Dali Huang

Renal cell carcinoma with novel VCL–ALK fusion: new representative of ALK-associated tumor spectrum

Renal cell carcinoma represents a model for contemporary classification of solid tumors; however, unusual and unclassifiable cases exist and are not rare in children and young adults. The anaplastic lymphoma kinase (ALK) gene has recently been implicated in subsets of pulmonary, esophageal, breast, and colon cancers. These findings strengthen the importance of molecular classification of carcinomas across different organ sites, especially considering the evolving targeted anticancer therapies with ALK inhibitors. In the current study of six pediatric renal cell carcinomas, two cases exhibited structural karyotypic abnormalities involving the ALK locus on chromosomal band 2p23. Fluorescence in situ hybridization (FISH) studies were positive for an ALK rearrangement in one case, and subsequent 5′ rapid amplification of cDNA ends analysis of this tumor revealed that the 3′ portion of the ALK transcript encoding for the kinase domain was fused in frame to the 5′ portion of vinculin (VCL, NM_003373). The new fusion gene is predicted to have an open reading frame of 4122 bp encoding for a 1374-aa oncoprotein; its expression was shown by immunoblotting with anti-VCL and anti-ALK antibodies in tumor tissue lysates. Immunohistochemistry with the same antibodies demonstrated cytoplasmic and subplasmalemmal localization of the oncoprotein determined by its N-terminal VCL portion. FISH with a custom-designed VCL–ALK dual-fusion probe set confirmed the presence of the fusion in neoplastic cells and demonstrated the potential clinical utility of this approach for detecting VCL–ALK in routinely processed tissue. The five remaining pediatric renal cell carcinomas did not show ALK rearrangement by FISH or ALK expression by immunohistochemistry. The data identify the kidney as a new organ site for ALK-associated carcinomas and VCL as a novel ALK fusion partner. The results should prompt further studies to advance the molecular classification of renal cell carcinoma and help to select patients who would benefit from appropriate targeted therapies.

Identification and characterization of a novel gene disrupted by a pericentric inversion inv(4)(p13.1q21.1) in a family with cleft lip.

Cleft lip with or without cleft palate is a common birth defect affecting 1 in every 700 live births. Several genetic loci are believed to be involved in the pathogenesis of syndromic and non-syndromic clefting. We identified a pericentric inversion of chromosome 4, inv(4)(p13q21) that segregates with cleft lip in a two-generation family. By using a combination of fluorescence in situ hybridization, yeast artificial chromosome, bacterial artificial chromosome contig mapping, and database searching we mapped and sequenced the inversion breakpoint region. The pericentric inversion disrupts a gene (ACOD4) on chromosome 4q21 that codes for a novel acyl-CoA desaturase enzyme. The 3.0 kb human ACOD4 cDNA spans approximately 170 kb and is composed of five exons of ACOD4. The inversion breakpoint is located in the second exon. The 3.0 kb mRNA is expressed at high level in fetal brain; a lower expression level was found in fetal kidney. No expression of ACOD4 was detected in fetal lung or liver or in adult tissues. The five exons code for a protein of 330 amino acids, with a predicted molecular weight of 37.5 kDa. The protein is highly similar to acyl-CoA desaturases from Drosophila melanogaster to Homo sapiens. The catalytically essential histidine clusters and the potential transmembrane domains are well conserved.

C11orf95-MKL2 is the Resulting Fusion Oncogene of t(11;16)(q13;p13) in Chondroid Lipoma

Chondroid lipoma, a rare benign adipose tissue tumor, may histologically resemble myxoid liposarcoma or extraskeletal myxoid chondrosarcoma, but is genetically distinct. In this study, an identical reciprocal translocation, t(11;16)(q13;p13), was identified in three chondroid lipomas, a finding consistent with previously isolated reports. A fluorescence in situ hybridization (FISH)‐based positional cloning strategy using a series of bacterial artificial chromosome (BAC) probe combinations designed to narrow the 16p13 breakpoint revealed MKL2 as the candidate gene. Subsequent 5′ RACE studies demonstrated C11orf95 as the MKL2 fusion gene partner. MKL/myocardin‐like 2 (MKL2) encodes myocardin‐related transcription factor B in a megakaryoblastic leukemia gene family, and C11orf95 (chromosome 11 open reading frame 95) is a hypothetical protein. Sequencing analysis of reverse transcription‐polymerse chain reaction (RT‐PCR) generated transcripts from all three chondroid lipomas defined the fusion as occurring between exons 5 and 9 of C11orf95 and MKL2, respectively. Dual‐color breakpoint spanning probe sets custom‐designed for recognition of the translocation event in interphase cells confirmed the anticipated rearrangements of the C11orf95 and MKL2 loci in all cases. The FISH and RT‐PCR assays developed in this study can serve as diagnostic adjuncts for the identification of this novel C11orf95‐MKL2 fusion oncogene in chondroid lipoma.

