Overview on Pediatric Myelodysplastic Syndrome: A Review

Myelodysplastic syndrome (MDS) is a set of clonal bone marrow diseases in children that are characterised by peripheral cytopenia, dysplastic alterations in the bone marrow, and inefficient hematopoiesis. MDS is uncommon in children, with just 1-4 occurrences per million children afflicted. Adults, particularly the elderly, are more susceptible to the disease. Some hereditary disorders, such as Fanconi's anaemia, Shwachman's, and Down's syndromes, are known to predispose children to developing MDS. JCML and monosomy 7 syndrome are the two most frequent paediatric MDS types, both of which affect children in their early years. Approximately 20% of juvenile myelodysplastic syndrome (MDS) cases are discovered by chance during normal laboratory testing or during the course of a suspected hereditary bone marrow failure (IBMF). Differentiating MDS with low blast numbers from aplastic anaemia (AA) and MDS with excess blasts from AML are the two key diagnostic issues in this condition. Bone marrow transplantation and stem cell transplantation is the treatment of choice in most cases. In this article we discuss the disease epidemiology, diagnosis, and treatment.

Non-Intensive Continuous Treatment with a Tyrosine Kinase Inhibitor (TKI) Followed By Allo-HSCT Is an Effective Therapeutic Strategy for Adult Ph-Positive Acute Lymphoblastic Leukemia: Outcomes of the Russian Prospective Multicenter RALL Study

Introduction. As Ph-positive (Ph+) ALL in adults remains less favorable in prognosis than other ALL, and by expert opinion needs non-intensive chemotherapy protocols and new generation TKI with the majority of pts undergoing allo-HSCT, the results of treatment based on the different approach: de-escalated but continuous treatment with the change of TKI according to the molecular response and allo-HSCT may be of interest and provide new insights to the treatment of Ph+ ALL. Aim. To evaluate survival and outcomes in different risk groups in pts with Ph+ ALL in the RALL-study (Ph+ALL-2009, Ph+ALL-2012 and Ph+ALL-2012m protocols). Patients and methods. Between January 2010 and June 2021, 74 new Ph+ ALL cases were diagnosed in 6 centers of the RALL-group and 63 of them were evaluable for analysis (median age 37 years (17-73), m/f 32(43%)/42(57%), CNS disease in 13(21%) pts, WBC>30*10 9/l in 27(43%) pts, bcr/abl transcript p190/p210/p190+210 in 31(60%)/12(23%)/9(17%) cases). Standard cytogenetic was performed in all 63 pts, 1 had no mitosis, 6(10%) monosomy 7 and 2 (3%) complex karyotypes were detected. All pts were treated according to RALL protocols with continuous Imatinib. Ph+ALL-2009 protocol included 600 mg Imatinib with prednisone, VNCR, L-asp, Dauno, Cph, followed by 6-MP and MTX. Imatinib had to be changed to Dasatinib (140 mg) after non-achievement of molecular complete response (MolCR) on day 70. MolCR was defined as bcr/abl chimeric transcript <0,01% by PCR with 10 -4 sensitivity. In protocols Ph+ALL-2012 and Ph+ALLm, we de-intensified chemotherapy: reduced Dauno, Cph and L-asp doses, accordingly. All pts were considered as candidates for allogeneic HSCT in CR1 if HLA-identical donor was available. 36 (57%) pts underwent HSCT in the first-line therapy: 2(6%) autologous, 9 (25%) matched related, 20 (56%) matched unrelated and 5 (13%) haplo-HSCT. Results. Hematological complete remission (CR) was achieved in 60 (95%) of 63 pts (1 early death and 2 refractory cases occurred). On day 70, MolCR was achieved in 21(38%) of 56 pts. Death on therapy in CR (within 5 months of induction/consolidation) was registered in 4 (6%) cases. The major causes of the non-relapsed mortality in unrelated allo-HSCT (n=9) were aGVHD and severe infections, at a median +4 months after HSCT. The 5-year overall survival (OS) and disease-free survival (DFS) for all 63 pts were 58% and 45%, respectively. The long-term outcome on different protocols (Ph+ALL-2009, Ph+ALL-2012 and Ph+ALL-2012m) were similar: 3-year OS - 55% vs 51% vs 75% (p=0,27), 3-year DFS - 56% vs 44% vs 50% (p=0,54), respectively. The 5-year OS was 65% vs 61% (p=0,84), and DFS was 57% vs 31% (p=0,24) in transplanted vs non-transplanted patients by landmark analysis with a median 5,3 month of CR. Landmark analysis of 5-year OS for transplanted and non-transplanted pts depending on age showed no significant difference for both groups: >45y 40% vs 80%; and ≤45y 70% vs 49%, respectively (p=0,1625), although data for 5-year OS was still not mature at the time of analysis. DFS was significantly different in transplanted vs. non-transplanted pts: >45y 40% vs 71%; ≤45y 61% vs 0%; respectively (p=0,0439). In a multivariate analysis for Ph+ ALL among common risk factors (age > 45y, WBC>30, LDH>2N, immunophenotype, late MolCR >70d, CNS leukemia) WBC>30, HSCT were significant risk factors for OS and DFS. Conclusions. Our data demonstrate that de-intensification of chemotherapy does not affect the efficacy of Ph+ ALL therapy in the era of TKIs. We confirmed that patients older than 45y old could be treated by chemotherapy with TKI (new generation TKI if needed) only, but all pts younger than 45y should be considered for HSCT. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Single-Cell Transcriptomic and Proteomic Analysis of Acute Myeloid Leukemia (AML) Patients with Abnormalities on Chromosome 7

