-specific congenital abnormalities. A review was conducted for patients and their relatives on whom subtelomeric DNA fluorescence in situ hybridization (telo-FISH) studies were performed. Patients were identified through a search of the Mayo Genetics System (MGS) database. Of 2,170 consecutive telo-FISH index case studies completed in our laboratory between January 2002 and December 2003, 121 or 5.6% had abnormalities of the subtelomere region. The present report includes 18 other abnormal index cases seen prior to 2002 to yield a total of 139 abnormal index cases. This represents 71 index patients with deletions, 53 index patients with derivative chromosomes, and 15 index patients with balanced rearrangements. A familial abnormality was identified in 29 (51.8%) of 56 families in whom parents and/or sibs were available for testing. Among 28 patients with deletions, 9 (32%) had an inherited deletion, whereas 19 (68%) were de novo. Family members of 20 index patients with derivative chromosomes were tested. Of these, 13 (65%) patients inherited the abnormality from a parent (12 from a parent who had a balanced translocation and 1 from a parent with the same abnormality), while 7 (35%) apparently arose de novo. Seven (88%) of 8 with balanced translocations inherited the translocation from one parent. The most common familial abnormalities involved 8pter deletion or rearrangement. The incidence of familial subtelomeric abnormalities is significantly high making parental telo-FISH studies an essential part of the investigation of patients with subtelomeric chromosome abnormalities.

Relationship of patient survival and chromosome anomalies detected in metaphase and/or interphase cells at diagnosis of myeloma.

The clinical efficacy of evaluating genetic anomalies in metaphase cells versus interphase nuclei for multiple myeloma (MM) is poorly understood. Therefore, survival for 154 patients with newly diagnosed untreated MM was compared with results from analysis of metaphase and interphase cells. Metaphases were studied by conventional cytogenetics and fluorescent-labeled DNA probes (fluorescence in situ hybridization [FISH]), whereas inter-phase nuclei were evaluated only by FISH. All FISH studies were done using DNA probes to detect t(4;14)(p16;q32), t(11;14)(q13;q32), t(14;16)(q32;q23), del(17) (p13.1), and chromosome 13 anomalies. Metaphases were abnormal by cytogenetics and/or metaphase FISH in 61 (40%) patients. Abnormal interphase nuclei were observed in 133 (86%) patients, including each patient with abnormal metaphases. FISH was a necessary adjunct to cytogenetics to detect t(4;14) and t(14;16) in metaphase cells. Patient survival was especially poor for patients with greater than 50% abnormal interphase nuclei, although this result was more likely due to level of plasma cells than specific chromosome anomalies. For metaphase data, patients with t(4;14), t(14;16), del(17) (p13.1), and/or chromosome 13 anomalies (primarily monosomy 13) had poor survival. A different outcome was observed for interphase data as patients with t(4;14) or t(14;16) had poor survival, whereas patients with chromosome 13 anomalies had intermediate survival: interphase FISH did not substitute for metaphase analysis.

Familial 22q11.2 deletions in DiGeorge/velocardiofacial syndrome are predominantly smaller than the commonly observed 3Mb.

PURPOSE: DiGeorge/velocardiofacial syndrome (DG/VCFS) is the most common cytogenetically characterized microdeletion of 22q11.2 region. In approximately 90% of patients, the deletion size is 3 Mb, whereas the remaining range from 1.5 to 2.5 Mb. The purpose of this study was to test the hypothesis that small deletions may be more easily tolerated in a familial fashion than larger deletions, especially for this syndrome. METHOD: Sixteen FISH probes designed from bacterial artificial chromosomes (BACs) and P1 artificial chromosomes (PACs) mapped to 22q11.2 were used to determine the deletion sizes in 22 individuals from ten families with familial 22q11.2 deletion detected by standard FISH tests. RESULT: Seven families had deletions of < 3 Mb ( approximately 1.5 Mb) in size and 3 families had the common 3-Mb deletion. The 70% frequency of smaller sized deletions among this group of patients with familial del(22)(q11.2) is significantly higher than that reported among unselected group of patients with del(22)(q11.2) (P < 0.0001, Fisher exact test). CONCLUSION: Familial del(22)(q11.2) are predominantly smaller than the common deletion size of 3 Mb, indicating that there may be some underlying mechanisms that favor parent-to-child transmission of smaller deletions in individuals with del(22)(q11.2), therefore, underscoring the need to exclude a familial basis in cases of del(22)(q11.2) smaller than 3 Mb.

Developmental changes in insulin-like growth factor I receptor gene expression in the mouse mammary gland.

