bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel KMT2A Partner Gene NUTM2A Revealed By Anchored Multiplex PCR in ALL
Authors: Lebedeva Svetlana , Zerkalenkova Elena , Soldatkina Olga , Maschan Michael , Maschan Alexey A. , Novichkova Galina , Olshanskaya Yulia 
Published: November 2019

Objectives
Chromosomal rearrangements of the human MLL/KMT2A gene are associated with infant, pediatric and adult acute leukemias. Such rearrangements are more frequent in infants, in whom they are found in 60% - 80% of acute lymphoblastic leukemias (ALL). KMT2A-r group itself is genetically heterogeneous. KMT2A-r can occur with at least 94 partner genes previously described in «THE MLL RECOMBINOME <…> IN 2017». Detection of KMT2A-r is an essential part of AL initial diagnostics. Also, the accurate detection of all KMT2A-r types is crucial in order to perform minimal residual disease (MRD) monitoring, as it is clear now that MRD-based therapy adjustment has a very strong impact on outcome. Here we report a case of novel KMT2A partner in pediatric ALL - NUT family member 2A (NUTM2A).
Methods
The patient is 8 y.o. girl with T-cell acute lymphoblastic leukemia with pleural effusion. Bone marrow and pleural fluid aspirates were analyzed by G-banded karyotyping and FISH with KMT2A breakapart probe. Pleural fluid aspirates were also analyzed by real-time RT-PCR for 8 most common KMT2A rearrangements screening, long-distance inversed PCR and targeted RNA-seq with FusionPlex Myeloid kit (ArcherDX, CO, USA). Sanger sequencing was used for validation.
Results
Conventional cytogenetics and FISH showed 47,XX,t(10;11)(q22;q23),+mar[5] karyotype with 100% KMT2A-rearranged nuclei. Gene fusion analysis identified novel fusion KMT2A-NUTM2A with exon 11 - exon 1 breakpoint junction.
NUTM2A is a gene at 10q23.2. This gene is not fully described in the literature. Rearrangements of this gene were identified in endometrial stromal sarcomas (ESS) (Cheng-Han Lee et al. 2012) and small round cell sarcoma (SRCS) (Sugita et al. 2017). In case of ESS, this rearrangement results in an in-frame fusion between YWHAE and NUTM2A (or highly homologous gene NUTM2B), and in case of SRCS it results in an in-frame fusion between NUTM2A and CIC. To our knowledge, KMT2A-NUTM2A fusion in our study is the first case demonstrating NUTM2A rearrangement in hematological malignancies.
Conclusions
Here we for the first time show the novel KMT2A-NUTM2A fusion transcript, which was found in pediatric T-cell acute lymphoblastic leukemia. Anchored multiplex PCR is one of the most sensitive way to detect rare variants of KMT2A rearrangements. It also allows selecting patient-specific primers for further PCR detection of MRD.

Disclosures
No relevant conflicts of interest to declare.
Subtyping Diffuse Large B-Cell Lymphoma with Cell-of-Origin Using 32-Gene Expression Assay in Formalin-Fixed Paraffin-Embedded Tissue
Authors: Jiang Xiangnan , Yan Wanhui , Sun Yifeng , Xu Qinghua , Zhou Xiaoyan , Cao Junning , Hong Xiaonan , Li Xiaoqiu 
Published: November 2019

