Belachew, Alem A.

Abstract Background: Genome-wide association studies (GWAS) of multiple myeloma in populations of European ancestry (EA) identified and confirmed 24 susceptibility loci. For other cancers (e.g., colorectum and melanoma), risk loci have also been associated with patient survival. Methods: We explored the possible association of all the known risk variants and their polygenic risk score (PRS) with multiple myeloma overall survival (OS) in multiple populations of EA [the International Multiple Myeloma rESEarch (IMMEnSE) consortium, the International Lymphoma Epidemiology consortium, CoMMpass, and the German GWAS] for a total of 3,748 multiple myeloma cases. Cox proportional hazards regression was used to assess the association between each risk SNP with OS under the allelic and codominant models of inheritance. All analyses were adjusted for age, sex, country of origin (for IMMEnSE) or principal components (for the others) and disease stage (ISS). SNP associations were meta-analyzed. Results: SNP associations were meta-analyzed. From the meta-analysis, two multiple myeloma risk SNPs were associated with OS (P < 0.05), specifically POT1-AS1-rs2170352 [HR = 1.37; 95% confidence interval (CI) = 1.09–1.73; P = 0.007] and TNFRSF13B-rs4273077 (HR = 1.19; 95% CI = 1.01–1.41; P = 0.04). The association between the combined 24 SNP MM-PRS and OS, however, was not significant. Conclusions: Overall, our results did not support an association between the majority of multiple myeloma risk SNPs and OS. Impact: This is the first study to investigate the association between multiple myeloma PRS and OS in multiple myeloma.

AbstractGene expression profiling can be used for predicting survival in multiple myeloma (MM) and identifying patients who will benefit from particular types of therapy. Some germline single nucleotide polymorphisms (SNPs) act as expression quantitative trait loci (eQTLs) showing strong associations with gene expression levels. We performed an association study to test whether eQTLs of genes reported to be associated with prognosis of MM patients are directly associated with measures of adverse outcome. Using the genotype‐tissue expression portal, we identified a total of 16 candidate genes with at least one eQTL SNP associated with their expression with P < 10−7 either in EBV‐transformed B‐lymphocytes or whole blood. We genotyped the resulting 22 SNPs in 1327 MM cases from the International Multiple Myeloma rESEarch (IMMEnSE) consortium and examined their association with overall survival (OS) and progression‐free survival (PFS), adjusting for age, sex, country of origin and disease stage. Three polymorphisms in two genes (TBRG4‐rs1992292, TBRG4‐rs2287535 and ENTPD1‐rs2153913) showed associations with OS at P < .05, with the former two also associated with PFS. The associations of two polymorphisms in TBRG4 with OS were replicated in 1277 MM cases from the International Lymphoma Epidemiology (InterLymph) Consortium. A meta‐analysis of the data from IMMEnSE and InterLymph (2579 cases) showed that TBRG4‐rs1992292 is associated with OS (hazard ratio = 1.14, 95% confidence interval 1.04‐1.26, P = .007). In conclusion, we found biologically a plausible association between a SNP in TBRG4 and OS of MM patients.

Abstract So far, 23 germline susceptibility loci have been associated with multiple myeloma (MM) risk. It is unclear whether the genetic variation associated with MM susceptibility also predisposes to its precursor, monoclonal gammopathy of undetermined significance (MGUS). Leveraging 2434 MM cases, 754 MGUS cases, and 2 independent sets of controls (2567/879), we investigated potential shared genetic susceptibility of MM and MGUS by (1) performing MM and MGUS genome-wide association studies (GWAS); (2) validating the association of a polygenic risk score (PRS) based on 23 established MM loci (MM-PRS) with risk of MM, and for the first time with MGUS; and (3) examining genetic correlation of MM and MGUS. Heritability and genetic estimates yielded 17% (standard error [SE] ±0.04) and 15% (SE ±0.11) for MM and MGUS risk, respectively, and a 55% (SE ±0.30) genetic correlation. The MM-PRS was associated with risk of MM when assessed continuously (odds ratio [OR], 1.17 per SD; 95% confidence interval [CI], 1.13-1.21) or categorically (OR, 1.70; 95% CI, 1.38-2.09 for highest; OR, 0.71; 95% CI, 0.55-0.90 for lowest compared with middle quintile). The MM-PRS was similarly associated with MGUS (OR, 1.19 per SD; 95% CI, 1.14-1.26 as a continuous measure, OR, 1.77, 95%CI: 1.29-2.43 for highest and OR, 0.70, 95%CI: 0.50-0.98 for lowest compared with middle quintile). MM and MGUS associations did not differ by age, sex, or MM immunoglobulin isotype. We validated a 23-SNP MM-PRS in an independent series of MM cases and provide evidence for its association with MGUS. Our results suggest shared common genetic susceptibility to MM and MGUS.

