Introduction: Enteropathy-type T-cell Lymphoma (ETL) is a highly aggressive extranodal T-cell non-Hodgkin’s lymphoma that is often associated with underlying celiac disease. In this study we used whole genome tiling resolution array comparative genomic hybridization (CGH) to delineate genomic changes that may be critical in disease pathogenesis in 30 well-characterized cases of ETL, among them 14 cases of CD56+ monomorphic small to medium-sized ETL, so-called small cell variant (CD56+smETL).

Experimental Approach: Whole genome tiling array CGH was used to generate high resolution segmental copy number profiles of 30 ETL specimens, the array platform consisting of 26,819 bacterial artificial chromosome (BAC) derived amplified fragment pools spotted in duplicate.

Results: Alignment of these profiles with the human genome map has resulted in the identification of both previously reported and novel regions of recurrent genomic alteration. The most frequently identified recurrent chromosomal gains were 9q34.11-qter (approx. 10.2 Mb; 70%), 9q33.2-q33.2 (6.6 Mb; 67%), 9q31.3-q33.2 (13.8 Mb; 60%), 5q34-q35.2 (6.5 Mb), 7q33-q34 (2.4 Mb, 47% each), 1q25.3-q31.2 (8.4 Mb), 1q32.2-q41 (7.9 Mb), 7q22-q31.1 (5.6Mb), 7q36.1-qter (9.6Mb, 43% each), 8q13.3–8q21.11 (3Mb), and 8q22.1-q24.3 (46.2 Mb, 40% each). Frequent recurrent chromosomal losses were observed on 8p22-p23.2 (15.3Mb, 37%), 10q26.2-q26.3 (5.5Mb, 27%), and 9p21.2-p21.3 (4.9Mb, 23%). Interestingly, the most frequent gains at 9q34.11-qter were inversely correlated with losses at 16q12.1 (2.5Mb, 23%, p=0.0139), suggesting these regions may accomplish similar biological effects. CD56-positive monomorphic small cell ETL were characterized by highly recurrent gains of 8q13.3-q21.11 and 8q22.1-q24.3 (71.4% in CD56+smETL vs 18.8% in non-monomorphic ETL, p=0.0086) and the rare occurrence of gains on 1q25.3-q31.2 and 1q32.2-q41 (21.4% in CD56+smETL vs 62.5% in non-monomorphic ETL, p=0.0329) and 5q34-q35.2 (21.4% in CD56+smETL vs 68.8% in non-monomorphic ETL, p=0.0136) which are common within non-monomorphic ETL.

Conclusions: ETL show highly recurrent and characteristic gains and losses of chromosomal material. While gains of chromosome 9q (detected in 70% of ETL) appear to be the hallmark genetic alteration in ETL, ETL, in line with differences in morphology, immunophenotypes and clinical features, seems to be also genetically subdivided into two distinct sub-groups: CD56+monomorphic small to medium sized ETL characterized by gains of 8q and CD56-negative non-monomorphic ETL characterized by gains of 1q and 5q.

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