Introduction
Diffuse large B-cell lymphoma (DLBCL) is a group of heterogeneous disease with distinct molecular subtypes. The most established subtyping algorithm, the Cell-of-Origin (COO) model, categorizes DLBCL into activated B-cell (ABC) and germinal center B-cell (GCB)-like subgroups through gene expression profiling. COO subtyping is mandatory for every newly diagnosed DLBCL patients, as it is critical for determining the therapeutic and surveillance strategies. We evaluated a newly developed assay using 32-gene expression profiling to determine the COO of DLBCL with formalin-fixed paraffin-embedded (FFPE) tissue.
Methods
The DLBCL-COO Test is a qPCR-based 32-gene expression assay for COO determination in FFPE samples. Biopsy of DLBCL patients with paired FFPE and fresh tissue were identified to assign COO, based on the immunohistochemistry (IHC) algorithm (Han's algorithm), DLBCL-COO qPCR assay and global gene expression profiling with RNA-seq, respectively. The global gene expression profiling with RNA-seq was taken as the "gold standard" for reference. Clinical information including the survival data were collected.
Results
160 cases of DLBCL with evaluable COO assignments with IHC, DLBCL-COO 32-gene assay and global gene expression profiling with RNA-seq were identified. Comparing with the 77.5% concordance between IHC algorithm and gold standard, there is 91.9% concordance between DLBCL-COO 32-gene assay and gold standard (P =0.005). 72 patients assigned as ABC subtype and 14 patients assigned as Type-3 subtype demonstrated a significantly inferior overall survival than 42 patients assigned as GCB subtype using DLBCL-COO assay (P =0.023). However, COO based the IHC algorithm failed to provide the predictive value regarding overall survival (P =0.09).
Conclusions
DLBCL-COO assay provides flexibility and accuracy in DLBCL subtype characterization. These subtype distinctions should help guide disease prognosis and treatment options within DLBCL clinical practice.

Disclosures
Sun: Canhelp Genomics: Employment. Xu:Canhelp Genomics: Employment.
LIM Domain Protein 1 (Ldb1) Is Required for Lmo2 Oncogene-Induced Thymocyte Self-Renewal and T-Cell Leukemia in a Mouse Model of Human T-ALL
Authors: Li Liqi , Mitra Apratim , Zhao Bin , Choi Seeyoung , Lee Jan , Stamos Daniel , Warzecha Claude , Pfeifer Karl , Hardwick Joyce , Venters Bryan , Love Paul , Dave Utpal 
Published: November 2019

LIM domain Only-2 (LMO2) is one of the most frequently deregulated oncogenes in T-cell acute lymphoblastic leukemia (T-ALL) and is generally expressed in the clinically aggressive Early Thymocyte Precursor ALL. LMO2 encodes a small protein with 2 LIM domains that is part of a large multiprotein complex in hematopoietic stem and progenitor cells (HSPC), where it is required for HSC specification and maintenance. Many of LMO2's protein partners in HSPCs are expressed in T-ALL implying that protein complexes like those scaffolded by LMO2 in HSPCs also play a role in leukemia. LDB1 is concordantly expressed with LMO2 in human T-ALL although its expression is more widespread than LMO2. In this study, we analyzed a critical component of the Lmo2 associated complex, LIM domain binding 1 (Ldb1), in the CD2-Lmo2 transgenic mouse model of human T-ALL. To further define Ldb1's role in leukemia, we induced its conditional knockout in CD2-Lmo2 transgenic mice with the use of Lck-Cre, Rag1-Cre, and Il7r-Cre transgenic mice. CD2-Lmo2 transgenic mice develop T-ALL with high penetrance and closely model the human disease.
We discovered that the penetrance and latency of Lmo2-induced T-ALL were markedly attenuated in the Lck-Cre model and T-ALL onset was completely abrogated in the Rag1-Cre and Il7r-Cre models. The latter two models induced more efficient deletions of Ldb1, earlier in the T-cell differentiation program compared to Lck-Cre. Interestingly, Lck-Cre deletion was efficient in thymocytes without the Lmo2 transgene. In striking contrast, Ldb1 deletion could not be induced in CD2-Lmo2 transgenic T-cell progenitors. Consistent with this finding, T-ALLs that developed in CD2-Lmo2/floxed-Ldb1/Lck-Cre mice had incomplete deletion of Ldb1. These results imply that Ldb1 is a required factor for Lmo2 to induce T-ALL. To further probe the pathogenesis of Lmo2-induced T-ALL, we analyzed preleukemic phenotypes in the Rag1-Cre (or Il7r-Cre) conditional knockout models. Our results showed that Ldb1 is required for the induction of thymocyte self-renewal and radioresistance. Ldb1 was also required for the acquisition of the pre-leukemic ETP gene expression signature observed in immature CD2-Lmo2 transgenic thymocytes. Detailed biochemical experiments show that LMO2 protein is directly stabilized by LDB1 in leukemia cells perhaps on chromatin.
In conclusion, these results support a model where Lmo2-induced T-ALL is caused by a failure to downregulate Ldb1/Lmo2 nucleated transcription complexes that normally function to enforce self-renewal in bone marrow hematopoietic progenitor cells.

