ALBERT

Description: Glutathione S-transferases (GST) are phase II detoxification enzymes, involved in the metabolism of carcinogens and anti-cancer drugs. Since GSTs have been also shown to interact with kinase complexes during oxidative or chemical stress-induced apoptosis, their polymorphic variants may account for differences in outcome following chemotherapy between individuals. Studying 106 patients (pts) with acute myeloid leukaemia (AML), we have shown that individuals with a GSTM1 and/or GSTT1 deletion were at higher risk of relapse and of shorter overall survival (Voso et al, Blood100:2703, 2002). The aim of the present study was to confirm or previous findings and to better define the role of GSTM1 and GSTT1 deletions in the context of a molecularly well-characterized cohort of AML-patients who were treated within two prospective clinical trials of the German-Austrian Acute Myeloid Leukemia Study Group (AMLSG) In addition to polymorphisms in GSTM1 and GSTT1, we were also interested in the role of the GSTP1(Ile105Val) polymorphism on outcome. Based on our previous work, we intended to show a 20% difference in the 3-year survival rate. Therefore the estimated power for our current study including 350 patients to confirm the previous findings was 98%. We studied 354 patients (pts) with AML, treated according to two AMLSG prospective multicenter clinical trials (HD98-A for pts with age 〈 60 years, 254 pts; HD98-B for pts 〉 60 yrs, 100 pts). The Ile105Val polymorphism of the GSTP1 gene (GSTP1*105) was analyzed by PCR-RFLP, while GSTM1 and GSTT1 homozygous deletions (GSTM1*0 and GSTT1*0) were studied using a multiplex PCR technique, including the housekeeping gene BCL-2 as internal control. GST genotypes were not associated to patients’ characteristics, including type of AML, cytogenetic risk group, presence of FLT3-ITD and abnormal laboratory parameters, and response to induction chemotherapy. GSTP1*105Val was associated with a significant better relapse-free survival using age-stratified test (adjusted HR, 0.7; 95% C.I., 0.51–0.98), while GSTT1 and GSTM1 genotypes had no impact on RFS. A Cox proportional hazard model on RFS including GST genotypes, LDH level, cytogenetic risk group, and FLT3-ITD mutation status showed that the GSTP1 genotype was a significant variable associated with a favourable outcome (n= 236 pts, HR, 0.62; 95% C.I., 0.44–0.88). Limiting the analysis to patients with a normal karyotype, the GSTP1 105Val allele was associated in the multivariable model on RFS with a 51% risk reduction (HR, 0.49; 95%C.I., 0.30–0.81). In conclusion, GSTP1*105Val seems to be of prognostic value, whereas the prognostic value of GSTM1 and GSTT1 reported in previously could not be confirmed.

Description: Background: Several studies have suggested that genetic variability related with single nucleotide polymorphisms (SNPs) of the BER system, DNA synthesis and folate-metabolizing pathway genes could modulate DNA repair capacity. Moreover, these genes are supposed to be related to cancer risk. However, the prognostic impact of the association of individual and/or combined genetic variants in patients with myelodysplastic syndromes (MDS) remains undetermined. Methods: We genotyped 113 MDS patients, 54 with IPSS low/int-1 receiving only best supportive care (BSC group) and 59 with IPSS int-2/high treated with azacitidine (AZA-group), for the following polymorphisms: XRCC1 194 and 399, APE1 148, XRCC3 241, TS5'-UTR (2R/3R and G/C) and 3'-UTR (6bp+/6bp-), MTHFR 677 and 1298. Genomic DNA was analyzed by High Resolution Melting assay and restriction digests of PCR products. Overall survival (OS) was calculated using the Kaplan-Meier estimate probabilities, and differences between survival curves were analyzed by the log-rank test. Multivariate analyses were performed using the Cox method. Results: For all the target genes, the distribution of genotypes was consistent with the Hardy-Weinberg equilibrium. Among the baseline characteristics analyzed (age, sex, diagnosis according to WHO, hemoglobin) there was no statistically significant difference in the genotype distribution of studied polymorphisms. In the BSC group, the variants XRCC1 399 GG [Hazard ratio (HR)=7.07; p=0.02], -6/-6 of TS3'-UTR (HR=4.65; p=0.05), 2R/3G, 3C/3G, 3G/3G of TS5'-UTR (HR=11.44; p=0.02) and TT of MTHFR 677 (HR=67.12; p

