Variant Fusion Gene Research Articles

Genetic diversity in alveolar soft part sarcoma: A subset contain variant fusion genes, highlighting broader molecular kinship with other MiT family tumors.

Alveolar soft part sarcoma (ASPS) is a rare malignancy that, since its initial description, remains a neoplasm of uncertain histogenesis. The disease-defining molecular event characterizing the diagnosis of ASPS is the ASPSCR1-TFE3 fusion gene. Following identification of an index case of ASPS with a novel TFE3 fusion partner, we performed a retrospective review to determine whether this represents an isolated event. We identified two additional cases, for a total of three cases lacking ASPSCR1 partners. The average patient age was 46 years (range, 17-65); two patients were female. The sites of origin included the transverse colon, foot, and dura. Each case exhibited a histomorphology typical of ASPS, and immunohistochemistry was positive for TFE3 in all cases. Routine molecular testing of the index patient demonstrated a HNRNPH3-TFE3 gene fusion; the remaining cases were found to have DVL2-TFE3 or PRCC-TFE3 fusion products. The latter two fusions have previously been identified in renal cell carcinoma; to our knowledge, this is the first report of a HNRNPH3-TFE3 gene fusion. These findings highlight a heretofore underrecognized genetic diversity in ASPS, which appears to more broadly molecularly overlap with that of translocation-associated renal cell carcinoma and PEComa. These results have immediate implications in the diagnosis of ASPS since assays reliant upon ASPSCR1 may yield a false negative result. While these findings further understanding of the molecular pathogenesis of ASPS, issues related to the histogenesis of this unusual neoplasm remain unresolved.

Acute promyelocytic leukemia associated with rare variant fusion gene STAT5b-RARα: report of two cases and review of literature

Objective To improve the recognition of clinical characteristics and treatment outcome of acute promyelocytic leukemia (APL) with STAT5b-RARα fusion gene. Methods The clinical features, therapeutic effects and prognosis of 2 cases of APL associated with STAT5b-RARα fusion gene were analyzed retrospectively, and the related literature was reviewed. Results Both two patients with positive STAT5b-RARα were resistant to retinoic acid and arsenic trioxide therapy. Subset of this disease also showed higher recurrence tendency. Meanwhile, the relapsed patients still had the potential of no response to chemotherapy. Conclusions Till now, there is no specific treatment for this rare genotype APL. Treatment should be adjusted according to the status of the disease, and hematopoietic stem cell transplantation may improve the prognosis and prolong overall survival. Key words: Leukemia, promyelocytic, acute; STAT5b-RARαfusion gene; Tretinoin; Arsenic trioxide

Molecular genetics, diagnosis and management of clear cell sarcoma of hand

Synonyms: Clear cell sarcoma of soft tissue, Clear cell sarcoma of the tendons and aponeuroses, malignant melanoma of the soft parts. Background: Rodriguez-Martin, Ortiz-Cruz, Del Rio, Vivanco, & Lopaz-Amor in 2011 stated “Clear cell sarcoma is a high-grade soft tissue sarcoma seen in adolescents and young adults, with melanosytic differentiation typically involving tendons and aponeuroses”. Clear cell sarcoma of soft tissue (CCSST) was originally described by Dr. Franz M. Enzinger in 1965 as a distinct entity of tumors arising from tendons and aponeuroses in young adults. Clear cell sarcoma (CCS) of soft tissue is a rare sarcoma with morphologic similarities to malignant melanoma. They are characterized by a distinct genetic background including a chromosomal translocation t(12;22)(q13;q12), or a resultant EWSR1-ATF1 fusion gene. The lower limbs are involved more commonly. Clear cell sarcoma has been reported in other tissues such as bone, colon and gastrointestinal tract. The clear cell sarcoma that occurs in relation to the gastrointestinal tract has a variant fusion gene EWSR1-CREB1 and they are re-designated as gastrointestinal neuroectodermal tumor (GNET). Material and method: A 21 years old female with a chronic recurrent swelling of the left mid finger was diagnosed as epithelioid sarcoma on histopathological examination. Immunohistochemistry was done with basic tumor markers panel and a diagnosis of clear cell sarcoma was confirmed. Result: Immunohistochemistry staining is used for sub-typing of the tumor, predicts the prognosis of the tumor and also the response to the specific type of therapy.