Disclosures
No relevant conflicts of interest to declare.
Monoclonal Gammopathies and Their Significance: A Retrospective Analysis of Monoclonal Gammopathy and Renal Disease
Authors: Kumar Anupama , Drew David , Inker Leslie , Comenzo Raymond L , Varga Cindy 
Published: November 2019

Background:Monoclonal gammopathy of renal significance (MGRS) describes a subtype of patients with monoclonal gammopathy of unknown significance (MGUS) who have kidney disease due to immunoglobulin deposition. Early identification of MGRS and treatment with chemotherapy can prevent progression to kidney failure. There is limited data on the characteristics of populations with concomitant MGUS and chronic kidney disease (CKD), and on the prevalence of diagnosed MGRS in this population in the real world. Methods: Through retrospective chart review, we identified 246 patients with ICD-9 or -10 codes denoting both MGUS and chronic kidney disease (CKD) between the years of 2000 and 2017. Patients with related overt malignancies such as multiple myeloma, Waldenstrom's macroglobulinemia, and amyloidosis at onset were excluded, leaving 144 evaluable patients. Results:The median age was 78, and females made up 41.0% of the population. At time of MGUS diagnosis, the median eGFR was 48 mL/min/1.73 m2, and in patients with a quantifiable gammopathy, the median M-protein was 0.54 g/dL. A total of 53/144 (36.8%) patients had a bone marrow biopsy and 19/144 (13.2%) underwent kidney biopsy. MGRS was considered as a cause of kidney dysfunction in 20/144 patients (13.9%), but only 6 were further worked up by kidney biopsy. In 3/144 (2.1%) patients, MGRS was confirmed by kidney biopsy. Ten of (6.9%) the total population and 1 (5%) of the patients with suspected or confirmed MGRS (n=20) developed malignant transformation. Conclusion: MGRS should be considered in the differential diagnosis of patients with MGUS and co-existing chronic kidney disease. Based on our findings, renal biopsy is underutilized in the work up of this treatable disease. We propose a simple algorithm for workup of suspected MGRS (see Figure 1).
Figure 1

Disclosures
Comenzo: Myself: Patents & Royalties: Patent 9593332, Pending 20170008966; Caelum: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Karyopharm: Research Funding; Prothena Biosciences: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Sanofi-Aventis: Membership on an entity's Board of Directors or advisory committees; Takeda: Research Funding; Unum: Membership on an entity's Board of Directors or advisory committees, Research Funding.
Insulin-like Growth Factor-1-Induced Epithelial-Mesenchymal Transition Promotes Multiple Myeloma Progression
Authors: Peng Yue , Wang Xiaman , Shen Ying , Li Fangmei , Zhang Ru , Jia Yachun , He Aili 
Published: November 2019

