Search

PDF file - 175K, Supplementary Table S1. Clinical and prognostic parameters of cases analyzed by gene expression profiling arrays (45 cMBL and 115 Rai0-CLL) and by miRNA expression profiling arrays (39 cMBL and 111 Rai0-CLL). Supplementary Table S2. List of the 302 modulated genes identified by the supervised multiclass analysis comparing cMBL and Rai0-CLL samples stratified according to IGVH mutational status at the 90th percentile of false discovery rate (FDR) equal to 0. The SAM score(d) and the contrast values of each class are reported for each gene. Negative values indicates down-regulation, positive up-regulation. In bold italic are marked the eight genes that showed different modulation depending on Rai0-CLL or cMBL configuration. Supplementary Table S3. List of the 18 modulated miRNAs in the supervised multiclass analysis comparing cMBL and Rai0-CLL samples stratified according to IGVH mutational status at q-value 0. The SAM score(d) and the contrast values of each class are reported for each gene. Negative values indicates down-regulation, positive up-regulation.

PDF file - 59K, Forty-seven genes differentially expressed in t(11;14), t(4;14) and MAF-associated translocations group.

Purpose: Deregulated expression of miRNAs has been shown in multiple myeloma (MM). A promising strategy to achieve a therapeutic effect by targeting the miRNA regulatory network is to enforce the expression of miRNAs that act as tumor suppressor genes, such as miR-34a.Experimental Design: Here, we investigated the therapeutic potential of synthetic miR-34a against human MM cells in vitro and in vivo.Results: Either transient expression of miR-34a synthetic mimics or lentivirus-based miR-34a-stable enforced expression triggered growth inhibition and apoptosis in MM cells in vitro. Synthetic miR-34a downregulated canonic targets BCL2, CDK6, and NOTCH1 at both the mRNA and protein level. Lentiviral vector-transduced MM xenografts with constitutive miR-34a expression showed high growth inhibition in severe combined immunodeficient (SCID) mice. The anti-MM activity of lipidic-formulated miR-34a was further shown in vivo in two different experimental settings: (i) SCID mice bearing nontransduced MM xenografts; and (ii) SCID-synth-hu mice implanted with synthetic 3-dimensional scaffolds reconstituted with human bone marrow stromal cells and then engrafted with human MM cells. Relevant tumor growth inhibition and survival improvement were observed in mice bearing TP53-mutated MM xenografts treated with miR-34a mimics in the absence of systemic toxicity.Conclusions: Our findings provide a proof-of-principle that formulated synthetic miR-34a has therapeutic activity in preclinical models and support a framework for development of miR-34a–based treatment strategies in MM patients. Clin Cancer Res; 18(22); 6260–70. ©2012 AACR.

PDF file - 111K, In vivo activity of miR-34a in RPMI-8226 xenografts

PDF file - 395K, Expression plots and functional annotations charts of miRNAs identified as differentially expressed between pPCL and MM patients.

PDF file - 29K, Multivariate analysis comparing each of the four miRNA-model (A: miR-22, B: miR-146a, C: miR-92a, D: miR-330-3p) with biological and molecular variables in pPCL series.

PDF file - 358K, MiRNA expression profiles in pPCL patients.

PDF file - 106K, Systemic delivery of formulated miR34a mimics affects the growth of MM xenografts

PDF file - 862K, Boxplot distributions of the expression levels of the 26 progression-associated genes.

PDF file - 78K, Quantitative analysis of miR-34a levels in retrieved tumors

PDF file - 122K, Boxplot distribution of NF-kB and proliferation indexes in the 21 PPCL and the 55 MM patients.

Supplementary Figures S1-S2 and Supplementary Tables S1-S5.

PDF file - 22K, Distribution of the most frequently utilized IGHV. The histogram shows the percentages of VH sequences used in cMBL compared to Rai0-CLL cases.

PDF file - 199K, Mir-301a/b ACVR1 anticorrelation in MM.