Cutaneous Clear Cell Sarcoma: A Clinicopathologic, Immunohistochemical, and Molecular Analysis of 12 Cases Emphasizing its Distinction from Dermal Melanoma

Clear cell sarcoma (CCS) of tendons and aponeuroses/malignant melanoma (MM) of soft parts is a rare tumor and in the majority of cases presents a characteristic reciprocal translocation t(12;22)(q13;q12) that results in fusion of the EWS and ATF1 genes. Although the melanocytic differentiation of CCS is indisputable, its precise lineage remains unclear. Typically, the slowly growing tumor affects the extremities of adolescents or young adults, especially around the ankle and foot. CCS is classically regarded as a deep soft tissue tumor associated with tendons or aponeuroses. This traditional view is put into perspective by the description of primary CCS of the gastrointestinal tract that may have a variant fusion gene EWSR1-CREB1. We describe 12 cases of cutaneous CCS and discuss the differential diagnoses. These 12 cases share an identical immunohistochemical profile with MM and thus can easily be confused with a dermal variant of spindle cell MM or metastasis of MM. The patients' ages ranged from 6 to 74 years (median: 25 y), and there was a female predominance (10 females, 2 males). Most tumors (n = 9) were located on the extremities, 2 tumors arose on the back, and 1 on the abdomen. The mean tumor size was 0.97 cm (range, 0.4 to 1.7 cm). Six cases showed invasion of the subcutis, the other 6 cases were entirely dermal. Tumor necrosis was evident in 2 cases, melanin pigment in 2 cases, and ulceration in 1 tumor. All cases showed uniform nests and fascicles of pale spindled or slightly epitheloid cells with finely granular eosinophilic or clear cytoplasm. There was fair pleomorphism with plump spindled nuclei and significantly prominent nucleoli. Multinucleated wreath-like tumor giant cells were observed in two-thirds of cases, but were usually present only focally. The dense cellular aggregates were encased by delicate fibrous septa. The stroma showed a sclerotic reticulated pattern. Partly, the nests of spindle cells bordered the epidermis, prima vista mimicking junctional nests of melanocytes. The specific translocation pattern was confirmed in all cases by fluorescence in situ hybridization. Local recurrences and metastases developed in 2 and 3 patients, respectively, and 1 patient died of the disease.

Technical aspects and clinical applications of measuring BCR‐ABL1 transcripts number in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is a myeloproliferative disorder characterized by a triphasic clinical course, the morphologic expansion of a terminally differentiated myeloid cell and the presence of the BCR-ABL1 fusion gene, the hallmark of CML. The fusion gene is usually, but not always, associated with a Philadelphia chromosome, the result of a reciprocal exchange of genetic material between chromosome 22 and chromosome 9, which leads to the production of the activated BCR-ABL1 gene and oncoprotein. The breakpoint in the BCR gene occurs commonly downstream of exons e13 or e14 (M-BCR) and less frequently downstream of exons e1 and e2 (m-BCR). Less than 1% of cases carry a breakpoint downstream of exon 6 or 8 ("variant fusion genes") or exon 19 (mu-BCR). Breakpoints in the ABL1 gene cluster upstream of exon a2 (or of exon a3 in less than 5% of patients with CML). Conventional cytogenetic, fluorescence in situ hybridization, and molecular testing for the BCR-ABL1 fusion gene are key investigations for the diagnosis and monitoring of CML. Treatment using tyrosine kinase inhibitors has revolutionized the management of CML with hematologic and cytogenetic response within 12-18 months observed in >85% of patients. Nevertheless, between 15 and 20% of patients may evolve to blastic phase. Measurement of low level or "minimal" residual disease using molecular tests is becoming the gold-standard approach to measure response to therapy due to its higher sensitivity compared to other routine techniques. The technical aspects and clinical applications of molecular monitoring will be the main focus of this article.