Description: Introduction Erythrocytosis is characterized by persistently raised hemoglobin (HB) and hematocrit (Ht) levels. Differential diagnosis includes Polycythemia Vera (PV), secondary, hereditary (HE) and idiopathic erythrocytosis (IE). Recently, Randi et al. (Br J Haematol, 2018) demonstrated the recurrence of HFE single nucleotide variants (SNVs) in patients with IE, postulating a possible link between Hemochromatosis genes and erythrocytosis. The most frequent HFE SNVs are C282Y and H63D, reported at allele frequencies of about 13% and 4% in Caucasian countries. HE has also been associated with mutations in genes members of the complex pathway of "oxygen sensing" (EPOR, VHL, HIF-2a and PHD2). To date, 30 mutations have been described in the PHD2 gene, all localized in the catalytic domain, which impair binding to HIF-2a. The PHD2p.C127S variant is frequently observed in Tibetans with D4E in cis (overall prevalence of this haplotype is 88.6% at altitudes above 3000m), in linkage disequilibrium with other missense mutations (in particular HIF-2a/EPAS1). Surprisingly, the combination of PHD2/HIF-2a variants result in a gain-of-function effect that blunts the hypoxic response, providing a molecular mechanism for the observed protection of Tibetans from erythrocytosis at high altitude. In normoxic conditions and in low-landers, the PHD2p.C127S variant may lead to increased erythropoiesis as reported in the literature. Patients and Methods Twenty-three patients with erythrocytosis (21 males and 2 females with a median age of 56 years, range 18-76, Table 1) negative for JAK2 mutations (both V617F and exon 12 variants), and with a bone marrow histology not suggestive of a myeloproliferative syndrome were studied for secondary causes of erythrocytosis using an appropriate algorithm (EPO levels, chest and abdomen imaging, spirometry, venous p50 of HB, arterial blood gas analysis). Since all tests were negative, HE genes mutation analysis was carried out, using Sanger sequencing of EPOR exon 8, the VHL coding region, PHD2 exon 1-3 and HIF-2a exon 12. HFE SNVs were studied using allele-specific real-time PCR. Results Sequencing of HE genes identified 4 carriers of PHD2 variants in 23 patients (17%). One patient had a novel missense heterozygous mutation (PHD2p.I269N). The study of his kindred showed that his sister and one daughter have HE and both carried the same heterozygous mutation of the propositus. Furthermore, his father had died with a diagnosis of PV in the pre-JAK2 era. In contrast, the patient's brother and the other daughter, both with normal Hb and Hct, had wild-type PHD2. Of note, the propositus and his two daughters were heterozygous for H63D in the HFE gene. The patient's pedigree is illustrated in Figure 1. Interestingly, three further patients tested positive for the PHD2 missense heterozygous variant (PHD2p.C127S) previously reported in the Tibetan population, and whose role in patients with erythrocytosis is still unclear. HFE SNVs real-time PCR revealed 7 carriers of the H63D, 1 of C282Y and 1 of S65C SNV in the HFE gene (about 40% of our cohort). Interestingly, two H63D heterozygous patients were a father and his son. They were all males with a median age of 48 years (range 18-64). The prevalence of HFE SNVs in our cohort of patients with erythrocytosis is higher than expected for H63D and S65C for Caucasians (30% vs 13% for H63D and 4.35 vs 1.5% for S65C), while the allele frequency of C282Y was similar to that of the general population. Finally, the patient with the S65C SNV also had the "Tibetan" PHD2 polymorphism. Conclusions In addition to previously known PHD2 gene alterations, we report here the occurrence in HE patients of a novel PHD2 mutation with an autosomal-dominant inheritance likely involved in disease pathogenesis. The milder phenotypic features of this patient's daughter and sister in terms of erythocytosis, may be explained by the childbearing age and the absence of H63D SNV, respectively. The increased prevalence of HFE SNVs in patients with IE may indicate an effect of impaired iron metabolism on erythropoiesis. Our data show that the inclusion of HFE SNVs and oxygen pathway mutational analysis in the diagnostic algorithm of erythrocytosis may help to better define the genetic basis of erythrocytosis. Further studies -including the analysis of molecules involved in iron storage pathway- in larger IE patient cohorts are warranted in order to clarify the link between HFE gene and IE. Disclosures Voso: Celgene: Research Funding, Speakers Bureau.