PDF file - 73K

Purpose: To investigate the incidence and clinical relevance of classic and new prognostic markers, IGHV gene mutational status, and chromosomal abnormalities in clinical monoclonal B lymphocytosis (cMBL) compared with Rai stage 0 chronic lymphocytic leukemia (Rai0-CLL).Experimental Design: A group of 136 patients with cMBL and a group of 216 Rai0-CLL cases were investigated prospectively.Results:IGHV-mutated cases were significantly more frequent among cMBLs (P = 0.005), whereas the distribution of CD38 and ZAP-70 positive cases, of patients with NOTCH1 and SF3B1 mutations or exhibiting the major CLL cytogenetic abnormalities, was similar in the two groups. Moreover, no significant differences were found either in IGHV/IGHD/IGHJ gene usage or in the overall prevalence of stereotyped IGHV gene sequences. Cells from cMBL and Rai0-CLL exhibited similar gene and microRNA (miRNA) signatures; in addition, when grouped according to the IGHV mutational status, IGHV-unmutated cases showed different transcriptional signatures compared with IGHV-mutated patients, irrespective of the cMBL or Rai0-CLL classification. cMBL diagnosis per se was predictive of longer progression-free survival.Conclusions: Our study based on a prospective series of patients indicates that no major differences exist between the circulating cells from cMBL and Rai0-CLL, at least based on a comparison of the markers used in the study. This possibly suggests that the two conditions mainly differ in the initial size of the monoclonal cell population, which may influence the subsequent timing of clonal expansion and clinical manifestations. Clin Cancer Res; 19(21); 5890–900. ©2013 AACR.

PDF file - 289K, Unsupervised analyses in cMBL and Rai0-CLL cases. (A) Gene and (B) miRNA expression profiling analyses by hierarchical clustering. Information about IGHV mutational status ('+' = M, '-' = UM), CD38, ZAP-70, chromosome 12 trisomy, chromosome 17, 11, and 13 deletions ('+' = positive, '-' = negative) are included alongside the patient ID. In the legend bar: turquoise indicates Rai0-CLL and yellow cMBL samples, respectively. The color scale bar represents the relative gene expression changes normalized by the standard deviation, and the color changes in each row represent gene expression relative to the mean across the samples.

Purpose: Plasma cell leukemia (PCL) is a rare form of plasma cell dyscrasia that presents either as a progression of previously diagnosed multiple myeloma, namely secondary PCL, or as initial manifestation of disease, namely primary PCL (pPCL). Although the presenting signs and symptoms include those seen in multiple myeloma, pPCL is characterized by several aspects that define a more aggressive course. Here, we have investigated the transcriptome of pPCLs and correlated differential expression profiles with outcome to provide insights into the biology of the disease.Experimental Design: The expression profiles of 21 newly diagnosed pPCLs included in a multicenter prospective clinical trial were generated using high-density microarray, then evaluated in comparison with a representative series of patients with multiple myeloma and in association with clinical outcome.Results: All but one of the pPCLs had one of the main immunoglobulin heavy-chain locus translocations, whose associated transcriptional signatures resembled those observed in multiple myeloma. A 503-gene signature distinguished pPCL from multiple myeloma, from which emerged 26 genes whose expression trend was associated with progressive stages of plasma cells dyscrasia in a large dataset from multiple institutions, including samples from normal donors throughout PCL. Finally, 3 genes were identified as having expression levels that correlated with response to the first-line treatment with lenalidomide/dexamethasone, whereas a 27-gene signature was associated with overall survival independently of molecular alterations, hematologic parameters, and renal function.Conclusions: Overall, our data contribute to a fine dissection of pPCL and may provide novel insights into the molecular definition of patients with poorer prognosis. Clin Cancer Res; 19(12); 3247–58. ©2013 AACR.

PDF file - 39K

PDF file - 39K, Anticorrelation results and functional annotations analysis of differentially expressed miRNAs between pPCL and MM patients.

PDF file - 93K

PDF file - 22K, Results of correlation analysis between miRNA expression and copy number.

PDF file - 114K, Boxplots of differentially expressed genes between pPCL and MM patients as determined by Q-RT-PCR.

Purpose: To assess biologic features related to the development of immune thrombocytopenia (ITP) in patients with chronic lymphocytic leukemia (CLL).Experimental Design: We retrospectively analyzed 463 patients with CLL with available immunoglobulin heavy-chain variable (IGHV) gene status and B-cell receptor (BCR) configuration [heavy-chain complementary-determining region 3 (HCDR3)], of whom thirty-six developed ITP, according to previously defined criteria. Most of them had available cytogenetic analysis.Results: We observed a significant association between ITP occurrence and IGHV unmutated gene status (P < 0.0001), unfavorable cytogenetic lesions (P = 0.005), and stereotyped HCDR3 (P = 0.006). The more frequent stereotyped HCDR3 subsets were #1 (IGHV1-5-7/IGHD6-19/IGHJ4; 16 of 16 unmutated) and #7 (IGHV1-69 or IGHV3-30/IGHD3-3/IGHJ6; 13 of 13 unmutated), both being significantly more represented among patients developing ITP (P = 0.003 and P = 0.001, respectively). Moreover, restricting the analysis to unmutated patients, subset #7 confirmed its independent significant association with the occurrence of ITP (P = 0.013). Both unmutated IGHV mutational status, del(11)(q23) and stereotyped BCR were significantly associated with shorter time to ITP development (P < 0.0001, P = 0.02, and P = 0.005, respectively) than other patients.Conclusion: Our data suggest that patients with CLL and peculiar BCR conformations are at higher risk of developing secondary ITP and that stereotyped BCR may be involved in the pathogenesis of this complication. Clin Cancer Res; 18(7); 1870–8. ©2012 AACR.