Abstract Background : Approximately 25% of patients with primary myelofibrosis (PMF) harbor calreticulin (CALR) mutations, which have been associated with longer survival (Klampf et al. NEJM 2013). More than 80% of CALR mutated patients harbor one of two mutation variants: type 1, a 52-bp deletion (p.L367fs*46) or type 2, a 5-bp TTGTC insertion (p.K385fs*47). Recent studies have suggested phenotypic and prognostic differences between these two variants (Tefferi et al. Blood 2014, Leukemia 2014 and AJH 2014). Furthermore, data are emerging that suggest functionally-relevant structural differences between type 1 and type 2 CALR variants, including a higher alpha-helix content of the mutant C-terminus in type 2, compared to type 1 (Eder-Azanza et al. Leukemia 2014). Objectives : We used statistical models to calculate helix propensity for thirty-one unique amino acid sequences that were altered by CALR mutations and used the results to subclassify non-type 1/2 CALR mutations into “type 1-like” and “type 2-like” variants. Subsequently, we examined the prognostic relevance of these subgroups. Methods : Calculation of helix propensity, which is the percentage of residues that are predicted to be involved in the formation of an alpha-helix, was performed using AGADIR, which is a statistical approximation algorithm (Munoz et al. Biopolymers 1997). The helix tendency calculations were performed using conditions of pH 7.0, 5 and 25 °C, an ionic strength of 0.1 M and no N- or C-terminal protection. Results : 532 PMF patients were screened for JAK2, CALR and MPL mutations; the respective mutational frequencies were 58%, 24.6% and 7.3%. Among the 131 CALR-mutated cases, 98 (74.8%) harbored type 1, 15 (11.5%) type 2 and 18 (13.7%) other variants. Based on predicted helix propensity scale, the “other” CALR mutations were subclassified as type 1-like (n=12) or type 2-like (n=6) and respectively grouped with type 1 and type 2 variants, for purposes of phenotypic and prognostic comparisons. The AGADIR-derived predicted helix propensity scale was 29.69 for wild-type CALR and 8.6 or 34.17 for type 1 and type 2 mutant CALR, respectively; accordingly, CALR variants with values that are close to or above the value for wild-type CALR were classified as “type 2-like” (range 26.47-36.12) and those with values close to or below the value for type 1 as “type 1-like” (range 2.11-17.3). Comparison of “type 1/type 1-like” (n=110) and “type 2/type 2-like” (n=21) CALR mutations showed the latter to be associated with higher DIPSS-plus score (p=0.01), EZH2 mutations (p<0.01), leukocyte count >25 x 10(9)/L (p<0.01), higher circulating blast percentage (p=0.02) and palpable spleen size >10 cm (p<0.01). Comparison of “type 1/type 1-like” CALR and JAK2 mutations (n=309) showed the former to be associated with younger age, higher platelet count, lower transfusion need, higher hemoglobin level, lower leukocyte count and lower DIPSS-plus score (p<0.01 for all comparisons). None of these associations was evident during comparison of “type 2/type 2-like” CALR with JAK2 mutations. Survival was similar between patients with type 1 and “type 1-like” (p=0.8) and between type 2 and “type 2-like” (p=0.63) CALR mutations. In contrast, survival was significantly shorter in patients with type 2 (HR 2.4, 95% CI 1.2-4.8) and “type 2-like” (HR 3.2, 95% CI 1.0-10.6), when compared to those with type 1 CALR mutations. Survival was also significantly shorter with “type 2/type 2-like” vs “type 1/type 1-like” CALR mutations (p=0.003; HR 2.5, 95% CI 1.4-4.5) and the difference remained significant when analysis was adjusted for age (p=0.047), ASXL1 (p=0.003) or EZH2 (p=0.001) mutations. Similarly, compared to JAK2-mutated cases (n=309), survival was longer in patients with “type 1/type 1-like” (HR 0.4, 95% CI 0.3-0.5) but not in those with “type 2/type 2-like” (HR 0.9, 95% CI 0.5-1.6) CALR mutations; the difference in survival between JAK2 and “type 1/type 1-like” CALR mutated cases remained significant (P<0.01) when analysis was adjusted for age, ASXL1 or EZH2 mutations or DIPSS-plus score. Conclusions : CALR mutations in PMF might be subclassified into type 1-like and type 2-like variants, based on predicted helical propensity of their mutant C-terminus. The favorable impact of CALR mutations in PMF might be restricted to type 1 or “type 1-like” variants. Disclosures No relevant conflicts of interest to declare.