Background: Chromosome 7 (chr7) abnormalities are commonly seen in patients with acute myeloid leukemia (AML) or myelodysplastic syndrome and are associated with poor prognosis. Flow cytometry (FCM) is typically used clinically to quantify residual malignancy during treatment but the relationship of cell surface immunophenotype with genetic features is incompletely defined. Single-cell RNA sequencing (scRNA-seq) with oligonucleotide-conjugated antibodies may be able to integrate cytogenetic genotypes found within leukemic clones with specific transcriptomic and immunophenotypic signatures. Methods: Bone marrow (BM) aspirate was collected from 12 AML patients with known abnormalities on chr7 according to cytogenetics and 3 healthy donors (HDs). We previously established a reference for normal immune cells where we assessed the BM of 20 HDs (PMID:30518681). HDs in present study were selected from this same cohort. Multi-parameter FCM was performed as previously described and scRNA-seq with 31 antibodies (10x Genomics, 3'v2) was performed on BM mononuclear cells. Data from 16 samples (including 1 patient replicate) were mapped onto the atlas with dimension reduction in gene expression (GEX) by principal component analysis and Uniform Manifold Approximation and Projection (UMAP). Cell clusters were constructed and surface proteins were utilized to determine cellular annotation. Patient GEX profiles were compared to those of HDs, and two algorithms were used to identify malignant cells with chromosomal abnormalities. Alterations of large chromosomal segments were identified by Hidden Markov Model. Clinical cytogenetics and expression matrices from the model output were combined to annotate individual cells as malignant or normal for all potential regions. Machine learning classifiers were applied to predict malignant cells using protein expression and important proteins were selected by models with measure for significant features. Results: After quality control, 132,658 cells were included, of which 43,441 and 12,572 cells from AML patients and HD respectively had additional cell surface immunophenotyping data. Samples were well-integrated by UMAP (Figure 1A) and cell annotation overlapped with previously reported annotations by GEX of HDs (Figure 1B), with 15,270 malignant cells identified (Figure 1C). Malignant groups were created if more than 20 cells shared the same chromosomal alterations. Among all 12 patients, 3 of them only had monosomy 7 as the sole genetic aberration, while 9 patients had abnormalities on other chromosomes. The correlation between cell types showed distinct features among patients, and cells in different groups had different protein expression profiles. For example, 22% of the cells (n = 432) from the myeloid population of patient 1 (n = 1957) were identified as normal and 77% had a loss of chr7 (Figure 2A). Clustering in lower resolution separated them into two groups: CD11b+CD33+ (n = 1026) and CD133+CD34+ (n = 931). The CD133+CD34+ group had a higher percentage of malignant cells overall (74% vs. 83%) while a subset of the CD11b+CD33+ group (CD16+CD13+) had the highest percentage of cells with losses on both chr2 and chr7 (60%). Data from patient 2 also suggested that cells with different immunophenotypes were estimated to have different chromosomal changes (Figure 2B). While 69% of the malignant cells had a loss on chr7, most of those without changes on chr7 were from CD45+CD11b+ group where 62% of the cells did not have a detectable change on chr7. The top significant proteins for distinguishing malignant from normal cells among all patients were CD117, CD33, CD34, CD44, and CD47. FCM intensity was compared with the scRNA-seq immunophenotyping data, confirming the similarity in distribution. The scRNA-seq data with immunophenotyping can capture and recapitulate the leukemic immunophenotype, further linking it with copy number changes to reveal potential subclonal structures. Conclusion: By comparing the expression profile of AML patients with abnormalities on chr7 to HDs, this study provides evidence that leukemic immunophenotype is correlated with chromosomal structural changes. The experiments on a single-cell level were able to identify clones in higher resolution and revealed potential cell surface protein markers that could be used clinically to identify specific malignant populations in patients with myeloid malignancies. Figure 1 Figure 1. Disclosures Ghiaur: Syros Pharmaceuticals: Consultancy; Menarini Richerche: Research Funding. Hourigan: Sellas: Research Funding.