Description: The myeloid transcription factors C/EBPalpha and PU.1 play a pivotal role in normal hematopoiesis and alterations of their function are involved in the pathogenesis of Acute Myeloid Leukemia (AML). So far, different mechanisms have been shown to affect their function and are important in some AML subsets. However most AML patients do not apparently show any alteration of these transcription factors. Here, we investigated C/EBPalpha and PU.1 mRNA levels by real time RT-PCR in 109 AML patients and correlated these data to morphology, FLT3 mutations and cytogenetics. C/EBPalpha and PU.1 levels were expressed as percentage of 18S. Twelve normal bone marrow mononuclear cells, four CD34+ cells isolated from normal bone marrow samples and 8 peripheral blood granulocytes and monocytes, were used as controls. Heterogeneous PU.1 expression was observed in AML patients (median 0.657, range 0.004 – 24.148), while PU.1 levels were more homogeneous in normal bone marrows (median 1.5, range 0.328 – 4.737). In particular, 55 AML patients (50.5%) had PU.1 levels similar to controls, while 37 patients (33.9%) and 17 patients (15.6%) expressed PU.1 levels at levels lower and higher, than the control range, respectively. In the same way, also C/EBPalpha mRNA expression was variable (median 0.047, range 0.0002 – 1.858 in AML and median 0.064, range 0.008 – 0.138 in normal bone marrows). Fourty-five AML patients (41.%) displayed C/EBPalpha levels similar to the normal range, while 26 patients (23.8%) had lower and 37 (33.9%) higher C/EBPalpha expression. Looking at different AML subsets, we found low C/EBPalpha mRNA in patients carrying recurrent chromosomal abnormalities, such as t(8;21) and inv16, as previously reported. On the other hand, patients carrying 11q23 rearrangements showed higher PU.1 levels than normal controls. No association was found between C/EBPalpha and PU.1 levels and therapy-related AML, AML with normal karyotype, AML with multilineage dysplasia, and AML not otherwise characterized (including previous F.A.B. categories). Although experimental models showed that FLT3 internal tandem duplications (ITD) downregulate both transcription factors, we did not find any association between the presence of FLT3 ITD and D835 mutations and C/EBPalpha and PU.1 levels, both in the whole patient group and in patients with normal karyotype. We then analyzed expression of two PU.1 and C/EBPalpha target genes, the M-CSF and G-CSF receptors, in patients expressing high and low levels of these transcription factors. A direct correlation was found between C/EBPalpha and G-CSFR levels (Spearman r = 0.5; p=0.02, 95% C.I. 0.07 – 0.78), while there was a tendency to correlation between PU.1 and M-CSFR, that did not reach the statistical significance. Since mutations and post-trascriptional events may affect C/EBPalpha and PU.1 function, we analyzed protein expression of 18 patients by Western Blotting. PU.1 protein was expressed by all patients. The functional p42 C/EBPalpha isoform was absent in 2 patients that expressed only the 30 kDa isoform, and was undetectable in 5 of 18 patients. In conclusion, down regulation of PU1 mRNA was found in one third of AML patients, consistently with the oncosuppressive role recently described. On the other side, C/EBPalpha is down-regulated in specific AML subsets, with recurrent cytogenetic abnormalities, while mutations and post-translational events could affect C/EBPalpha expression in other patients.

