Philip N. Mowrey

Deletions of the PRKAR1A Locus at 17q24.2-q24.3 in Carney Complex: Genotype-Phenotype Correlations and Implications for Genetic Testing

BACKGROUND Carney complex (CNC) is a multiple neoplasia syndrome caused by PRKAR1A-inactivating mutations. One-third of the patients, however, have no detectable PRKAR1A coding sequence defects. Small deletions of the gene were previously reported in few patients, but large deletions of the chromosomal PRKAR1A locus have not been studied systematically in a large cohort of patients with CNC. SETTING A tertiary care referral center was the setting for analysis of an international cohort of patients with CNC. METHODS Methods included genome-wide array analysis followed by fluorescent in situ hybridization, mRNA, and other studies as well as a retrospective analysis of clinical information and phenotype-genotype correlation. RESULTS We detected 17q24.2-q24.3 deletions of varying size that included the PRKAR1A gene in 11 CNC patients (of 51 tested). Quantitative PCR showed that these patients had significantly lower PRKAR1A mRNA levels. Phenotype varied but was generally severe and included manifestations that are not commonly associated with CNC, presumably due to haploinsufficiency of other genes in addition to PRKAR1A. CONCLUSIONS A significant number (21.6%) of patients with CNC that are negative in currently available testing may have PRKAR1A haploinsufficiency due to genomic defects that are not detected by Sanger sequencing. Array-based studies are necessary for diagnostic confirmation of these defects and should be done in patients with unusual and severe phenotypes who are PRKAR1A mutation-negative.

Incidence and patterns of ALK FISH abnormalities seen in a large unselected series of lung carcinomas

BackgroundAnaplastic lymphoma receptor tyrosine kinase (ALK) gene rearrangements have been reported in 2-13% of patients with non-small cell lung cancer (NSCLC). Patients with ALK rearrangements do not respond to EGFR-specific tyrosine kinase inhibitors (TKIs); however, they do benefit from small molecule inhibitors targeting ALK.ResultsIn this study, fluorescence in situ hybridization (FISH) using a break-apart probe for the ALK gene was performed on formalin fixed paraffin-embedded tissue to determine the incidence of ALK rearrangements and hybridization patterns in a large unselected cohort of 1387 patients with a referred diagnosis of non-small cell lung cancer (1011 of these patients had a histologic diagnosis of adenocarcinoma). The abnormal FISH signal patterns varied from a single split signal to complex patterns. Among 49 abnormal samples (49/1387, 3.5%), 32 had 1 to 3 split signals. Fifteen samples had deletions of the green 5′ end of the ALK signal, and 1 of these 15 samples showed amplification of the orange 3′ end of the ALK signal. Two patients showed a deletion of the 3′ALK signal. Thirty eight of these 49 samples (38/1011, 3.7%) were among the 1011 patients with confirmed adenocarcinoma. Five of 8 patients with ALK rearrangements detected by FISH were confirmed to have EML4-ALK fusions by multiplex RT-PCR. Among the 45 ALK-rearranged samples tested, only 1 EGFR mutation (T790M) was detected. Two KRAS mutations were detected among 24 ALK-rearranged samples tested.ConclusionsIn a large unselected series, the frequency of ALK gene rearrangement detected by FISH was approximately 3.5% of lung carcinoma, and 3.7% of patients with lung adenocarcinoma, with variant signal patterns frequently detected. Rare cases with coexisting KRAS and EGFR mutations were seen.

Translocation (2;8)(q35;q13): a recurrent abnormality in congenital embryonal rhabdomyosarcoma.

We report a case of congenital embryonal rhabdomyosarcoma (ERMS), a rare form of rhabdomyosarcoma, featuring a karyotype with a t(2;8)(q35;q13) in a 2-week-old male infant. This is the third reported case of congenital ERMS with cytogenetic findings. The previous cases also showed a similar or possibly identical translocation. We postulate that the t(2;8)(q35;q13) is a specific abnormality in congenital ERMS, and that it involves the PAX3 gene at 2q35 and a non-yet identified gene at 8q13.