Pre-Clinical Efficacy of Targeting TBL1/R-β-Catenin-TCF7L2 Axis Against AML with 3q26 Lesions and EVI1 Overexpression

EVI1 gene maps to the MECOM locus at chromosome 3q26.2 and encodes for a zinc finger domain-containing transcriptional regulator. EVI1 supports hematopoietic stem cell self-renewal and blocks hematopoietic differentiation. EVI1 is overexpressed in up to 10% of AML, including those harboring chromosome translocation t(3;3)(q21;q26.2) or inv(3)(q21;q26.2), where the distal GATA2 hematopoietic enhancer is repositioned to induce EVI1 overexpression while repressing GATA2. EVI1 overexpression due to 3q26.2 lesions in MDS and AML is frequently associated with monosomy 7 and confers poor response to therapy and inferior relapse-free and overall survival. We had previously reported the pre-clinical efficacy of targeting TBL1/R1-nuclear β-catenin-TCF7L2 by tegavivint (BC-2059, Iterion Therapeutics) against AML stem/progenitor cells. This led us to interrogate the anti-AML activity of tegavivint (TV) in AML models harboring 3q26.2 lesions, where EVI1 overexpression has been documented to drive the biology of AML stem/progenitor cells. For this, we utilized AML cell lines with 3q26.2 lesions with/without monosomy 7 (UCSD-AML1, OCI-AML20, AML191 / MUTZ-3, AML194, HNT34), as well as patient-derived (PD) AML cells with 3q26 lesions with or without monosomy 7. Treatment with TV (10 to 100 nM) dose-dependently induced apoptosis in these cellular models. This was associated with attenuation of protein levels (determined by immunoblot analyses) of EVI1, TCF7L2, c-Myc, c-Myb, RUNX1, CEBPα, c-KIT, BCL2, Bcl-xL and MCL1, but upregulation of CD11b, BIM and cleaved PARP levels. Additionally, pan-BET protein inhibitor OTX015 (100 to 1000 nM) dose-dependently induced apoptosis of AML cell lines and PD AML cells with t(3:3)/inv(3). Following TV treatment, RNA-Seq and gene set enrichment analysis in UCSD-AML1 and OCI-AML20 cells showed log2 fold-changes in gene expression and positive enrichment of pathway genes and/or reactomes of inflammatory response, TNFα and interferon signaling, TGFβ, NOTCH and apoptosis signaling, as well as negative enrichment of gene sets of c-Myc, E2F, G2M checkpoint, DNA replication and repair and chromosome maintenance (all with FDR q-values < 0.1). QPCR analysis showed repression of EVI1, MYC and KIT, but upregulation of Axin2 mRNAs. Following TV treatment, confocal microscopy showed reduction of nuclear protein levels of EVI1 and β-catenin, as well as disrupted their co-localization with TBL1. Proximity ligation assay also demonstrated that exposure to TV significantly reduced the proximity of TBL1 and EVI1 as well as of TBL1 and β-catenin. Mass cytometry (CyTOF) analysis of patient-derived (PD) AML samples with t(3:3)/inv(3) confirmed that TV treatment attenuated protein levels of EVI1, c-Myc, RUNX1, β-catenin, TBL1/R1, Bcl-xL, BCL2, MCL1 