Description: Myelodysplastic syndromes (MDS) are a genetic and epigenetic disease of the hematopoietic stem cell. Aberrant CpG islands methylation in the contex of the promoter of multiple genes plays a pivotal role in the pathogenesis of MDS and leads to silencing of tumor suppressor genes, including cell-cycle inhibitors, inducers of apoptosis, DNA repair genes, transcription factors, cell adhesion mediators, hormonal receptors and detoxifiers. Demethylating agents, such as decitabine and azacitidine, are able to revert epigenetic silencing induced by hypermethylation and are currently used to treat all subtypes of MDS. Some of the target genes of demethylating drugs have been well studied and correlated to clinical response of patients, such as p15INK4B, but most of them remain to be identified and characterized. We isolated CD34+ cells from two patients with previously untreated MDS, a 70 year old female, with a diagnosis of Refractory Anemia with Excess Blasts (RAEB) and a complex karyotype including deletion of 5q11–q34 and trisomy 8, and a 59 years old male, with a diagnosis of RAEB in transformation, according to FAB and a normal karyotype. CD34+ cells were isolated from bone marrow samples by immunomagnetic beads, with a yield of about 2 x 106 cells per patients. Purity of the CD34+ cell fraction, evaluated by flow cytometry, was 58% and 86%, respectively. Cells were cultured in 24-well plates in IMDM medium with L-Glutamine, antibiotics, 30% of inactivated Foetal Bovine Serum and 10 ng/ml each of IL-3, Stem Cell Factor (SCF), Thrombopoietin and FLT3-ligand. After 24 hours, decitabine was added to the culture medium to a final concentration of 1 m M. A corresponding amount of acetic acid was added to different wells for the mock treatment control. Each experiment was conducted in triplicate. Cells were collected after 72 hours of treatment and RNA was extracted by the Qiagen RNeasy Kit, processed by two-cycle cDNA synthesis kit (Invitrogen), in vitro transcripted to cRNA and hybridized on Affymetrix HG-U133A chips. Five chips were used for each patient: three for treated cells and two for mock -treated cells. Microarray data were normalized and analysed by GeneSpring software version 7.2 and the ANOVA Welch’s test was applied. We selected genes with a p value less than 0.01 and a fold change higher than 2. Using these conditions, 60 genes were upregulated by decitabine in both patients. Some of the most interesting genes were GATA binding protein 2 (GATA2), cyclin-dependent kinase inhibitor 1A (CDKN1A, p21), cyclin A1 (CCNA1), decay accelerating factor for complement (CD55, DAF), immediate early response 3 (IER3), nuclear factor interleukin 3 regulated (NFIL3) and chemokine (C-X-C motif) receptor 4 (CXCR4). Interestingly, the patient with a normal karyotype showed a higher percentage of up-regulated genes after decitabine treatment compared to the patient with the 5q11-q34 deletion and a trisomy 8. This suggests that epigenetic changes in gene expression may have higher impact when the karyotype is normal. Functional significance of these data remains to be elucidated. Expression and methylation status of these genes will be investigated in a larger group of MDS patients. This approach aims to characterize new genes, as methylation targets in MDS and possible markers of disease, and to identify patients responding to demethylating agents.

Description: Clonal haematopoiesis of indeterminate potential (CHIP) is defined by the detection of somatic mutations in genes recurrently mutated in myeloid neoplasms (MNs), in the blood of healthy individuals with normal blood values and lack of morphological evidence of MN. Recent studies have highlighted the potential association between CHIP and the development of MN, in particular therapy-related MN (t-MN) in patients with lymphoma treated with chemotherapy and/or autologous stem-cell transplantation. In the present study, we investigated whether the presence of CHIP is associated with a higher risk for the development of t-MN in patients with chronic lymphocytic leukemia (CLL) treated with chemo(immuno)therapy, including fludarabine and cyclophosphamide combinations. To this end, we studied 9 patients with CLL who developed a t-MN [acute myeloid leukemia (AML): n=6, myelodysplastic syndrome (MDS): n=3] after the administration of chemo(immuno)therapy (FCR: n=7, other, n=2), with available samples collected both before CLL treatment and at diagnosis of t-MN. The median interval between the two samples was 26 months (range: 9-38months). NGS was performed on DNA extracted from bone marrow mononuclear cells (MNCs) at t-MN diagnosis, using the Trusight Myeloid Sequencing Panel (n=4) and the Archer VariantPlex Myeloid kit (n=5). Backtracking of the variants detected at the t-MN phase was performed by NGS of DNA extracted from peripheral blood MNCs (n=8) or CD19+ selected cells (n=1) in the samples from the CLL phase. In case no variants were detected in the t-MN phase, targeted digital droplet PCR (ddPCR) was also performed in paired CLL samples to confirm the presence of the variants. Moreover, using the Trusight Myeloid Sequencing Panel, we evaluated the prevalence of CHIP in a population cohort of 285 patients with CLL at the time of diagnosis. The variant allele frequency (VAF) cut-off for the detection of the variants was set to 5%. Variants were reported if meeting the following criteria: (i) located within an exonic or splicing region; (ii) be non-synonymous; (iii) not listed in the gnomAD database, if not also recurrently reported in Cosmic v85. Overall, 16 variants were detected in 7/9 cases analyzed at the time of t-MN [NRAS (n=4), DNMT3A (n=3), TET2 (n=2), EH2 (n=2), TP53 (n=2), KRAS (n=1), U2AF1 (n=1) and SF3B1 (n=1)], while no variants were detected in 2 t-MN samples. In 6/7 cases with detectable variants at t-MN diagnosis, the same variants were present at the CLL phase with either lower (n=4) or similar (n=2) VAF. Overall, CHIP was detectable in 6/9 (66.7%) CLL patients who later developed a t-MN. Among the untreated CLL patients, 45 CHIP-related variants were detected in 35/285 cases (12%) as 7 patients harbored more than one variant. The median VAF was 12.7% (5.1-58.6%) with 27/45 (60%) having a VAF