The insulin-like growth factor I receptor (IGF-IR), which mediates the mitogenic action of IGF-I, has been shown to play an essential role in normal growth and development. However, the precise role of IGF-IR in the growth and differentiation of the mammary gland has not been elucidated. This study examines the profile of the IGF-IR gene and protein expression during normal postnatal mammary gland development in order to gain further insight into the role of the IGF-I/IGF-IR during mammary gland morphogenesis. Gene and protein expression were examined in developing mouse mammary glands (virgin, pregnant, lactating, involuting) by real time PCR analysis and Western blotting. Both IGF-IR gene and protein expression levels were high during early pregnancy. Interestingly, the level of gene expression was significantly down-regulated during late pregnancy (5.4 fold) and lactation (9-13 fold) and significantly up-regulated (3.9 fold) during late involution, to the level observed in the virgin mammary gland. By in situ hybridization, the IGF-IR transcripts were localized to the proliferating ductal epithelium of the mammary glands of virgin mice and to the differentiating ductal and alveolar epithelium of the mammary glands during pregnancy and lactation. In the involuting gland, the transcripts were localized to the regressing ductal epithelium. These data are direct evidence that IGF-IR expression is important for alveolar cell proliferation and suggest that the progression of involution may require the down-regulation of IGF-IR gene expression. Altogether, these results demonstrate that a developmental IGF-IR gene expression pattern exists in the mouse mammary gland and that increases in gene expression at specific phases of development may reflect an important role for IGF-I/IGF-IR at those phases of development.

Relationship between mammaglobin expression and estrogen receptor status in breast tumors.

Mammaglobin (SCGB2A2) is a breast-specific member of the secretoglobin (SCGB) gene family. SCGB2A2 has previously been found overexpressed in breast tumors but possible associations between its expression and established prognostic tumor characteristics such as the levels of estrogen and progesterone receptors have not yet been investigated. We evaluated SCGB2A2 expression at the mRNA and at the protein level by reverse-transcription polymerase chain reaction and immunocytochemistry in 52 and 32 breast tumors, respectively. Both SCGB2A2 mRNA and protein expression were significantly higher in estrogen-receptor-positive compared to estrogen-receptor-negative tumors (Mann- Whitney rank sum test, p = 0.04; chi-square test, p = 0.01; respectively). In contrast, SCGB2A2 expression did not correlate with progesterone receptor levels or Nottingham grade. As estrogen and antiestrogen treatment of estrogen-positive breast cancer cell lines does not modify SCGB2A2 expression we suggest that SCGB2A2 may be a new independent breast cancer prognostic marker.

Characterization of a novel breast carcinoma xenograft and cell line derived from a BRCA1 germ-line mutation carrier.

A human tumor xenograft (L56Br-X1) was established from a breast cancer axillary lymph node metastasis of a 53-year-old woman with a BRCA1 germ-line nonsense mutation (1806C>T; Q563X), and a cell line (L56Br-C1) was subsequently derived from the xenograft. The xenograft carries only the mutant BRCA1 allele and expresses mutant BRCA1 mRNA but no BRCA1 protein as determined by immunoprecipitation or Western blotting. The primary tumor, lymph node metastasis, and xenograft were hypodiploid by DNA flow cytometry, whereas the cell line displayed an aneuploidy apparently developed via polyploidization. Cytogenetic analysis, spectral karyotyping, and comparative genomic hybridization of the cell line revealed a highly complex karyotype with numerous unbalanced translocations. The xenograft and cell line had retained a somatic TP53 missense mutation (S215I) originating from the primary tumors, as well as a lack of immunohistochemically detectable expression of steroid hormone receptors, epidermal growth factor receptor, human epidermal growth factor receptor 2 (HER-2), and keratin 8. Global gene expression analysis by cDNA microarrays supported a correlation between the expression profiles of the primary tumor, lymph node metastasis, xenograft, and cell line. We conclude that L56Br-X1 and L56Br-C1 are useful model systems for studies of the pathogenesis and new therapeutic modalities of BRCA1-induced human breast cancer.

Microduplication 22q11.2, an emerging syndrome: clinical, cytogenetic, and molecular analysis of thirteen patients.

Chromosome 22, particularly band 22q11.2, is predisposed to rearrangements due to misalignments of low-copy repeats (LCRs). DiGeorge/velocardiofacial syndrome (DG/VCFS) is a common disorder resulting from microdeletion within the same band. Although both deletion and duplication are expected to occur in equal proportions as reciprocal events caused by LCR-mediated rearrangements, very few microduplications have been identified. We have identified 13 cases of microduplication 22q11.2, primarily by interphase fluorescence in situ hybridization (FISH). The size of the duplications, determined by FISH probes from bacterial artificial chromosomes and P(1) artificial chromosomes, range from 3-4 Mb to 6 Mb, and the exchange points seem to involve an LCR. Molecular analysis based on 15 short tandem repeats confirmed the size of the duplications and indicated that at least 1 of 15 loci has three alleles present. The patients' phenotypes ranged from mild to severe, sharing a tendency for velopharyngeal insufficiency with DG/VCFS but having other distinctive characteristics, as well. Although the present series of patients was ascertained because of some overlapping features with DG/VCF syndromes, the microduplication of 22q11.2 appears to be a new syndrome.