MM is an incurable B cell neoplasm, which is characterized by the clonal proliferation of plasma cells in the bone marrow (BM), accounts for approximately 10% of hematological malignancies. Insulin-like growth factor-1 (IGF-1) is a vital proliferation factor in myeloma cells, recent researches demonstrated that it may be involved in MM cell metastasis. In last decade, studies have demonstrated that IGF-1 induces epithelial-mesenchymal transition (EMT), which has been tightly correlated with increased motility and invasive capacity in several cancers including gastric cancer, hepatocellular carcinoma, and melanoma. However, it remains unclear whether IGF-1 induces EMT and promote myeloma progression.
In this study, we firstly observed the morphology of the myeloma cell line Karpas707 changed from tight polygon to loose spindle, a mesenchymal phenotype after treated with IGF-1 (50 ng/ml) after 72h. We supposed IGF-1 may induced EMT in myeloma cells. Furthermore, when serum-starved MM cell lines RPMI8226 and MM1.S were stimulated with 50ng/mL of IGF-1, we found that the expression of mesenchymal features was significantly upregulated in a time-dependent manner, as determined by both flow cytometry analysis and western blotting. Next we confirmed that IGF-1 can activate the PI3K/Akt signaling pathway by inducing the phosphorylation of Akt in MM cells. To investigated whether PI3K/Akt signaling pathway involved in the IGF-1 mediated EMT, we blocked PI3K/Akt signaling pathway using Akt inhibitor MK2206 in IGF-1 treated MM.1S cells. We found MK2206 reversed these changes of EMT markers. Moreover, we found the IGF-1-induced EMT promotes myeloma progression, including migration, invasion, adhesion and clone formation in MM cells, using transwell migration and invasion assay, cell adhesion assay, colony formation assay and flow cytometry. Furthermore, to further validate IGF-1-induced EMT promote MM progression, we knocked down mesenchymal marker vimentin using siRNA in MM.1S cells (VIM k/d cells). We detected that these function IGF-1 plays in myeloma was impaired in Vim k/d cells, indicating that IGF-1-induced EMT promotes MM progression. Finally, we validated that IGF1 expression is aberrantly upregulated and correlated with the expression of the EMT markers by analyzing the mRNA data of BM samples from normal donors and patients in different stages of plasma cell neoplasm from the GEO database. Taken together, these data demonstrate that the mesenchymal phenotype induced by IGF1 contributes to MM progression via PI3K/Akt pathway.

Disclosures
No relevant conflicts of interest to declare.
Efficacy and Safety of Apatinib in Relapsed or Refractory Diffuse Large B Cell Lymphoma: An Open-Label, Single-Arm, Prospective Study
Authors: Ma Xinran , Li Ling , Zhang Lei , Li Xin , Fu Xiaorui , Wang Xinhua , Wu Jingjing , Zhang Xudong , Feng Xiaoyan , Zhou Zhiyuan , Chang Yu , Li Zhaoming , Young Ken H. , Zhang Mingzhi 
Published: November 2019

Background
Treatment options for relapsed or refractory diffuse large B-cell lymphoma (RR DLBCL) represent an unmet medical need. Apatinib is a new oral tyrosine kinase inhibitor mainly targeting vascular endothelial growth factor receptor 2 (VEGFR-2) to inhibit tumor angiogenesis, and has shown encouraging anti-tumor effects in multiple solid tumors. Yet clinical evidence of apatinib as a potential treatment choice for RR DLBCL remains rare. In current study, we evaluated the efficacy and safety of Apatinib for patients with RR DLBCL.
Methods
In this open-label, single-arm, prospective study, we enrolled patients aged 14-70 years with treatment failure of at least two chemotherapeutic regimens using Simon's two stage design. All patients took Apatinib at an initial dose of 500mg on a 4 weeks cycle at home and visited outpatient clinic every 2 cycles to evaluate the efficacy and to record the adverse events. Dose interruptions and reductions were only allowed when there were grade 3 haematological adverse events or grade 2 non-haematological adverse events. We considered objective response rate (ORR) as the primary end point, and progression-free survival (PFS), overall survival (OS) plus duration of response (DoR) as the secondary end point. (This trial was registered at ClinicalTrials.gov, identifier: NCT03376958.)
Results
From January 2017 to February 2019, we screened 35 and enrolled 32 eligible patients. At the cutoff point (April 2019), we noted 2 (6.3%) complete responses, 12 (37.5%) partial responses and 9 (28.1%) stable diseases, attributing to an ORR of 43.8% and a disease control rate (DCR) of 71.9%. The median PFS was 6.9 months (95%CI 5.8-7.9) and the median OS was 7.9 months (95%CI 7.0-8.7). Kaplan-Meier estimates of PFS and OS are shown in Figure 1. For patients achieved PR, The median DoR was 5.0 months (95%CI 3.5-6.5). At data analysis time, the median duration of follow-up was 8.6 months (95%CI 7.3-9.4), and 16 (50.0%) patients remained on treatment. 21 patients showed tumor shrinkage comparing with their baseline data and the best percentage changes from baseline are shown in Figure 2. The most common grade 3-4 adverse events (AE) were hypertension (12.6%), hand-foot syndrome (9.4%) and leukopenia (6.3%). No Apatinib-related deaths were noted. AEs arose in at least one patient are shown in Table 1.
Conclusion
With the potential superiority of home administration without frequent hospitalization, apatinib can be an arrow in the bow for RR DLBCL patients considering its favorable efficacy, manageable AEs, improved patient adherence and economic effectiveness. Further investigations into this topic will be of profound significance.

