Case Reports in Oncological Medicine Myoepithelioma: A New Rearrangement Involving the LPP Locus in a Case of Multiple Bone and Soft Tissue Lesions

Figure 2

Cytogenetic characterization. (a) Conventional karyotype on the bone tumor (calcaneum): 46,XY,add(2)(q?21),der(3)t(2;3)(q?21;q?21),-8,-19,+mar1,+mar2[8]. The soft tissue tumor harbor the same chromosomal aberrations: 46,XY, add(2)(q?21),der(3)t(2;3)(q?21;q?21),-8,-19,+mar1,+mar2[2]. (b) FISH experiments with break-apart probes on fixed cells: deletion of the BAC probe located 5’/centromeric (RP11-1144D2 labelled in green) to the LPP (lipoma preferred partner or LIM Domain Containing Preferred Translocation Partner In Lipoma) locus in a metaphasic cell and in a nucleus (soft tissue tumor): ish der(?)t(3,?)(RP11-1144D2-,RP11-67E18-;RP11-67E18+[5].nuc ish(RP11-1144D2x1,RP11-67E18x2)(RP11-1144D2 con RP11-67E18x1)[334/400]. (c, d) Molecular karyotyping (soft tissue tumor): 2 interstitial deletions within the long arm of chromosome 3 (c) and the telomeric one delete the 5’ part of the LPP locus (d) arr[hg19] 3q22.1q26.2(133,374,187–169,925,119),3q27.2q28(185,628,780-188,411,171)x1. Culturing, harvesting, and G-banding of the tumor samples for karyotyping were performed according to standard procedures [21]. Culturing, harvesting, and G-banding of the tumor samples for karyotyping were performed according to standard procedures [21]. Dual-color FISH experiments were performed on fixed nuclei and on formalin-fixed paraffin-embedded tissue sections (4 μm-thick), using commercial probes (LSI-EWSR1, LSI-FUS, LSI-TP53/CEP17, LSI-9p21/CEP9, LSI-TP53/CEP17 from Abbott Molecular/Vysis; ON-TFE3 from Kreatech) and bacterial artificial chromosome (BACs) probes. The BAC clones were purchased from the Chori BACPAC Resources Center (Oakland, USA) to study the following loci: NR4A3/9q31.1 (RP11-412F16, RP11-47M15, RP11-266D8, and RP11-282C24); HMGA2/12q14.3 (RP11-317J13, RP11-412I20, RP11-945G8, and RP-347J7); and LPP/3q27.3-q28 (RP11-1144D2 and RP11-67E18). Extraction, labeling, and hybridization were performed, as previously reported [22]. Two hundred interphasic cells and all hybridized metaphases were analysed. Molecular karyotyping was performed with Cytoscan 750K SNP-arrays according to the manufacturer’s instructions (Affymetrix). Results were analysed as previously reported [23]. Aberrations greater than 100 kb involving at least 20 consecutive SNPs were considered for copy number variant (CNV) analysis. Constitutional CNV polymorphisms were excluded based on comparisons with the Database of Genome Variants (hg19). The quality control metrics were within the normal range (SnpQC = 17.656, Mapd = 0.195, and Waviness = 0.088).

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