A case of lipoblastoma with seven copies of chromosome 8

Fig. 1. Biopsy specimen of lipoblastoma showing lobules of mature and immature adipose tissue, separated by well-vascularized fibrous septae. Hematoxylineeosin stain; original magnification, 40. Lipoblastoma is a rare benign mesenchymal tumor of embryonal white fat that usually occurs in infancy and early childhood [1]. Histologically, these lesions are composed of variably differentiated lipoblasts, spindled to stellate mesenchymal cells, a plexiform capillary network, myxoid stroma, and mature adipocytes [2]. Infrequently, mainly in older children and young adults, lipoblasts may be limited in number, or the matrix may show a myxoid appearance with a plexiform vascular pattern, making it difficult to distinguish a lipoblastoma from a typical lipoma or a myxoid liposarcoma, respectively [2]. In such cases, cytogenetic analysis may prove helpful in establishing the final diagnosis. Here, we present a case of lipoblastoma in a 4-year-old boy. The tumor was located on the left shoulder and, upon removal, measured 5.0 3.0 0.5 cm. The cut surface of the tumor mass was yellow-brown, glistening with whiteyellow areas possibly consisting of fat necrosis. Microscopically, the sections examined revealed lobules of mature and immature adipose tissue, separated by wellvascularized fibrous septa (Fig. 1). Myxoid stroma was present, and fat cells showed a spectrum of maturation from primitive stellate cells to spindle cells. Mucoid microcysts were also present. A diagnosis of lipoblastoma was made at that time. Metaphase harvest and slide preparation from tumor cell cultures were as described previously, with minor modifications. G banding was performed using trypsineWright staining. [3]. Twenty G-banded metaphases were analyzed, and the chromosome findings were interpreted according to ISCN 2005 [4]. Of the 20 metaphases analyzed, 10 showed the presence of 7 copies of an apparently normal chromosome 8 (Fig. 2). The first cytogenetic cases of lipoblastoma were reported in 1986 by Sandberg et al. [5]. Since then, O40 cases have been reported [6e10]. These studies demonstrate the importance of chromosome 8 in these tumors, and particularly the chromosomal region 8q11wq13 [11,12]. It has been proposed that rearrangements involving the region 8q11wq13 cause upregulation of the PLAG1 gene through promoter swapping [13]. An alternative mechanism for upregulation of PLAG1 is gain of multiple copies of chromosome 8. Previous FISH and chromosome studies have shown the presence of extra copies of chromosome 8 in lipoblastoma [14,15]. The highest number of apparently normal chromosomes 8 previously detected in

Long-term persistence of nonpathogenic clonal chromosome abnormalities in donor hematopoietic cells after allogeneic stem cell transplantation.

We describe the cases of two unrelated patients who exhibited multiple chromosomal abnormalities in donor cells after allogeneic peripheral blood stem cell transplantation (PBSCT). The patients were diagnosed with chronic myeloid leukemia and chronic lymphocytic leukemia, respectively, and both underwent nonmyeloablative conditioning with cyclophosphamide and fludarabine followed by PBSCT from their HLA-matched opposite-sex siblings. Post-transplant bone marrow cytogenetics showed full engraftment, and the early post-transplant studies demonstrated only normal donor metaphases. Subsequent studies of both patients, however, revealed a population of metaphase cells with abnormal, but apparently balanced, donor karyotypes. Chromosome studies performed on peripheral blood cells collected from both donors after transplantation were normal. Both patients remained in clinical remission during follow-up of approximately 8 years in one case, and 6 years in the other case, despite the persistence of the abnormal clones. Chromosomal abnormalities in residual recipient cells after bone marrow or PBSCT are not unusual. In contrast, only rare reports of chromosome abnormalities in donor cells exist, all of which have been associated with post-bone marrow transplant myelodysplastic syndrome or acute leukemias. The present cases demonstrate the rare phenomenon of persistent clonal nonpathogenic chromosome aberrations in cells of donor origin.

Deletion 6p as the sole chromosome abnormality in a patient with therapy-related myelodysplastic syndrome: case report and review of the literature

Rearrangement or deletion of 6p in hematologic malignancies is an unusual finding [1,2]. The majority of cases appear to be associated with therapy-related myelodysplastic syndrome (t-MDS) and therapy-related acute myeloid leukemia (t-AML), where deletion 6p is present in the context of a complex karyotype that frequently includes 5/del(5q) or 7/del(7q) [2]. To our knowledge, deletion 6 p has not previously been reported as a sole abnormality in t-MDS or t-AML. We present the case of a 62-year-old woman with refractory anemia with excess blasts type 2 (RAEB2). The patient has a history of stage I breast carcinoma diagnosed in 2002. At that time, she underwent