Abstract Background : Cytogenetic abnormalities in PMF have been broadly classified into “favorable” and “unfavorable” risk categories. The latter include +8, -7/7q-, i(17q), inv(3), -5/5q-, 12p-, 11q rearrangements and complex karyotype (Leukemia. 2011;25:82). In a more recent study, we had demonstrated an even worse prognosis for patients with monosomal karyotype (MK), inv(3) and i(17q) abnormalities (Blood. 2011;118:4595). In the current study, we revisited the topic using a larger database. Methods: PMF diagnosis was according to World Health Organization criteria (Blood. 2009;114:937). Cytogenetic analysis and reporting was done according to the International System for Human Cytogenetic Nomenclature (Cytogenetic and genome research. 2013. Prepublished on 2013/07/03 as DOI 10.1159/000353118). Assignment to “normal” karyotype required a minimum of 10 metaphases analyzed. A complex karyotype was defined as the presence of 3 or more distinct structural or numeric abnormalities. MK was defined as 2 or more distinct autosomal monosomies or single autosomal monosomy associated with at least one structural abnormality (JCO. 2008;26:4791). Results : A total of 903 patients (median age 65 years; range 19-92; 63% males) met the above stipulations for study eligibility. Dynamic International Prognostic Scoring System (DIPSS)-plus risk distribution (JCO. 2011;29:392) was high in 344 (38%) patients, intermediate-2 in 334 (37%), intermediate-1 in 128 (14%) and low in 97 (11%). 472 patients were annotated for JAK2/CALR/MPL mutations; 276 (58%) harbored JAK2, 117 (25%) CALR and 33 (7%) MPL mutations. Abnormal karyotype was documented in 437 (48%) patients and included sole abnormalities of 20q- (n=71; 16%), 13q- (n=57; 13%), +8 (n=25; 5%), -7/7q- (n=17; 4%) and +9 (n=16; 3%). 22 (5%) patients displayed MK and 31 (7%) complex karyotype without MK. At a median follow-up time of 3 years, 634 (70%) deaths and 65 blast transformations (BT; 7%) were recorded. A step-wise survival analysis, using “normal karyotype” and “MK/inv(3)/i(17q)” as comparators for “low” and “very high risk” categories, respectively, resulted in four distinct cytogenetic risk designations: very high (MK, inv(3), i(17q), -7/7q-, 11q or 12p abnormalities; n=67), high (complex without MK, two abnormalities not included in very high risk category, 5q-, +8, other autosomal trisomies except +9, and other sole abnormalities not included in other risk categories; n=164), intermediate (sole abnormalities of 20q-, 1q duplication or any other translocation, and -Y or other sex chromosome abnormality; n=133) and low (normal or sole abnormalities of 13q- or +9; n=539); the corresponding median survivals were 0.9, 2.6, 3.8 and 4.6 years, with respective HR (95% CI) of 4.4 (3.3-5.8), 2.0 (1.6-2.4) and 1.3 (1.03-1.6). Very high (HR 6.1, 95% CI 2.9-13.2) and high (HR 2.2, 95% CI 1.1-4.1) risk categories were also associated with higher risk of BT. There was no significant correlation between the revised cytogenetic risk stratification and JAK2/CALR/MPL mutational categories (p=0.22), but none of the triple-negative or MPL-mutated patients displayed “very high risk” karyotype. The revised cytogenetic model was also effective in risk-stratification of JAK2 or CALR mutated patients, when analyzed separately, and its prognostic relevance for survival was generally independent of JAK2/CALR/MPL mutational status (p<0.01), DIPSS (p<0.01) or DIPSS-plus (p<0.01). Comparison of the currently used “favorable” vs “unfavorable” with the revised cytogenetic risk model showed a significant number of patients with “favorable” karyotype (n=213 of total 753) being re-assigned to high (n=82) or intermediate (n=131) risk categories. Conclusions : The currently used cytogenetic risk stratification in PMF is too broad and underestimates prognosis in a significant number of patients with “favorable” karyotype. We have developed a revised four-tier risk model that is independent of conventional risk models and JAK2/CALR/MPL mutational status and is expected to facilitate the development of genetics-based prognostic scoring systems in PMF. Disclosures No relevant conflicts of interest to declare.