and Ki67, but augmented protein levels of APC and cleaved PARP in phenotypically characterized AML stem cells (with high expression of CLEC12A, CD123, CD244, CD99, but low expression of CD11b). Consistent with effects of TV on gene-expressions that regulate cell death pathways, in vitro co-treatment with TV and BCL2 inhibitor venetoclax or OTX015 synergistically induced apoptosis (as determined by the SynergyFinder algorithm) of AML cell lines and PD AML cells with t(3:3)/inv(3) and EVI1 overexpression. In the in vivo HNT-34 model of flank-implanted and established tumors in athymic nude mice, treatment with TV (50 mg/kg, TIW, IP) and venetoclax (30 mg/kg, PO, daily) for 5-weeks yielded more tumor growth delay than vehicle control or TV alone. Additionally, following tail vein infusion and engraftment of luciferized AML191 cells in NSG mice, treatment with TV and/or venetoclax or OTX015 (30 mg/kg, PO, daily) was evaluated for 6 weeks. Co-treatment with TV and venetoclax or TV and OTX015 significantly reduced AML growth (determined by reduction in bioluminescence by Xenogen camera) (p < 0.05), as well as improved overall survival of the NSG mice more than treatment with each drug alone or vehicle control, without any toxicity. Collectively, these findings highlight that targeted inhibition of TBL1/R1-nuclear β-catenin-TCF7L2 by treatment with TV also inhibits EVI1 and its targets. They also demonstrate superior pre-clinical efficacy of novel TV-based combinations with BCL2 or BET protein inhibitor against AML models harboring 3q26 lesion and EVI1 overexpression. Disclosures DiNardo: Celgene, a Bristol Myers Squibb company: Honoraria, Research Funding; Forma: Honoraria, Research Funding; Foghorn: Honoraria, Research Funding; GlaxoSmithKline: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Honoraria, Research Funding; ImmuneOnc: Honoraria, Research Funding; Notable Labs: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria; Novartis: Honoraria; AbbVie: Consultancy, Research Funding; Agios/Servier: Consultancy, Honoraria, Research Funding. Takahashi: Symbio Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; GSK: Consultancy; Novartis: Consultancy; Celgene/BMS: Consultancy. Horrigan: Iterion Therapeutics: Current Employment. Kadia: Astellas: Other; Cure: Speakers Bureau; Genfleet: Other; Ascentage: Other; Jazz: Consultancy; Sanofi-Aventis: Consultancy; Dalichi Sankyo: Consultancy; Cellonkos: Other; Novartis: Consultancy; AstraZeneca: Other; BMS: Other: Grant/research support; Liberum: Consultancy; Amgen: Other: Grant/research support; Pulmotech: Other; Pfizer: Consultancy, Other; Genentech: Consultancy, Other: Grant/research support; Aglos: Consultancy; AbbVie: Consultancy, Other: Grant/research support.

Der(1;7)(q10;p10) Presents with a Unique Genetic Profile and Frequent ETNK1 Mutations in Myeloid Neoplasms