Proteome-Wide Identification of Novel Binding Partners to the Oncogenic Fusion Gene Protein, NPM-ALK, using Tandem Affinity Purification and Mass Spectrometry

Nucleophosmin-anaplastic lymphoma kinase (NPM-ALK), an oncogenic fusion gene protein that is characteristically found in a subset of anaplastic large cell lymphomas, promotes tumorigenesis through its functional and physical interactions with various biologically important proteins. The identification of these interacting proteins has proven to be useful to further our understanding of NPM-ALK-mediated tumorigenesis. For the first time, we performed a proteome-wide identification of NPM-ALK-binding proteins using tandem affinity purification and a highly sensitive mass spectrometric technique. Tandem affinity purification is a recently developed method that carries a lower background and higher sensitivity compared with the conventional immunoprecipitation-based protein purification protocols. The NPM-ALK gene was cloned into an HB-tagged vector and expressed in GP293 cells. Three independent experiments were performed and the reproducibility of the data was 68%. The vast majority of the previously reported NPM-ALK-binding proteins were detected. We also identified proteins that are involved in various cellular processes that were not previously described in association with NPM-ALK, such as MCM6 and MSH2 (DNA repair), Nup98 and importin 8 (subcellular protein transport), Stim1 (calcium signaling), 82Fip (RNA regulation), and BAG2 (proteosome degradation). We believe that these data highlight the functional diversity of NPM-ALK and provide new research directions for the study of the biology of this oncoprotein.

Clear Cell Sarcoma of Soft Tissue

Clear cell sarcoma (CCS) of soft tissue is a rare sarcoma with morphologic similarities to malignant melanoma but a distinct genetic background including a chromosomal translocation, t(12;22)(q13;q12), or a resultant EWSR1-ATF1 fusion gene. In addition, the tumors occurring in the gastrointestinal tract may have a variant fusion gene EWSR1-CREB1. This study analyzed the clinicopathologic and molecular genetic features of 33 CCSs of soft tissue. The patients' ages ranged from 13 to 73 years (median, 30 y), and there was a male predominance (20 males, 13 females). The tumors were located in the deep soft tissues of the extremities (N=25) or in the trunk or limb girdles (N=8). The median tumor size was 4 cm (range, 1 to 15 cm). The tumor cells were either spindle or epithelioid, and they were arranged predominantly in a short fascicular (N=19) or a solid sheetlike growth pattern (N=14). Minor histologic variations included the existence of rhabdoid cells (N=8), bizarre pleomorphic cells (N=6), alveolar structures due to loss of cellular cohesion (N=3), and a seminomalike pattern (N=2). Tumor necrosis was evident in 14 tumors, and the mitotic activity ranged from 0 to 43 mitotic figures (MF)/10 high-power fields (HPF) (mean: 4 MF/10 HPF). Immunohistochemically, the tumors were consistently positive for S-100 protein (33/33) and variably or focally for HMB45 (32/33), microphthalmia transcription factor (26/32), Melan A (23/32), CD57 (25/33), bcl-2 (30/32), synaptophysin (14/32), CD56 (7/32), epithelial membrane antigen (12/33), cytokeratin (AE1/AE3) (1/32), CD34 (3/32), c-erbB-2 (10/32), c-kit (5/32), and c-met (5/32). alpha-Smooth muscle actin, desmin, and cytokeratin (CAM5.2) were negative. Reverse transcription-polymerase chain reaction using RNA extracted from formalin-fixed, paraffin-embedded tissues demonstrated transcripts of the EWSR1-ATF1 (31/33) or EWSR1-CREB1 fusion gene (2/33). In 26 cases with available clinical information, local recurrences and metastases developed in 2 and 15 patients, respectively. Ten patients were dead of the disease, and the overall survival rate was 63% at 5 years. However, no clinicopathologic or molecular variables associated with the patients' prognosis were identified. This study confirms that CCS is an aggressive soft tissue tumor with a melanocytic phenotype and wider morphologic variations than had been generally considered. In cases with unusual histologic findings, molecular detection of the EWSR1-ATF1/CREB1 fusion genes provides critical information regarding the diagnosis of the tumor.

