Identification of ERBB4 and COL29A1 as specific outliers in ALK-negative ALCL. (A) COPA of T-NHL microarray data revealed ERBB4 and COL29A1 as outlier genes in ALK-negative ALCL. ALK, ERBB4, and COL29A1 expression (normalized expression units) are shown from all profiled samples (data set from Agnelli et al¹¹ ). Sample classes are indicated according to the color scale. Angioimmunoblastic lymphoma (AILT; 41 samples), ALK-negative ALCL (24 samples), ALK-positive ALCL (30 samples), normal T cells (69 samples), PTCL-NOS (74 samples); adult T-cell leukemia/lymphoma (ATLL; 11 samples), cell lines (4 samples). (B) Hierarchical clustering of transcripts correlated to ERBB4 expression in ALCL samples (ALK-positive, yellow; ALK-negative, blue), as revealed by the average linkage method using Euclidean distance. Each column represents a sample, and each row a gene. The color scale bar represents relative gene expression changes, normalized by the standard deviation. Microarray data analysis was performed as described in Piva et al¹⁵ . (C) Unbalanced expression of ERBB4 transcripts. Expression of ERBB4 (exons 1-2 and 24-25) was assessed by qRT-PCR in 8 ALCL cases and in the breast cancer cell line T47D, used as a positive control. (D) Distribution of ERBB4 and COL29A1 RNA sequencing reads in a representative ERBB4-positive ALCL case. (E) Electropherograms of 2 ERBB4-truncated transcripts: I20Δ (exon 21 carrying at 5′ a portion of intron 20 (GRCh37:2:212329687:212330078) and I12Δ (exon 13 carrying at 5′ a portion of intron 12 (GRCh37:2:212558507:212558780). Fragments were identified by RLM-RACE in a representative ERBB4-positive ALCL case. Arrows point to the position of intron-exon junctions.