PDF file - 164K, Cell culture methods, in vitro assays, in vivo models

PDF file - 749K, Histogram of the expression values of MAFA gene in the 21 PPCL and the 55 MM patients.

XLSX file - 33K, Features of CLL samples.

Purpose: Primary plasma cell leukemia (pPCL) is a rare and very aggressive form of plasma cell dyscrasia. To date, no information on microRNA (miRNA) expression in pPCL has been reported. This study aimed at investigating the involvement of miRNAs in pPCL and their possible relationship with higher tumor aggressiveness.Experimental design: Global miRNA expression profiles were analyzed in highly purified malignant plasma cells from 18 pPCL untreated patients included in a prospective clinical trial. MiRNA expression patterns were evaluated in comparison with a representative series of multiple myeloma patients, in relation to the most recurrent chromosomal abnormalities (as assessed by fluorescence in situ hybridization and single-nucleotide polymorphism-array analysis), and in association with clinical outcome. MiRNA expression was also integrated with gene expression profiles in pPCL and multiple myeloma samples.Results: We identified a series of deregulated miRNAs in pPCL (42 upregulated and 41 downregulated) in comparison with multiple myeloma. Some of them, on the basis of their reported functions and putative target genes computed by integrative analysis, might have a role in the pathobiology of pPCL. As regards chromosomal aberrations, the expression of some miRNAs mapped to hotspot altered regions was associated with DNA copy number of the corresponding loci. Finally, 4 miRNA (miR-497, miR-106b, miR-181a*, and miR-181b) were identified as having expression levels that correlated with treatment response, and 4 (miR-92a, miR-330-3p, miR-22, and miR-146a) with clinical outcome.Conclusions: Overall, our study provides insights into the possible contribution of miRNAs in the pathogenesis of pPCL and suggests targets for future therapeutic investigations. Clin Cancer Res; 19(12); 3130–42. ©2013 AACR.

Purpose: Despite its indolent nature, chronic lymphocytic leukemia (CLL) remains an incurable disease. To establish the potential pathogenic role of miRNAs, the identification of deregulated miRNAs in CLL is crucial.Experimental Design: We analyzed the expression of 723 mature miRNAs in 217 early-stage CLL cases and in various different normal B-cell subpopulations from tonsils and peripheral blood.Results: Our analyses indicated that CLL cells exhibited a miRNA expression pattern that was most similar to the subsets of antigen-experienced and marginal zone–like B cells. These normal subpopulations were used as reference to identify differentially expressed miRNAs in comparison with CLL. Differences related to the expression of 25 miRNAs were found to be independent from IGHV mutation status or cytogenetic aberrations. These differences, confirmed in an independent validation set, led to a novel comprehensive description of miRNAs potentially involved in CLL. We also identified miRNAs whose expression was distinctive of cases with mutated versus unmutated IGHV genes or cases with 13q, 11q, and 17p deletions and trisomy 12. Finally, analysis of clinical data in relation to miRNA expression revealed that miR26a, miR532-3p, miR146-5p, and miR29c* were strongly associated with progression-free survival.Conclusion: This study provides novel information on miRNAs expressed by CLL and normal B-cell subtypes, with implication on the cell of origin of CLL. In addition, our findings indicate a number of deregulated miRNAs in CLL, which may play a pathogenic role and promote disease progression. Collectively, this information can be used for developing miRNA-based therapeutic strategies in CLL. Clin Cancer Res; 20(15); 4141–53. ©2014 AACR.

PDF file - 64K, Supervised analysis comparing cMBL and Rai0-CLL samples. Haetmaps of the differentially expressed (A) gene and (B) miRNA. Information about IGHV mutational status ('+' = M, '-' = UM), CD38, ZAP-70, chromosome 12 trisomy, chromosome 17, 11, and 13 deletions ('+' = positive, '-' = negative) are included alongside the patient ID. In the legend bar: turquoise indicates Rai0-CLL and yellow cMBL samples, respectively. The color scale bar represents the relative gene expression changes normalized by the standard deviation, and the color changes in each row represent gene expression relative to the mean across the samples.