Nuclear Localization of the NuMA-RARα/RXRα Complex Is Necessary for Leukemogenesis in hCG-NuMA-RARα Transgenic Mice.

Acute promyelocytic leukemia (APL) is a model system for the role of aberrant transcription in cancer, and differentiation therapy in cancer treatment. APL is characterized by accumulation of abnormal promyelocytes in patient bone marrow, and by reciprocal chromosomal translocations involving retinoic acid receptor alpha (RARα). RARα heterodimerizes with the retinoid X receptor alpha (RXRα) and regulates transcription of genes associated with myeloid differentiation, in response to all trans retinoic acid (ATRA). Though PML-RARα is the most prevalent fusion gene in APL, four variant fusion genes (X-RARα) are currently known. By understanding the role that each fusion gene plays in APL, we may better understand the mechanism of this leukemia, and, by extension, the role of aberrant transcription factors and transcriptional regulation in cancer. Several lines of evidence suggest that X-RARα interact with and delocalize RXRα. We previously characterized the phenotype of the hCG-NuMA-RARα transgenic model (Sukhai et al, Oncogene, 2004). We observed that mice developed a myeloproliferative disease-like myeloid leukemia with promyelocytic features, with a variable onset peripheral blood phenotype (2–17 months). To further elucidate the role of RXRα in APL, we conditionally knocked out RXRα in hCG-NuMA-RARα mice. Phenotype analysis of NuMA-RARα+ mice was consistent with our previous results; animals developed a myeloproliferative disease-like myeloid leukemia within 4 months of birth. Hemizygous and homozygous RXRα conditional knockout mice were phenotypically normal as late as 12 months of age. The leukemic phenotype in NuMA-RARα+ mice was dependent on the presence of functional RXRα, as indicated by a progressive decrease in accumulation of promyelocytes, as well as Gr-1+, CD11b+, CD13+ and CD117+ cells in the bone marrow and peripheral blood of NuMA-RARα+ mice hemizygous and homozygous for the RXRα mutation, as compared to NuMA-RARα+ RXRα+/+ controls. We further observed that downstream target genes (e.g., C/EBPα) of NuMA-RARα were regulated in an RXRα-dependent manner, as these genes exhibited the greatest extent of deregulation in the presence of both alleles of functional RXRα, but had progressively less deregulated expression with loss of one or two functional alleles of RXRα. Furthermore, the NuMA-RARα/RXRα heterodimer was observed to bind to retinoic acid response elements in vitro. Strikingly, these observations mirrored what we observed in single transgenic mice with low vs. high transgene copy number. Mice with low copy number exhibited nuclear localization of the NuMA-RARα/RXRα complex, the greatest extent of deregulation of gene expression, and a rapid-onset phenotype. On the other hand, mice with high transgene copy number exhibited cytoplasmic localization of NuMA-RARα/RXRα, the least extent of gene deregulation, and an ameliorated leukemia similar to that observed in NuMA-RARα mice carrying the conditional mutation in RXRα. We therefore propose that NuMA-RARα cooperates with RXRa in the development of leukemia in hCG-NuMA-RARα transgenic mice, and that the localization of this complex to the nucleus is required for leukemogenesis in transgenic mice.

Clinicopathologic and molecular genetic characterization of low-grade fibromyxoid sarcoma, and cloning of a novel FUS/CREB3L1 fusion gene