Disclosures
No relevant conflicts of interest to declare.
Genomic Landscape and Risk-Stratification for De Novo Acute Myeloid Leukemia with Normal Cytogenetics and No NPM1 or FLT3-itd Mutation
Authors: Zhou Ya-Lan , Wu Li-Xin , Gale Robert Peter , Wang Zi-Long , Li Jin-Lan , Jiang Hao , Jiang Qian , Jiang Bin , Cao Shan-Bo , Lou Feng , Sun Ying , Wang Chengcheng , Li Ting , Liu Yan-Rong , Wang Yu , Chang Ying-Jun , Xu Lan-Ping , Zhang Xiaohui , Liu Kaiyan , Ruan Guorui , Huang Xiaojun 
Published: November 2019

Introduction-About 25% of persons with new-diagnosed acute myeloid leukemia (AML) have normal cytogenetics and no NPM1 or FLT3-ITD mutation. The prognosis and best therapy of these persons is controversial.
Methods-We evaluated 809 consecutive newly diagnosed adult with normal cytogenetics and 231 of whom had no NPM1 or FLT3-ITD mutation identified by targeted regional sequencing. 158 achieved a complete remission within 2 cycles of induction therapy and were assigned to 2 different post-remission strategies: (1) 6 courses of consolidation chemotherapy (N=95); or (2) 2-4 courses of consolidation chemotherapy and an allotransplant (N=63).
Results-In multi-variable analyses a WBC ≥13·6×10E+9/L, mutated IDH2, not having a bi-allelic CEBPA mutation at diagnosis, a positive measurable residual disease (MRD)-test during consolidation and not receiving an allotransplant were independently associated with a higher cumulative incidence of relapse (CIR) and worse event-free survival (EFS). Amongst subjects with IDH2 mutations, non-bi-allelic CEBPA mutations or a positive MRD-test, subjects receiving an allotransplant had a lower 5-year CIR (16% [95% confidence interval, 6, 26%]; vs. 83% [72, 95%]; hazard ratio, HR=8·77 [4·05, 13·49]; P &lt; 0·001) and better 5-year EFS (74% [60, 88%] vs. 15% [5, 25%]; HR=0·16 [0·09, 0·29]; P &lt; 0·001). In contrast, in subjects with none of these adverse predictive variables there was no difference in CIR and EFS between those receiving an allotransplant and those who did not.
Conclusions-Our data suggest a strategy to identify which persons with AML with normal cytogenetics and no NPM1 or FLT3-ITD mutation benefit from an allotransplant.
Trial Registration: Registered in the www.clinicaltrials.gov, NCT01455272 and NCT02185261.
Keywords: Acute myeloid leukemia, mutations, prognosis, targeted regional sequencing, measurable residual disease, risk stratification.
*Correspondence
Profs. Guo-Rui Ruan and Xiao-Jun Huang
Peking University Peoples Hospital and Institute of Hematology
No.11 Xi-Zhi-Men South Street, Beijing 100044, China
T 86-10-88324672
F 86-10-88324672

Disclosures
No relevant conflicts of interest to declare.
The Role of Direct Oral Anticoagulants in Antiphospholipid Syndrome
Authors: Alsheef Mohammed Abdullah , Alomar Mukhtar , Alarfaj Ohoud , AlHamidi Hussam A , Zaidi Abdul Rehman Z. 
Published: November 2019

