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Transcriptional Features of Multiple Myeloma Patients with Chromosome 1Q Gain

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Transcriptional Features of Multiple Myeloma Patients with Chromosome 1Q Gain Letters to the Editor 1113 References 5 Dworzak MN, Froschl G, Printz D, Mann G, Po¨tschger U, Mu¨hlegger N et al. Prognostic significance and modalities of flow cytometric minimal residual disease detection in childhood acute 1 Woessmann W, Seidemann K, Mann G, Zimmermann M, Burkhardt lymphoblastic leukemia. Blood 2002; 99: 1952–1958. B, Oschlies I et al. The impact of the methotrexate administration 6 Hummel M, Bentink S, Berger H, Klapper W, Wessendorf S, Barth schedule and dose in the treatment of children and adolescents with TF et al. A biologic definition of Burkitt’s lymphoma from B-cell neoplasms: a report of the BFM Group Study NHL-BFM95. transcriptional and genomic profiling. N Engl J Med 2006; 354: Blood 2005; 105: 948–958. 2419–2430. 2 Busch K, Borkhardt A, Wossmann W, Reiter A, Harbott J. Combined 7 Dave SS, Fu K, Wright GW, Lam LT, Kluin P, Boerma EJ et al. polymerase chain reaction methods to detect c-myc/IgH rearrange- Molecular diagnosis of Burkitt’s lymphoma. N Engl J Med 2006; ment in childhood Burkitt’s lymphoma for minimal residual disease 354: 2431–2442. analysis. Haematologica 2004; 89: 818–825. 8 Attarbaschi A, Mann G, Dworzak M, Trebo M, Urban C, Fink FM 3 Mussolin L, Basso K, Pillon M, d’Amore ES, Lombardi A, Luzzatto L et al. Malignant non-Hodgkin’s lymphoma of childhood and et al. Prospective analysis of minimal bone marrow infiltration in adolescence in Austria – therapy results between 1986 and 2000. pediatric Burkitt’s lymphomas by long-distance polymerase chain Wien Klin Wochenschr 2002; 114: 978–986. reaction for t(8;14)(q24;q32). Leukemia 2003; 17: 585–589. 9 Canonico B, Zamai L, Burattini S, Granger V, Mannello F, 4 Dworzak MN, Fritsch G, Fleischer C, Printz D, Fro¨schl G, Buchinger Gobbi P et al. Evaluation of leukocyte stabilisation in P et al. Comparative phenotype mapping of normal vs malignant TransFix-treated blood samples by flow cytometry and trans- pediatric B-lymphopoiesis unveils leukemia-associated aberrations. mission electron microscopy. J Immunol Methods 2004; 295: Exp Hematol 1998; 26: 305–313. 67–78. Transcriptional features of multiple myeloma patients with chromosome 1q gain Leukemia (2007) 21, 1113–1116. doi:10.1038/sj.leu.2404616; TC3 including tumors that do not fall into any of the other published online 22 February 2007 groups, most of which express CCND2; TC4 showing high CCND2 levels and the presence of the t(4;14) translocation and TC5 expressing the highest levels of CCND2 in association with Abnormalities of chromosome 1 are among the most either the t(14;16) or t(14;20) translocation.3 frequent chromosomal alterations in multiple myeloma Assessment of 1q/gain by FISH was performed by using three (MM), being found in up to 45% of patients.1,2 It has been BAC clones specific for the BCL9 (1q21.1), CKS1B (1q22) and reported that the short arm of chromosome 1 is preferentially ARF1 (1q42.13) loci, and setting the threshold as 10%. Specific involved in deletions, whereas the long arm is associated alterations were identified in 40/77 (51.9%) patients; three with amplification. The gain of 1q (1q/gain) can occur as (75%) or four (12.5%) signals of all the 1q probes were found in isochromosomes, duplications or jumping translocations. It 35 patients and, in the remaining five samples (12.5%), the has been widely reported that 1q/gain MM patients are probes mapping to 1q21 and 1q22 showed more signals than characterized by complex karyotypes and aggressive disease, that mapping to 1q42. 1q/gain was observed in the majority of and a close association with poor-risk genetic features, such purified plasma cells (490%) in all but three patients (range as chromosome 13q deletion (D13) and the t(4;14) trans- 12–20%). 1q/gain was significantly absent in TC2 group location has also been described.1 It has been recently (Po10À4) and present in TC3 (P ¼ 0.008), whereas the correla- demonstrated that gains/amplification of 1q21 increase as tion was not significant in the TC1 (P ¼ 0.053) or TC4 the condition goes from smoldering to overt MM, thus (P ¼ 0.142) groups; in addition, 1q extra copies significantly suggesting that these regions contain critical genes for disease associated with D13 (Po10À4) and chromosome 11 polisomy progression.2 These findings along with the limited information (although at a limited significance level of P ¼ 0.038), but not concerning specific transcriptional profiles prompted us to ploidy status (P ¼ 0.0971). molecularly characterize 1q/gain MMs by FISH and microarray To identify a specific transcriptional fingerprint characterizing analyses. 