Low-grade fibromyxoid sarcoma (LGFMS) is an indolent, late-metastasizing malignant soft-tissue tumor that is often mistaken for either more benign or more malignant tumor types. Cytogenetic analyses have identified a recurrent balanced translocation t(7;16) (q32–34;p11), later shown by molecular genetic approaches to result in a FUS/CREB3L2 fusion gene. Whereas preliminary studies suggest that this gene rearrangement is specific for LGFMS, its incidence in this tumor type and the possible existence of variant fusion genes have not yet been addressed. For this purpose, a series of potential LGFMS were obtained from nine different soft-tissue tumor centres and subjected to molecular analysis as well as careful histopathologic review. Reverse transcriptase-polymerase chain reaction analysis disclosed a FUS/CREB3L2 fusion transcript in 22 of the 23 (96%) cases that remained classified as LGFMS after the histologic re-evaluation and from which RNA of sufficient quality could be extracted, whereas none of the cases that were classified as other tumor types was fusion-positive. In one of the tumors with typical LGFMS appearance, we found that FUS was fused to the CREB3L1 gene instead of CREB3L2. The proteins encoded by these genes both belong to the same basic leucine-zipper family of transcription factors, and display extensive sequence homology in their DNA-binding domains. Thus, it is expected that the novel FUS/CREB3L1 chimera will have a similar impact at the cellular level as the much more common FUS/CREB3L2 fusion protein. Taken together, the results indicate that virtually all LGFMS are characterized by a chimeric FUS/CREB3L2 gene, and that rare cases may display a variant FUS/CREB3L1 fusion.

Pathobiology of NPM-ALK and variant fusion genes in anaplastic large cell lymphoma and other lymphomas

Despite its clinical and histological heterogeneity, anaplastic large cell lymphoma (ALCL) is now a well-recognized clinicopathological entity accounting for 2% of all adult non-Hodgkin's lymphomas (NHL) and about 13% of pediatric NHL. Immunophenotypically, ALCL are of T cell (predominantly) or Null cell type; by definition, cases expressing B cell antigens are officially not included in this entity. The translocation (2;5)(p23;q35) is a recurring abnormality in ALCL; 46% of the ALCL patients bear this signature translocation. This translocation creates a fusion gene composed of nucleophosmin (NPM) and a novel receptor tyrosine kinase gene, named anaplastic lymphoma kinase (ALK). The NPM-ALK chimeric gene encodes a constitutively activated tyrosine kinase that has been shown to be a potent oncogene. The exact pathogenetic mechanisms leading to lymphomagenesis remain elusive; however, the synopsis of evidence obtained to date provides an outline of likely scenarios. Several t(2;5) variants have been described; in some instances, the breakpoints have been cloned and the genes forming a new fusion gene with ALK have been identified: ATIC-ALK, TFG-ALK and TPM3-ALK. Cloning the translocation breakpoint and identifying the ALK and NPM genes provided tools for screening material from patients with ALCL using various approaches at the chromosome, DNA, RNA, or protein level: positive signals in the reverse transcriptase-polymerase chain reaction (RT-PCR) and the immunostaining with anti-ALK monoclonal antibodies (McAb) serve as the most convenient tests for detection of the t(2;5) NPM-ALK since the fusion gene and ALK protein expression do not occur in normal or reactive lymphoid tissue. The wide range of NPM-ALK positivity reported in different series appears to be dependent on the inclusion and selection criteria of the ALCL cases studied. Overall, however, 43% of ALCL cases were NPM-ALK+ (83% of pediatric ALCL vs 31% of adult ALCL). Occasional non-ALCL B cell lymphomas (4%) with diffuse large cell and immunoblastic histology and Hodgkin's disease cases (3%) were NPM-ALK-, but these data are questionable. The aggregate results indicate that, in contrast to primary nodal (systemic) ALCL, the t(2;5) may be present in only 10-20% of primary cutaneous ALCL and rarely, if at all, in lymphomatoid papulosis, a potential precursor lesion; however, these 10-20% positive cases were not confirmed by anti-ALK McAb immunostaining and may represent an overestimate. Positivity for NPM-ALK is associated to various degrees with the following parameters: 44% and 45% of ALCL cases with T cell and Null cell immunophenotype, respectively, are positive, whereas only 8% of cases with a B cell immunoprofile are positive; the mean age of positive patients is significantly younger than that of negative patients; positive cases carry a better overall prognosis (but not in all studies). Recently, the homogenous category of ALK lymphoma ('ALKoma') has emerged as a distinct pathological entity within the heterogenous group of ALCL. The fact that patients with ALK lymphomas experience significantly better overall survival than ALK- ALCL demonstrates further that analysis of ALK expression has important prognostic implications. The term ALK lymphoma signifies a switch in the use of the diagnostic criteria: cases are selected on the basis of a genetic abnormality (the ALK rearrangement), instead of the review of morphological or immunophenotypical features which are clearly more prone to disagreement and controversy. Since its initial description in 1985 ALCL has become one of the best characterized lymphoma entities.