Background
Antiphospholipid Syndrome (APS) is defined by thrombosis and/or pregnancy morbidity in patients with antiphospholipid antibodies (aPL). There remains a pressing need for identification of clinical and laboratory parameters that define patients at most considerable risk for APS-related events on Direct oral anticoagulants (DOACs).
Aims
To demonstrate the efficacy and safety of DOAC (Rivaroxaban) compared with Warfarin (Vitamin K Antagonist) in patients with thrombotic APS.
Methods
A retrospective cohort study of thrombotic APS patients who were started on anticoagulant therapy, either VKA or DOAC, from 2010 -2016.
Results
We investigated 73 patients diagnosed with APS. 83.5% of the patients were female. The age range at diagnosis was between 26-40 (52%). 67% of the cases were diagnosed in the form of DVT while the rest had arterial or unusual site venous thrombosis. 43% of the patients had systemic lupus disease. 28% of the cases had a single-positive aPL profile, 23% had double-positive, and 49% had triple-positive aPL. 68.5% of the cases were treated with warfarin, while 31.5% of the cases were switched from warfarin to Rivaroxaban. 15% of patients had major and clinically relevant non-major bleeding (2 patients had major bleeding in the warfarin group, and four patients in the rivaroxaban group). Recurrence of thrombosis (arterial and venous) was 43% with Rivaroxaban and 30% with warfarin. The average duration from starting Rivaroxaban to development of complications such as bleeding and thromboembolic events was mostly after 1-2 years (70%).
Conclusions
Rivaroxaban should be used with extreme caution in APS patients, especially patients with a full positive aPL profile and arterial thrombosis.

Disclosures
No relevant conflicts of interest to declare.
CRISPR Dropout Screens Identify DHODH,PIK3C3, and Crkl as Potential Therapeutic Targets in Acute Myeloid Leukemia
Authors: Takacs Gregory , Zhou Yujia , King David J. , Meacham Amy , Alex Loguinov , Tagmount Abderrahmane , Sobh Amin , Russo Max , Vulpe Chris D , Cogle Christopher R. 
Published: November 2019

Relapsed disease is still a major challenge in AML despite recently approved targeted therapies. New therapeutic targets are needed. To identify vulnerabilities in AML, screening data from a lentiviral-based genome-wide pooled CRISPR-Cas9 library (DepMap) was analyzed by examining gene knockout (KO) dependency scores in 15 AML cell lines (HEL, MV411, OCIAML2, THP1, NOMO1, EOL1, KASUMI1, NB4, OCIAML3, MOLM13, TF1, U937, F36P, AML193, P31FUJ). 438 gene KOs were identified as essential to AML cell survival in 14/15 AML cell lines. 247/438 (56%) genes had no active compound or approved drug interacting with its gene-products (DGIdb, canSAR Black) but were tractable targets based on 3D modeling or ligand-based druggability scoring (canSAR Black). This refined list of targets made up a new screening platform termed disKO. For clinical relevance, a primary AML specimen was treated with a custom-made lentiviral-based pooled CRISPR-Cas9 library including disKO targets using guide RNA's constructed against a parsed version of the druggable genome. Following transduction, PCR and oligo-sequencing were performed on Days 0, 7, and 14. Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) was used to identify gene KOs associating with AML dropout over time. Four gene KOs from disKO were identified as essential in primary AML: NUP93, DHODH, CRKL, and PIK3C3. NUP93 loss of function mutations have been associated with steroid-resistant nephrotic syndrome in patients, suggesting inhibition may be toxic. DHODH inhibitors are currently being tested in AML. PIK3C3 codes for lipid kinases involved in autophagocytosis, and PIK3C3 inhibitors are in preclinical stage of development. CRKL is a proto-oncogene encoding src homology domains (SH2, SH3), which activate RAS and JNK signaling pathways. Although CRKL is a substrate of BCR-ABL CML, its essentiality in our study was found in AML cell lines and primary AML lacking the BCR-ABL fusion. Differential gene expression analysis showed CRKL to have lower expression in AML when compared to normal hematopoietic cells. Its druggability score based on six 3D structures and 1.3 ligand z-score indicates promising pharmacologic inhibition. In conclusion, a new CRISPR-Cas9 screening method termed disKO led to the identification of three viable targets for AML: PIK3C3, DHODH, and CRKL. Current efforts are focused on target validation followed by compound screening to find inhibitors with therapeutic potential.

Disclosures
No relevant conflicts of interest to declare.