1q/gain, we made a supervised analysis of 1q/gain versus 1q/ Our study includes a panel of 77 MM patients at diagnosis, normal MM patients using SAM algorithm. Seventy-two probe whose characteristics have been deposited in National Center sets (specific for 61 genes) distinguished the 40 1q/gain from the for Biotechnology Information’s Gene Expression Omnibus 37 1q/normal cases (Figure 1a and Table 1a, b). Notably, in the (GEO; http://www.ncbi.nlm.mih.gov/geo, accession number 1q/gain patients 41 of the 43 upregulated genes mapped to GSE6401). Bone marrow plasma cells were purified (490% in 1q12-q44, whereas a significant percentage of the down- all cases) using CD138-immunomagnetic bead selection and regulated genes was localized on chromosomes 13q (7/18; characterized by FISH for the presence of 11 polisomy, the most 39%) and 11 (6/18, 33%). To verify whether the 1q/gain recurrent IGH translocations, ploidy status, D13, and global reflected transcriptional imbalances of specific chromosomal gene expression profiling using the Affymetrix U133A gene regions, the expression data from the 1q/gain and 1q/normal chips, as described previously.3 Patients were then stratified samples were also analyzed in the context of the physical accordingly to the proposed translocation/cyclin D (TC) localization of the genes using a model-free statistical method classification in five groups: TC1 characterized by the t(11;14) (LAP),4 allowing the identification of five modulated chromoso- or t(6;14) translocations, with the consequent overexpression of mal regions (Figure 1b). In the 1q/gain patients, the region either CCND1 or CCND3, and a nonhyperdiploid status; TC2 1q21.1-q44 (absolute positions: 146,567,360-245,353,955) was showing low/moderate levels of the CCND1 gene in the absence upregulated and 13q12-14 (22,800,966-47,961,101) down- of any primary IGH translocations, and a hyperdiploid status; regulated, which is in line with the significant association Leukemia Letters to the Editor 1114 between 1q abnormalities and D13; regional downregulation 15q24.1-q25 (72,397,963-78,483,746), which may reflect the was also observed in chromosome regions 11p15 (2,380, higher frequency of hyperdiploid patients in the 1q/normal 098-6,372,930), 11q13-q23 (71,317,730-113,946,523) and group. Figure 1 (a) Supervised analysis of 1q/gain versus 1q/normal patients. The differentially expressed genes discriminating 1q/gain and 1q/normal classes were identified using Significant Analysis of Microarrays software version 2.21 (SAM; Excel front-end publicly available at http://www- stat.stanford.edu/~tibs/SAM/index.html; cutoff for significance: q-value ¼ 0 with median FDR ¼ 0%, 90th %ile FDR ¼ 0%) and visualized by means of dChip software. The color scale bar represents relative gene expression changes normalized by standard deviations. Information about chromosome 11 trisomy ( þ 11), D13, ploidy status (HD ¼ hyperdiploid), TC classes and 1q extra copies (1q þ ) are included (n ¼ data not available). (b) Regional analysis of 1q/gain versus 1q/normal patients. The whole genome plot of the differentially expressed 858 genes identified using LAP algorithm4 (q-value ¼ 0) shows five modulated chromosomal regions. The vertical axis represents the progressive chromosome number, and the horizontal axis (blue lines) the progressive absolute position of the probes represented on HG-U133A gene chips for each chromosome. The white bars indicate the exact chromosomal locations, and the colored perpendicular lines the locations and up- (red) or downregulation (green) of genes in the 1q/gain patients (see geneplotter package from Bioconductor for details). Table 1a Forty-three upregulated genes in 1q/gain, ordered by chromosomal location and gene name whenever more than one probe recognized the same gene, the one with the best score is shown Probe ID Gene symbol Chromosome location Probe ID Gene symbol Chromosome location 202337_at PMF1 1q12 208716_s_at TMCO1 1q22-q25 209044_x_at SF3B4 1q12-q21 201403_s_at MGST3 1q23 210386_s_at MTX1 1q21 208114_s_at ISG20L2 1q23.1 210417_s_at PIK4CB 1q21 215158_s_at DEDD 1q23.3 201771_at SCAMP3 1q21 208684_at COPA 1q23-q25 216591_s_at SDHC 1q21 202846_s_at PIGC 1q23-q25 209561_at THBS3 1q21 202427_s_at BRP44 1q24 202596_at ENSA 1q21.2 214838_at SFT2D2 1q24.2 222212_s_at LASS2 1q21.2 217748_at ADIPOR1 1q32 210460_s_at PSMD4 1q21.2 212165_at C1orf37 1q32.1 221189_s_at TARSL1 1q21.2 202187_s_at PPP2R5A 1q32.2-q32.3 216873_s_at ATP8B2 1q21.3 204478_s_at RABIF 1q32-q41 200052_s_at ILF2 1q21.3 208755_x_at H3F3A 1q41 209609_s_at MRPL9 1q21.3 202374_s_at RAB3GAP2 1q41 203515_s_at PMVK 1q21.3 200065_s_at ARF1 1q42 201378_s_at UBAP2L 1q21.3 221497_x_at EGLN1 1q42.1 217978_s_at UBE2Q1 1q21.3 214170_x_at FH 1q42.1 218270_at MRPL24 1q21-q22 202324_s_at ACBD3 1q42.12 200896_x_at HDGF 1q21-q23 212371_at C1orf121 1q44 201275_at FDPS 1q22 214831_at MED28 4p16 218296_x_at MSTO1 1q22 210859_x_at CLN3 16p12.1 218291_at MAPBPIP 1q22 Leukemia Letters to the Editor 1115 Table 1b
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