Description: Clonal hematopoiesis (CH) has been recognized as a predisposing factor for the development of myeloid malignancies. Its detection has been reported at different frequencies across studies, based on the type of genome scanning approach used and the population studied, but the latest insights recognize its virtual ubiquitous presence in older individuals. The discovery of CH in recent years paved the way for a shift in the paradigm of our understanding of the biology of therapy-related myeloid malignancies (t-MNs). Indeed, we moved from the concept of a treatment-induced lesion to a model where CH precedes the commencement of any cancer-related treatment in patients who subsequently develop a t-MN. Invariant patterns of genes seem to contribute to the arising of t-MN cases, with differences regarding the type of treatment received. Here, we review the principal studies concerning CH, the relationship with myeloid progression and the mechanisms of secondary t-MN development.

Description: Therapy-related myeloid neoplasms (t-MNs) include diseases onsetting in patients treated with chemo- and/or radiotherapy for a primary cancer, or an autoimmune disorder. Genomic variants, in particular, in familial cancer genes, may play a predisposing role. Recent advances in deep sequencing techniques have shed light on the pathogenesis of t-MNs, identifying clonal hematopoiesis of indeterminate potential (CHIP) as a frequent first step in the multihit model of t-MNs. CHIP is often detectable prior to any cytotoxic treatment, probably setting the fertile genomic background for secondary leukemogenesis. The evolution pattern toward t-MNs is then a complex process, shaped by the type of cancer therapy, the aging process, and the individual exposures, that favor additional hits, such as the acquisition of TP53 mutations and unfavorable karyotype abnormalities. The pathogenesis of t-MNs differs from MN associated with environmental exposure. Indeed, the genetic aberration patterns of MN developing in atomic bomb survivors show few mutations in classical DNA methylation genes, and a high prevalence of 11q and ATM alterations, together with TP53 mutations. Survival in t-MNs is poor. In addition to the biology of t-MNs, the patient’s previous disease history and the remission status at t-MN diagnosis are significant factors contributing to unfavorable outcome. New drugs active in secondary leukemias include CPX-351, or venetoclax in combination with hypomethylating agents, monoclonal antibodies as magrolimab, or targeted drugs against pathogenic mutations. Allogeneic stem cell transplantation remains the best currently available therapeutic option with curative intent for fit patients with unfavorable genetic profiles.

Description: The mechanism underlying cell type-specific gene induction conferred by ubiquitous transcription factors as well as disruptions caused by their chimeric derivatives in leukemia is not well understood. Here, we investigate whether RNAs coordinate with transcription factors to drive myeloid gene transcription. In an integrated genome-wide approach surveying for gene loci exhibiting concurrent RNA and DNA interactions with the broadly expressed Runt-related transcription factor 1 (RUNX1), we identified the long noncoding RNA (lncRNA) originating from the upstream regulatory element of PU.1 (LOUP). This myeloid-specific and polyadenylated lncRNA induces myeloid differentiation and inhibits cell growth, acting as a transcriptional inducer of the myeloid master regulator PU.1. Mechanistically, LOUP recruits RUNX1 to both the PU.1 enhancer and the promoter, leading to the formation of an active chromatin loop. In t(8;21) acute myeloid leukemia (AML), wherein RUNX1 is fused to ETO, the resulting oncogenic fusion protein, RUNX1-ETO, limits chromatin accessibility at the LOUP locus, causing inhibition of LOUP and PU.1 expression. These findings highlight the important role of the interplay between cell-type–specific RNAs and transcription factors, as well as their oncogenic derivatives in modulating lineage-gene activation and raise the possibility that RNA regulators of transcription factors represent alternative targets for therapeutic development.