Distinct leukemia phenotypes in transgenic mice and different corepressor interactions generated by promyelocytic leukemia variant fusion genes PLZF-RARalpha and NPM-RARalpha.

Acute promyelocytic leukemia (APL) is characterized by a specific chromosome translocation involving RARalpha and one of four fusion partners: PML, PLZF, NPM, and NuMA genes. To study the leukemogenic potential of the fusion genes in vivo, we generated transgenic mice with PLZF-RARalpha and NPM-RARalpha. PLZF-RARalpha transgenic animals developed chronic myeloid leukemia-like phenotypes at an early stage of life (within 3 months in five of six mice), whereas three NPM-RARalpha transgenic mice showed a spectrum of phenotypes from typical APL to chronic myeloid leukemia relatively late in life (from 12 to 15 months). In contrast to bone marrow cells from PLZF-RARalpha transgenic mice, those from NPM-RARalpha transgenic mice could be induced to differentiate by all-trans-retinoic acid (ATRA). We also studied RARE binding properties and interactions between nuclear corepressor SMRT and various fusion proteins in response to ATRA. Dissociation of SMRT from different receptors was observed at ATRA concentrations of 0.01 microM, 0.1 microM, and 1.0 microM for RARalpha-RXRalpha, NPM-RARalpha, and PML-RARalpha, respectively, but not observed for PLZF-RARalpha even in the presence of 10 microM ATRA. We also determined the expression of the tissue factor gene in transgenic mice, which was detected only in bone marrow cells of mice expressing the fusion genes. These data clearly establish the leukemogenic role of PLZF-RARalpha and NPM-RARalpha and the importance of fusion receptor/corepressor interactions in the pathogenesis as well as in determining different clinical phenotypes of APL.

Cytogenetics and experimental models of sarcomas

Bone and soft tissue sarcomas are diagnostically challenging. Recognition of specific cytogenetic abnormalities in these neoplasms has significantly reduced some of the associated difficulties and has provided valuable information on histopathogenesis. Commonly, translocations involving an exchange of chromosomal material and creation of novel chimeric genes are detected. These fusion genes frequently function as aberrant transcription factors that contribute to sarcomagenesis. New studies indicate that less commonly occurring variant fusion genes are also present in some tumors, eg, Ewing's sarcoma and alveolar rhabdomyosarcoma. The clinical consequences, if any, of these variant hybrids are not yet known. Reverse transcriptase polymerase chain reaction and are useful approaches in detecting these transcripts. In addition to translocations, supernumerary ring chromosomes are often encountered in sarcomas, particularly those of intermediate or borderline malignancy. Traditional fluorescence in situ hybridization, and recently, comparative genomic hybridization have uncovered the chromosomal composition of these rings as well as some associated gene amplifications in well-differentiated liposarcoma and dermatofibrosarcoma protuberans.

Expression of the human growth hormone variant gene in cultured fibroblasts and transgenic mice.

The nucleotide sequence of the human growth hormone variant gene, one of the five members of the growth hormone gene family, predicts that it encodes a growth hormone-like protein. As a first step in determining whether this gene is functional in humans, we have expressed a mouse metallothionein I/human growth hormone variant fusion gene in mouse L cells and in transgenic mice. The growth hormone variant protein expressed in transiently transfected L cells is distinct from growth hormone itself with respect to reactivity with anti-growth hormone monoclonal antibodies, behavior during column chromatography, and isoelectric point. Transgenic mice expressing the growth hormone variant protein are 1.4- to 1.9-fold larger than nontransgenic controls, suggesting that the protein has growth-promoting properties.