Genomic imbalances in benign metastasizing leiomyoma: characterization by conventional karyotypic, fluorescence in situ hybridization, and whole genome SNP array analysis

Benign metastasizing leiomyoma, a rare condition of controversial origin, is characterized by the occurrence of extrauterine smooth muscle tumors primarily affecting the lungs of women with a history of uterine leiomyomas. Numerous genetic studies of uterine leiomyoma with rearrangements of the HMGA2 and HMGA1 loci defined in prominent subgroups have been conducted. In contrast, cytogenetic and molecular descriptions of benign metastasizing leiomyoma are few, and, in particular, this entity has not been previously subjected to single nucleotide polymorphism (SNP) array analysis. In this study, conventional karyotypic, and/or molecular cytogenetic, and SNP array characterization of a pleuropulmonary benign mestasizing leiomyoma and a synchronous deep soft tissue leiomyoma of the thigh, which arose in a 56-year-old female with a remote history of uterine leiomyomata, revealed rearrangement of the HMGA1 (6p21) locus and nearly identical genomic profiles, including loss of chromosome 7 material in both lesions. These findings suggest that both the deep soft tissue and pleuropulmonary lesions were derived from the same abnormal clone and are genetically related to uterine leiomyomata.

Tumoral TP53 and/or CDKN2A Alterations are Not Reliable Prognostic Biomarkers in Patients with Localized Ewing Sarcoma: A Report from the Children’s Oncology Group

A growing collection of retrospective studies have suggested that TP53 mutations and/or CDKN2A deletions have prognostic significance in Ewing sarcoma. We sought to evaluate these variables in patients with localized disease treated prospectively on a single Childrens Oncology Group protocol.

Pericytoma with t(7;12) and ACTB-GLI1 fusion arising in bone

Cytogenetic analysis of a primary bone neoplasm with pericytic features in a 67-year-old man revealed a t(7;12)(p22;q13) among other karyotypic abnormalities. Subsequent molecular studies confirmed the presence of an associated ACTB-GLI1 fusion transcript. An identical 7;12 translocation is known to characterize a discrete group of soft tissue tumors belonging to the myopericytic category termed pericytoma with t(7;12). To the best of our knowledge, this is the first case of pericytoma with t(7;12) arising in bone. Cytogenetic and molecular analyses were useful, if not essential, in classifying this rare diagnostic entity.

Osseous myxochondroid sarcoma: A detailed study of 5 cases of extraskeletal myxoid chondrosarcoma of the bone

Extraskeletal myxoid chondrosarcoma (EMC) is a rare mesenchymal neoplasm with a characteristic translocation usually involving NR4A3 and EWSR1. EMC has rarely been reported in the bone and may be confused with conventional chondrosarcoma with myxoid features or various small round cell sarcomas. We present 5 cases of molecularly confirmed EMC arising primarily in the bone. Patients included 4 men and 1 woman, aged 38 to 77 years (median 54 y). Tumors arose in the ilium (2 cases), manubrium, rib, and humerus. Four tumors extensively infiltrated and destroyed preexisting bone with cortical breakthrough and associated soft tissue extension; 1 case demonstrated only focal cortical breakthrough. Microscopically, 2 cases had small round cell features; 1 of these was hypercellular, whereas the other was hypocellular with abundant myxochondroid matrix. Three cases were composed of eosinophilic spindled cells with variable fascicular to corded or wreath-like growth patterns. Fluorescence in situ hybridization was positive for both EWSR1 and NR4A3 translocation in 3 cases; rearrangement for EWSR1 or NR4A3, but not both, was seen in 2 tumors. After definitive therapy, 1 patient experienced multiple local recurrences at 36 months and died of disease at 61 months. Two patients developed lung metastases at 26 and 74 months and are alive with disease at 44 and 74 months, respectively. Two patients are disease free at 5 and 24 months. EMC of the bone is a diagnostic dilemma and requires molecular confirmation. We propose to classify tumors with the appropriate phenotype and molecularly confirmed NR4A3/EWSR1 rearrangements as myxochondroid sarcoma, either osseous or extraskeletal variants.

Extraskeletal Ewing's sarcoma of the thoracic epidural space: Case report and review of the literature

The occurrence of primary extraskeletal Ewings sarcoma (EES) of the spinal epidural space has been rarely reported in the literature. The clinical, radiologic and pathologic features of a case of EES occurring in the thoracic epidural space are presented. A 37-year-old woman presented with a one-year history of back pain. Magnetic resonance imaging demonstrated an epidural mass at the T8-9 level. Laminectomy and partial resection of the tumor were performed. The differential diagnosis of a spinal epidural mass is broad. Histopathological and molecular cytogenetic examinations confirmed an EES arising from the thoracic epidural space. Despite receiving both chemotherapy and radiotherapy, the patient died of respiratory insufficiency due to medulla oblongata metastasis 22 months after the initial consultation. Awareness of this entity will allow this rare diagnosis to be considered and facilitate appropriate management. A review of the literature on spinal epidural EES is also presented.

Translocation t(12;17)(q24.1;q21) as the sole anomaly in a nasal chondromesenchymal hamartoma arising in a patient with pleuropulmonary blastoma

The identification of recurrent chromosomal abnormalities in benign and malignant mesenchymal neoplasms has provided important pathogenetic insight as well as powerful diagnostic adjuncts. Nasal chondromesenchymal hamartoma (NCMH), an extremely rare benign tumor arising in the sinonasal tract of infants and children, has not been previously subjected to cytogenetic analysis. Histopathologically composed of mixed mesenchymal elements, NCMH exhibits a relatively wide differential diagnosis to include chondromyxoid fibroma, chondroblastoma, aneurysmal bone cyst, fibrous dysplasia, and osteochondromyxoma. An interesting association with pleuropulmonary blastoma has been reported in a small subset of NCMH patients. In the current study, cytogenetic analysis of a NCMH arising in an 11-year-old boy with a past medical history of pleuropulmonary blastoma revealed a novel 12;17 translocation, t(12;17)(q24.1;q21), as the sole anomaly.