Figure 2.
WES and bulk RNA-seq reveal genomic mechanisms of CD20 loss. (A) CD79A and CD20 protein expression determined using IHC on FFPE biopsy sections. The images show staining from a lesion located to the left axilla of patient 3 obtained shortly after the start of CD20 bispec treatment (sample 3.1) and at relapse (sample 3.2), which is representative of the CD20⁻ relapses. (B) Schematic illustration showing CD20 loss was accompanied by genomic alterations, namely an RNA fusion between NHLRC3- NXT1P1 intergenic region and MS4A1 in patient 1 (positions refer to hg19), an intronic T>C mutation leading to cryptic splicing and frameshift in patient 2 (exon5:c.573+2T>C; allelic frequency, 82.10%-100%; tumor content, 80%), a nucleotide deletion with frameshift in patient 3 (exon3:c.212delT:p.M71Rfs∗12; allelic frequency, 16.60%-20.60%; tumor content, 80%), and a biallelic deletion of MS4A1 in patient 6.

WES and bulk RNA-seq reveal genomic mechanisms of CD20 loss. (A) CD79A and CD20 protein expression determined using IHC on FFPE biopsy sections. The images show staining from a lesion located to the left axilla of patient 3 obtained shortly after the start of CD20 bispec treatment (sample 3.1) and at relapse (sample 3.2), which is representative of the CD20⁻ relapses. (B) Schematic illustration showing CD20 loss was accompanied by genomic alterations, namely an RNA fusion between NHLRC3- NXT1P1 intergenic region and MS4A1 in patient 1 (positions refer to hg19), an intronic T>C mutation leading to cryptic splicing and frameshift in patient 2 (exon5:c.573+2T>C; allelic frequency, 82.10%-100%; tumor content, 80%), a nucleotide deletion with frameshift in patient 3 (exon3:c.212delT:p.M71Rfs∗12; allelic frequency, 16.60%-20.60%; tumor content, 80%), and a biallelic deletion of MS4A1 in patient 6.

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