Colony stimulating factor 3 receptor gene (CSF3R) mutations have recently been associated with chronic neutrophilic leukemia (CNL). Fourteen patients with CSF3R‐mutated CNL (median age 67 years; 57% males) were screened for additional mutations; 8 (57%) and 5 (38%) harbored an ASXL1 and/or SETBP1 mutation (two patients expressed both), respectively. Two patients developed blastic transformation, both SETBP1‐mutated and ASXL1‐unmutated, whereas two other cases evolved into chronic myelomonocytic leukemia (CMML), both ASXL1‐mutated and SETBP1‐unmutated. Median survival was 23.2 months (10 deaths documented). On multivariable analysis mutated ASXL1 (P = 0.009; HR 19.6, 95% CI 2.1–184.1) and thrombocytopenia (P = 0.005; HR 28.8, 95% CI 2.8–298.2) were independently predictive of shortened survival. This study provides information on the natural history of CSF3R‐mutated CNL and identifies mutant ASXL1 and thrombocytopenia as risk factors for survival. The study also suggests pathogenetic roles for SETBP1 and ASXL1 mutations in disease evolution into blast phase disease and CMML, respectively. Am. J. Hematol. 90:653–656, 2015. © 2015 Wiley Periodicals, Inc.

Key Points Survival in ET is superior to that of PV, regardless of mutational status, but remains inferior to the sex- and age-matched US population. JAK2/CALR/MPL mutational status is prognostically informative in PMF, regarding overall and leukemia-free survival.

CALR (calreticulin) trails JAK 2 as the second most mutated gene in essential thrombocythemia (ET). Mutant CALR in ET is a result of frameshift mutations, caused by exon 9 deletions or insertions; type‐1, 52‐bp deletion (p.L367fs*46), and type‐2, 5‐bp TTGTC insertion (p.K385fs*47) variants constitute more than 80% of these mutations. The current study includes a total of 1027 patients divided into test ( n = 402) and validation ( n = 625) cohorts. Among the 402 ET patients in the test cohort, 227 (57%) harbored JAK 2, 11 (3%) Myeloproliferative leukemia virus oncogene ( MPL ), and 114 (28%) CALR mutations; 12% were wild‐type for all three mutations (i.e., triple‐negative). Among the 114 patients with CALR mutations, 51 (45%) displayed type‐1 and 44 (39%) type‐2 variants; compared to mutant JAK 2, both variants were associated with higher platelet and lower hemoglobin and leukocyte counts. However, male sex was associated with only type‐1 ( P = 0.005) and younger age with type‐2 ( P = 0.001) variants. Notably, platelet count was significantly higher in type‐2 vs. type‐1 CALR ‐mutated patients ( P = 0.03) and the particular observation was validated in the validation cohort that included 111 CALR ‐mutated ET patients ( P = 0.002). These findings, coupled with the recent demonstration of preferential expression of mutant and wild‐type CALR in megakaryocytes, suggest differential effects of CALR variants on thrombopoiesis. Am. J. Hematol. 89:E121–E124, 2014. © 2014 Wiley Periodicals, Inc.