Background Der(1;7)(q10;p10) (der(1;7) is an unbalanced translocation recurrently found in myeloid neoplasms, particularly in myelodysplastic syndromes (MDS) and related disorders. Caused by a recombination between two homologous alphoid sequencing D1Z7 and D7Z1 on chromosomes 1 and 7, respectively, it results in monosomy 7q and trisomy 1q, which is implicated in the pathogenesis of der(1;7)-positive myeloid neoplasms. Previous studies reported frequent co-occurrence of +8 and del(20q), as well as RUNX1 mutations, the genetic and clinical characteristics of this abnormality has not fully been elucidated. Methods In this study, we enrolled a total of 153 cases myeloid neoplasms positive for der(1;7) from Japanese and German cohorts, in which co-occurring genetic lesions were analyzed using whole exome and/or targeted-capture sequencing. An additional 3,223 MDS and related neoplasm cases were also analyzed using targeted-capture sequencing to identify der(1;7)-specific genomic features. Results Ethnicity was evaluated comparing the frequency of der(1;7) in 944 German MDS cases and 763 Japanese MDS cases. Der(1;7) cases were observed at a higher frequency in Japanese MDS cohort compared to German MDS cohort (73/763 cases versus 4/944 cases, p < 0.00001). Der(1;7) cases showed a strong male predominance (86.3%) (p<0.001). Of 153 myeloid neoplasm patients harboring der(1;7), 114 were diagnosed with MDS, 28 with AML, 5 with MDS-MPN and 1 with MPN. Targeted-capture sequencing revealed mutations in common myeloid drivers (n=61) in 96% of der(1;7) cases. The most frequently mutated gene was RUNX1 with 46%, followed by ETNK1 (24.5%) and EZH2 (24.5%). Of interest, ETNK1 mutation was identified as the most unique to der(1;7) when compared to myeloid neoplasm cases without der(1;7) (n=3,066) [odds ratio (OR)=15.06], followed by ETV6 (OR=9.35) and EZH2 (OR=6.52). To further examine the uniqueness of this mutation profile, the mutational profile of der(1;7) was compared to those myeloid neoplasm cases harboring amp(1q) (n=52) and monosomy 7 (n=105). Highly frequent ETV6 and ETNK1 mutations were highly unique to der(1;7) cases when compared to amp(1q) cases (OR=3.72, OR=2.57, respectively). BCOR and ETNK1 mutations were highly unique to der(1;7) cases when compared to monosomy 7 cases (OR=35.88, OR=4.29, respectively). Both amp(1q) and monosomy 7 cases showed a higher mutation rate in TP53 compared to der(1;7) cases (49.1% and 51%, respectively, vs 3.5 %) . From these mutational characteristics, ETNK1 was identified as being the most unique to der(1;7) when compared to amp(1q), monosomy 7 and other myeloid neoplasm cases. ETNK1-mutated der(1;7) cases were featured with eosinophilia (p < 0.0005), a lack of RAS pathway mutations and trisomy 8 when compared to ETNK1-wild type der(1;7) cases. Survival analysis was conducted to elucidate the difference in survival in der(1;7) cases (n=65) versus myeloid neoplasm cases (n=2066). Der(1;7)-harboring myeloid neoplasm cases had a median overall survival of 6.8 months (95% CI, 3.5 to 11.9) and non-der(1;7) harboring myeloid neoplasm cases were 11.8 months (95% CI, 10.5 to 12.6). Thus, der(1;7)-harboring myeloid neoplasm cases had poorer prognosis (p<0.001). Conclusion In conclusion, der(1;7) is an unbalanced translocation that occurs predominantly in males and is seen more frequently in Japanese than Caucasian populations. Der(1;7) cases present with a mutational profile that is distinct from other myeloid neoplasm cases such as those with amp(1q) and monosomy7/del(7q), showing frequency of ETNK1 mutations. Disclosures Nannya: Otsuka Pharmaceutical Co., Ltd.: Consultancy, Speakers Bureau; Astellas: Speakers Bureau. Kern: MLL Munich Leukemia Laboratory: Other: Part ownership. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Atsuta: Astellas Pharma Inc.: Speakers Bureau; Mochida Pharmaceutical Co., Ltd.: Speakers Bureau; AbbVie GK: Speakers Bureau; Kyowa Kirin Co., Ltd: Honoraria; Meiji Seika Pharma Co, Ltd.: Honoraria. Handa: Ono: Honoraria; BMS: Honoraria; Janssen: Honoraria; Daiichi Sankyo: Research Funding; Celgene: Honoraria, Research Funding; Chugai: Research Funding; Kyowa Kirin: Research Funding; Takeda: Honoraria, Research Funding; Sanofi: Honoraria, Research Funding; Abbvie: Honoraria; MSD: Research Funding; Shionogi: Research Funding. Ohyashiki: Novartis Pharma: Other: chief clinical trial; Bristol Myers Squibb: Membership on an entity's Board of Directors or advisory committees. Haferlach: MLL Munich Leukemia Laboratory: Other: Part ownership. Ogawa: Otsuka Pharmaceutical Co., Ltd.: Research Funding; Eisai Co., Ltd.: Research Funding; Kan Research Laboratory, Inc.: Consultancy, Research Funding; Dainippon-Sumitomo Pharmaceutical, Inc.: Research Funding; ChordiaTherapeutics, Inc.: Consultancy, Research Funding; Ashahi Genomics: Current holder of individual stocks in a privately-held company.

