5′-(RACE) Identification of Rare ALK Fusion Partner in Anaplastic Large Cell Lymphoma

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Anaplastic large-cell lymphoma (ALCL) is a subtype of aggressive non-Hodgkin’s lymphoma first described in 1985, 1 and characterized by the expression of CD30/Ki-1 antigen. By current definition, ALCLs exhibit a T-cell or null phenotype and the majority of cases demonstrate expression of the anaplastic lymphoma kinase (ALK) protein. 2 Most ALK-expressing ALCLs harbor the t(2;5)(p23;q35) chromosomal aberration 3, 4, 5 that involves the 5′-oligomerization motif region of nucleophosmin (NPM) gene on chromosome 5, and the 3′-cytoplasmic tyrosine kinase catalytic domain of anaplastic lymphoma kinase (ALK) gene of chromosome 2 to form the NPM-ALK fusion gene. 6 This rearrangement places the ALK gene under the control of the NPM promoter and results in deregulated expression of the ALK protein. Normal expression of ALK appears to be stringently controlled and limited to the cytoplasm of the testis, ganglion cells of the intestine, and neural tissues. 6 The NPM-ALK fusion protein has been shown by immunohistochemistry to localize in the cytoplasm and the nucleus of the neoplastic cells, thereby providing a distinctive marker for t(2;5)-positive ALCL. The t(2;5)-positive ALCLs account for 80 to 85% of the ALK-positive lymphomas. 7 The remaining 15 to 20% of ALK-positive ALCLs harbor variant fusion partners and exhibit immunohistological patterns different from that observed for t(2;5). 8 In these cases, ALK expression is predominantly cytoplasmic and is not present in a nuclear or nucleolar localization. 8 This is because of ALK forming fusion partners with genes other than NPM. Interestingly, a number of non-t(2;5) translocations have also been identified in a nonhematopoietic soft-tissue neoplasm known as inflammatory myofibroblastic tumor (IMT). 9, 10, 11 Remarkably, IMT may bear a histological resemblance to morphological variants of ALCL such as the lymphohistiocytic, small cell, and sarcomatoid variants. 8, 12 The propensity of ALK for partnering with a diverse variety of genes in both ALCLs and IMTs raises the possibility that other yet unidentified genes that partner with ALK may be involved in the pathogenesis of these tumors. In a quest to identify the ALK fusion partner in a non-t(2,5) ALCL with cytoplasmic expression of the ALK protein, we used the 5′-rapid amplification of cDNA ends (RACE) technique that revealed a fusion between tropomyosin 3 (TPM3) and the ALK genes. Molecular analysis for T-cell clonality also complemented immunohistochemical studies in the definitive assignment of T-cell lineage to the tumor.