PDF file - 1024K, Supplementary Figure 1. Purification of normal human B cell subset populations. Supplementary Figure 2. CLL miRNA expression profile is homogeneous and distinct from multiple myeloma and Sezary syndrome. Supplementary Figure 3. Quantitative PCR validation of miRNAs differentially expressed between CLL and normal memory B cells. Supplementary Figure 4. Expression of miR-29c* in M-CLL and UM-CLL. Supplementary Figure 5. Validation of some miRNAs differentially expressed in IGHV or FISH classes. Supplementary Figure 6. Cluster analysis of averaged miRNA expression in the different FISH subgroups of CLL.

PDF file - 145K, Q-RT-PCR validation of the microarray expression data of LOC400986 and miR-130a. The microarray and Q-RT-PCR data of LOC400986 (A) and miR-130a (C) scaled in the range 0-1 are shown in the charts together with Pearson correlation coefficient. Boxplots of LOC400986 and miR-130a Q-RT-PCR expression comparing Rai0-CLL vs cMBL cases are represented in charts B and D respectively with the corresponding P-values (Wilcoxon rank sum test).

PDF file - 133K, Differentially expressed miRNAs identified by supervised analysis of pPCL patients stratified according to response rate.

Purpose: Chromosome 13q14 deletion occurs in a substantial number of chronic lymphocytic leukemia (CLL) patients and it is believed to play a pathogenetic role. The exact mechanisms involved in this lesion have not yet been fully elucidated because of its heterogeneity and the imprecise knowledge of the implicated genes. This study was addressed to further contribute to the molecular definition of this lesion in CLL.Experimental Design: We applied single-nucleotide polymorphism (SNP)-array technology and gene expression profiling data to investigate the 13q14 deletion occurring in a panel of 100 untreated, early-stage (Binet A) patients representative of the major genetics, molecular, and biological features of the disease.Results: Concordantly with FISH analysis, SNP arrays identified 44 patients with del(13)(q14) including 11 cases with a biallelic deletion. The shorter monoallelic deletion was 635-kb long. The loss of the miR-15a/16-1 cluster occurred in all del(13)(q14) cases except in 2 patients with a monoallelic deletion, who retained both copies. MiR-15a/16 expression was significantly downregulated only in patients with the biallelic loss of the miRNA cluster compared to 13q normal cases. Finally, the natural grouping of SNP profiles by nonnegative matrix factorization algorithm showed that patients could be classified into 2 separate clusters, mainly characterized by short/biallelic versus wide/monoallelic 13q14 deletions. Supervised analyses of expression data showed that specific transcriptional profiles are correlated with these 2 genomic subgroups.Conclusions: Overall, our data highlight the presence of 2 distinct molecular types of 13q14 deletions, which may be of clinical relevance in CLL. Clin Cancer Res; 16(23); 5641–53. ©2010 AACR.

PDF file - 108K, Effects induced by stable expression of miR-34a

XLSX file - 248K, microRNAs exhibiting differential expression between CLL and normal antigen-experienced B cells.

PDF file - 171K, Distribution of unfavorable events in Rai0-CLL and cMBL and correlation with prognosis. (A) Boxplot of concomitant unfavorable events (y-axis)in cMBL and Rai0-CLL; (B) Kaplan-Meier estimated curves of time to first treatment in the whole cohort stratified according to the number of concomitant events (as indicated in each of the four legends). The p-value and the hazard ratios (with the 95% confidence interval) of the proportional hazard model are indicated above each plot.

Multiple myeloma (MM) has a highly heterogeneous genetic background, which complicates its molecular tracking over time. Nevertheless, each MM patient’s malignant plasma cells (PCs) share unique V(D)J rearranged sequences at immunoglobulin loci, which represent ideal disease biomarkers. Because the tumor-specific V(D)J sequence is highly expressed in bulk RNA in MM patients, we wondered whether it can be identified by single-cell RNA sequencing (scRNA-seq). To this end we analyzed CD138+ cells purified from bone marrow aspirates of 19 samples with PC dyscrasias by both a standard method based on bulk DNA and by an implementation of the standard 10x Genomics protocol to detect expressed V(D)J sequences. A dominant clonotype was easily identified in each sample, accounting on average for 83.65% of V(D)J-rearranged cells. Compared with standard methods, scRNA-seq analysis proved highly concordant and even more effective in identifying clonal productive rearrangements, by-passing limitations related to the misannealing of consensus primers in hypermutated regions. We next validated its accuracy to track 5 clonal cells with absolute sensitivity in a virtual sample containing 3180 polyclonal cells. This shows that single-cell V(D)J analysis may be used to find rare clonal cells, laying the foundations for functional single-cell dissection of minimal residual disease.