Accurate Prediction of Chromosome-Level CNVs from Targeted NGS

Background: Aneuploidy and large-scale Copy Number Variations (CNVs) are prominent features of cancer cells. While Fluorescence in situ hybridization (FISH) and conventional cytogenetics (CC) are the gold standard for detecting aneuploidy and CNVs, NGS-based assays are currently used for high-resolution detection of copy number alterations assessing the whole genome. However, although an increasing number of NGS-based tools have been developed for detecting aneuploidy or CNVs from whole genome or exome sequencing data, only a limited number of options are available for targeted gene panels. Despite mechanisms provided to establish normal profiles for a specific panel, the accuracy of these tools at the chromosome level suffer when only a small number of regions are targeted on each chromosome. Here we leveraged on a custom amplicon based NGS assay designed to detect somatic alterations (SNVs and indels) in 297 hematological cancer relevant genes, previously validated in our clinical laboratory. We introduce a simple approach to accurately predict chromosome-level CNVs such as monosomy and trisomy for a targeted gene panel, commonly used in a clinical setting. Methods: Mutation profiles, including SNVs, INDELs, and structural changes, were interrogated with an in-house bioinformatics pipeline that utilized PureCN and CNVkit algorithms to detect structural changes. The first step consists of finding optimal panel-specific decision thresholds for gains and losses at the gene level. This step was performed using an independent set of 1,314 clinical samples sequenced with the NeoType® Heme assay developed by NeoGenomics Laboratories, Inc. for which at least one FISH test was performed in addition to the sequencing. Three genes (ATM, TP53, and NF1) were used to find optimal decision thresholds based on the FISH result for these markers. These thresholds are used afterward to predict a gain or a loss for any other gene in the panel. The second step consists of predicting the chromosome-level gain or loss based on the individual predictions at the gene level by simply observing the frequency of targeted genes on the corresponding chromosome predicted as either gained or lost by the first step approach. The 19, 7, and 18 targeted genes in the NGS panel (Table 1) were respectively used to predict monosomy 7, trisomy 8, and trisomy 12 in a second set of over 7,000 clinical samples with known ploidy for chromosomes with clinically relevant ploidy abnormalities in hematological malignancies. Results: Evaluation of the first stage gene-level CNV prediction on 1,314 clinical samples shows a concordance rate of 97.95% between NGS and FISH results on ATM, TP53, and NF1. When we evaluated the second stage chromosome-level CNV prediction in clinical samples sequenced using the same targeted panel and assessed by FISH for chromosome-level variation on chromosomes 7, 8 and 12 (Table 1), a heatmap of the predicted Log 2 ratios for each sample and targeted gene from the first step shows a clear distinctive signal between aneuploidy and diploid samples (Figure 1). At the chromosome level, the concordance rate between the final prediction and the FISH results is consistently observed above 93% (Table 2). Roughly 50% of the 12, 78, and 40 discordant calls for monosomy 7, trisomy 8, and trisomy 12, respectively captured by FISH but not by NGS can be explained by low tumor content (less than 20%) in the tested samples. The concordance rate between NGS and FISH is consistently observed above 96% when leaving these samples aside. Note that results in Table 2 are obtained using all samples to decide the optimal decision threshold for the chromosome-level prediction, but are found identical when using a leave-one-out evaluation procedure, and nearly identical when using a repeated cross-validation procedure. Conclusion: This study demonstrates that chromosome-level CNVs can be accurately predicted in hematologic malignancies even when the number of targeted genes on a given chromosome is low. Despite the simplicity of the approach, the two stages bioinformatics pipeline based on an ensemble method allowed us to gain between 8% and 46% accuracy compared to relying only on the prediction of a single tool like PureCN. Samples with low tumor content remain, however, a difficult case to tackle with bulk NGS as it is difficult to distinguish a CNV from the natural variability of the sequencing coverage. Figure 1 Figure 1. Disclosures Nam: NeoGenomics Laboratories, Inc.: Current Employment. Magnan: NeoGenomics Laboratories, Inc.: Current Employment. Lopez-Diaz: NeoGenomics Laboratories, Inc.: Current Employment. Bender: NeoGenomics Laboratories, Inc.: Current Employment. Agersborg: NeoGenomics Laboratories, Inc.: Current Employment. Jung: NeoGenomics Laboratories, Inc.: Current Employment. Funari: NeoGenomics Laboratories, Inc.: Current Employment.

