1. ¹Department of Pathology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
2. ²Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
3. ³Department of HSCT Data Management, Nagoya University School of Medicine, Nagoya, Japan
4. ⁴Department of Pathology, Okayama University, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
5. ⁵Department of Clinical Laboratory, National Center for Child Health and Development, Tokyo, Japan
6. ⁶Department of Pathology and Clinical Laboratories, Nagoya University Hospital, Nagoya, Japan

Correspondence: Dr H Inagaki, MD, PhD, Department of Pathology, Graduate School of Medical Sciences, Nagoya City University, Kawasumi, Mizuho-ku, Nagoya 467-8601, Japan. E-mail: hinagaki@med.nagoya-cu.ac.jp

Received 15 November 2006; Revised 22 February 2007; Accepted 23 February 2007; Published online 20 April 2007.

Abstract

In anaplastic large-cell lymphomas positive for anaplastic lymphoma kinase (ALK) protein, the ALK gene is most commonly fused to the NPM gene, and less commonly to TPM3, TFG, ATIC, and other rare genes. Although this lymphoma is generally associated with a favorable clinical outcome, 25% of the patients die of the disease within 5 years. In this study, we developed three assays, all of which can be used with archival formalin-fixed, paraffin-embedded tissues: (1) a sensitive reverse transcription-polymerase chain reaction (RT-PCR) assay for various X-ALK fusion genes, (2) a 5' rapid amplification of cDNA ends (RACE) assay to identify unknown fusion partners, and (3) a real-time RT-PCR assay to quantify the amount of the NPM-ALK fusion transcript. In 26 cases of ALK⁺ anaplastic large-cell lymphoma, the RT-PCR assay showed that the ALK was fused to NPM in 21 cases, to TPM3 in three, and to TFG in one. The 5' RACE assay detected ATIC-ALK fusion in the remaining case. The real-time quantitative RT-PCR assay showed that the NPM-ALK transcript was over expressed in four of 20 quantifiable cases. Patients with NPM-ALK overexpression showed a significantly unfavorable overall survival compared with those with a low expression of this transcript. The RT-PCR and 5' RACE assays developed here may be useful for identification of known and unknown gene partners fused to the ALK gene. Overexpression of the NPM-ALK fusion transcript may be associated with a poor prognosis of the patients with ALK⁺ anaplastic large-cell lymphomas.