Chronic lymphocytic leukaemia (CLL) is characterised by a heterogeneous clinical course. Such heterogeneity is associated with a number of markers, including TP53 gene inactivation. While TP53 gene alterations determine resistance to chemotherapy, it is not clear whether they can influence early disease progression. To clarify this issue, TP53 mutations and deletions of the corresponding locus [del(17p)] were evaluated in 469 cases from the O-CLL1 observational study that recruited a cohort of clinically and molecularly characterised Binet stage A patients. Twenty-four cases harboured somatic TP53 mutations [accompanied by del(17p) in 9 cases], 2 patients had del(17p) only, and 5 patients had TP53 germ-line variants. While del(17p) with or without TP53 mutations was capable of significantly predicting the time to first treatment, a reliable measure of disease progression, TP53 mutations were not. This was true for cases with high or low variant allele frequency. The lack of predictive ability was independent of the functional features of the mutant P53 protein in terms of transactivation and dominant negative potential. TP53 mutations alone were more frequent in patients with mutated IGHV genes, whereas del(17p) was associated with the presence of adverse prognostic factors, including CD38 positivity, unmutated-IGHV gene status, and NOTCH1 mutations.

Monoclonal gammopathy of undetermined significance (MGUS) and clonal hematopoiesis (CH) are 2 preclinical clonal expansions of hematopoietic cells whose prevalence rises with age, reaching almost 10% in people of aged 70 years and older. The increased risk of myeloid malignancies in patients with myeloma is well defined, and the study of the association between CH and MGUS could help explain this phenomenon. Here, we analyzed a fully clinically annotated dataset of 777 older subjects (median age, 91 years) previously screened for prevalence of CH. The prevalence of MGUS and CH was 9.6% and 17.3%, respectively. We detected CH in 9.7% of the patients with MGUS and MGUS in 5.5% of the patients with CH. We did not find a significant correlation between the presence of MGUS and CH. Furthermore, the 2 conditions showed a differential association with clinical and laboratory covariates, suggesting that MGUS and CH may represent age-associated unrelated clonal drifts of hematopoietic cells. Confirmatory studies are needed to assess the relevance of CH in plasma cell disorders. This trial was registered at www.clinicaltrials.gov as #NCT03907553.

Simple Summary In this review we summarized the most relevant biological features concerning smoldering multiple myeloma (SMM). We outlined the genetic architecture of the disease and how it is entering in the SMM risk stratification. In particular, we pointed out how the identification of a high-risk setting, meaning the population with the risk of faster progression to the symptomatic phase, is crucial and, despite huge improvements in recent years, still represents an unmet clinical need. Indeed, the correct identification of these patients will drive to an early therapeutical intervention. Moreover, we also discussed the role of the microenvironment, which is highly relevant in the symptomatic disease but still understudied in the SMM setting. Finally, we debated the state-of-the-art current available therapies and ongoing clinical trials, and envisioned possible strategies to introduce a biological-based stratification approach within the daily clinical practice. Abstract Smoldering multiple myeloma (SMM) is an asymptomatic disorder of clonal bone marrow (BM) plasma cells (PCs) in between the premalignant condition known as monoclonal gammopathy of undetermined significance and overt multiple myeloma (MM). It is characterized by a deep biological heterogeneity that is reflected in a markedly variable progression risk among patients. Recently proposed risk stratification models mainly rely on indirect markers of disease burden and are unable to identify cases in whom clonal PCs have already undergone the “malignant switch” but major clonal expansion has not occurred yet. In the last years, the application of next-generation sequencing (NGS) techniques has led to profound advances in the understanding of the molecular bases of SMM progression, and in all likelihood, it will contribute to the needed improvement of SMM prognostication. In this Review, we describe the recent advances in characterizing the genomic landscape of SMM and intrinsic determinants of its progression, highlighting their implications in terms of understanding of tumor evolution and prognostication. We also review the main studies investigating the role of the microenvironment in this early disease stage. Finally, we mention the results of the first randomized clinical trials and discuss the potential clinical translability of the genomic insights.