HLA associations, somatic loss of HLA expression, and clinical outcomes in immune aplastic anemia

Immune aplastic anemia (AA) features somatic loss of HLA class I allele expression on bone marrow cells, consistent with a mechanism of escape from T cell-mediated destruction of hematopoietic stem and progenitor cells. The clinical significance of HLA abnormalities has not been well characterized. We examined somatic loss of HLA class I alleles, and correlated HLA loss and mutation-associated HLA genotypes with clinical presentation and outcomes after immunosuppressive therapy in 544 AA patients. HLA class I allele loss was detected in 92 (22%) of the 412 patients tested, in whom there were 393 somatic HLA gene mutations and 40 instances of loss of heterozygosity. Most frequently affected was HLA-B*14:02, followed by HLA-A*02:01, HLA-B*40:02, HLA-B*08:01, and HLA-B*07:02. HLA-B*14:02, HLA-B*40:02, and HLA-B*07:02 were also overrepresented in AA. High-risk clonal evolution was correlated with HLA loss, HLA-B*14:02 genotype, and older age, which yielded a valid prediction model. In two patients, we traced monosomy 7 clonal evolution from preexisting clones harboring somatic mutations in HLA-A*02:01 and HLA-B*40:02. Loss of HLA-B*40:02 correlated with higher blood counts. HLA-B*07:02 and HLA-B*40:01 genotypes and their loss correlated with late onset of AA. Our results suggest the presence of specific immune mechanisms of molecular pathogenesis with clinical implications. HLA genotyping and screening for HLA loss may be of value in the management of immune AA. This study was registered at clinicaltrials.gov as NCT00001964, NCT00061360, NCT00195624, NCT00260689, NCT00944749, NCT01193283, and NCT01623167.

Double paternal uniparental isodisomy 7 and 15 presenting with Beckwith-Wiedemann spectrum features

Here we describe for the first time double paternal uniparental isodisomy (iUPD) 7 and 15 in a baby boy with features in the Beckwith-Wiedemann syndrome spectrum (BWSp) (placentomegaly, hyperinsulinism, enlarged viscera, hemangiomas, and earlobe creases) in addition to conjugated hyperbilirubinemia. His phenotype was also reminiscent of genome-wide paternal uniparental isodisomy. We discuss the most likely origin of the UPDs; a maternal double monosomy 7 and 15 rescued by duplication of the paternal chromosomes after fertilization. So far, paternal UPD7 is not associated with an abnormal phenotype, while paternal UPD15 causes Angelman syndrome. Methylation analysis for other clinically relevant imprinting disorders, including BWSp, was normal. Therefore, we hypothesized that the double UPD affected other imprinted genes. To look for such effects, patient fibroblast RNA was isolated and analyzed for differential expression compared to six controls. We did not find apparent transcription differences in imprinted genes outside chromosomes 7 and 15 in patient fibroblast. PEG10 (7q21.3) was the only paternally imprinted gene on these chromosomes upregulated beyond double-dose expectation (6-fold). We speculate that a high PEG10 level could have a growth-promoting effect as his phenotype was not related to aberrations in BWS-locus on 11p15.5 after DNA, RNA, and methylation testing. However, many genes in gene sets associated with growth were upregulated. This case broadens the phenotypic spectrum of UPDs but did not show evidence of involvement of an imprinted gene network.