bluuebunny/crossref_metadata_2025_split huggingface dataset:
All Roads Lead to Rome: Phenotypic Channeling to Uniform Differentiation Structures from Diverse Leukemia Genotypes by Mass Cytometry
Authors: Nolan Garry 
Published: October 2019

Abstract
Emerging single-cell technologies have been pivotal in uncovering an extensive degree of heterogeneity between and within tissues (1). Analysis of single-cell data has shed light on many different cellular processes (2-7) and recent technological advances have enabled the study of a large number of parameters in single cells at unparalleled resolution. One such technology, mass cytometry (8), can measure up to 45 parameters simultaneously in tens of thousands of individual cells. Using mass cytometry and genomic sequencing of conventionally sorted subpopulations show that acute myelogenous leukemia (AML) in a given patient can simultaneously occupy multiple stages of differentiation. Occupation of these stages was correlated with the presence, or absence, of unique exonic mutation fingerprints. In another cancer, B-cell acute lymphoblastic leukemia (ALL), outgrowth of tumor at pro and pre-B cell stages was nearly always uniquely at a single stage - contrary to the results in AML. This suggests that evolutionary “niche” searching is not only for physical space in cancers, but also involves utilization of differentiation machinery as an additional elaboration mechanism. Each differentiation stage in both AML and B-cell ALL was characterized by utilization of cognate signaling networks which showed differential susceptibility to drug action. Using such deep profiling and signaling delineation approaches at the single-cell level will allow for fine structured indexing of patient disease and further tailoring of disease management. In addition, it will allow “heterogeneous” tumors to be organized by a maturation index associated with a granular catalog of mutations that drive cells to occupy these pseudo-differentiation niches.
1. Bendall, S.C., et al., A deep profiler's guide to cytometry.Trends Immunol, 2012. 33(7): p. 323-32.
2. Petilla Interneuron Nomenclature Group, et al., Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex.Nat Rev Neurosci, 2008. 9(7): p. 557-68.
3. Irish, J.M., et al., Single cell profiling of potentiated phospho-protein networks in cancer cells.Cell, 2004. 118(2): p. 217-28.
4. Sachs, K., et al., Causal protein-signaling networks derived from multiparameter single-cell data.Science, 2005. 308(5721): p. 523-9.
5. Majeti, R., C.Y. Park, and I.L. Weissman, Identification of a hierarchy of multipotent hematopoietic progenitors in human cord blood. Cell Stem Cell, 2007. 1(6): p. 635-45.
6. Tarnok, A., H. Ulrich, and J. Bocsi, Phenotypes of stem cells from diverse origin.Cytometry A, 2010. 77(1): p. 6-10.
7. O'Brien, C.A., A. Kreso, and J.E. Dick, Cancer stem cells in solid tumors: an overview.Semin Radiat Oncol, 2009. 19(2): p. 71-7.
8. Bandura, D.R., et al., Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. Anal Chem, 2009. 81(16): p. 6813-22.

Disclosures:
No relevant conflicts of interest to declare.
The Role of Chromatin Factors in Hematopoietic Development
Authors: Zon Leonard I. 
Published: October 2019

Abstract
The initiation of blood-specific programs is orchestrated by key transcription factors. To generate a complete compendium of chromatin factors that establish the epigenetic code during developmental hematopoiesis, a large-scale reverse genetic screen was conducted targeting orthologs of 425 human chromatin factors in zebrafish. A set of chromatin regulators was identified that function at distinct steps of primitive and definitive blood formation, including factors not previously implicated in blood development. We identified 15 factors that regulate development of primitive erythroid progenitors and 29 factors that regulate development of definitive stem and progenitor cells. These chromatin factors are associated with SWI/SNF and ISWI chromatin remodeling, SET1/MLL methyltransferase, CBP/P300/HBO1/NuA4 acetyltransferase, Sin3A/NuRD deacetylase, and Polycomb repressive complexes. Knockdown of a class of chromatin factors led to an expansion of hematopoietic stem cells (HSCs). In collaboration with Nancy Speck’s laboratory, we have investigated the activity of one of these chromatin factors, CHD7, that led to an expansion of hematopoietic stem and progenitor cells in the aorta. Using a T-cell line, a CBFβ protein pulldown, and a mass spectrometric sequencing approach led to the finding that CBFβ immunoprecipitated RUNX1 and CHD7. By studying a conditional allele of murine Chd7, inactivation does not have an effect on peripheral blood counts, but Chd7-deleted HSCs purified based on phenotypic markers contain an increased number of functional HSCs. Our studies suggest that CHD7 suppresses hematopoiesis, and provides a novel control mechanism for the regulation of HSCs. Our work provides a comprehensive view of how specific chromatin factors and their associated complexes play a major role in the establishment of hematopoietic cells in vivo.

Disclosures:
Zon: Scholar Rock: Consultancy, Equity Ownership, Founder, Founder Other, Membership on an entity’s Board of Directors or advisory committees, Patents & Royalties; Stemgent, Inc: Consultancy, Membership on an entity’s Board of Directors or advisory committees, Stocks, Stocks Other; FATE Therapeutics, Inc: Consultancy, Equity Ownership, Founder Other, Membership on an entity’s Board of Directors or advisory committees, Patents & Royalties.
TGF-Beta Signaling Favors Central Memory Phenotype Expression By Ex-Vivo Stimulated Human T Cells
Authors: Dahmani Amina , Carli Cédric , Taillefer Julie , Goupil Mathieu , Khalili Myriam , Delisle Jean-Sebastien 
Published: October 2019

Abstract
Adoptive immunotherapy using ex vivo differentiated and expanded T cell lines can be remarkably efficient to treat cancer and infections. Unfortunately, the process of ex vivo T cell stimulation can lead to terminal effector differentiation and functional exhaustion thereby limiting the persistence and therapeutic effects of these T cells after transfer. Accumulating evidence suggests that, owing to their proliferative capacity, self-renewal ability and long term persistence in vivo, T cells bearing a central memory (CD45RO+/CD62L+ - Tcm) instead of an effector memory (CD45RO+/CD62L- - Tem) phenotype before adoptive transfer can mediate more significant therapeutic activity. Transforming-growth factor-beta (TGF-β) is a pleiotropic cytokine that influences several aspects of T-cell biology and that is best known for its growth suppression and immunosuppressive activity. We show that TGF-β signaling can have a profound impact on the number of CD4 and CD8 T cells expressing the Tcm and Tem phenotype after anti-CD3e and anti-CD28 stimulation without altering the number of cells recovered at the end of the culture and without inducing regulatory T cells. By enhancing the percentage of the lymph-node homing receptors, L-selectin (CD62L) and CC-chemokine receptor 7 (CCR7) expressing cells, exogenous TGF-β, added to the culture medium to a concentration of 5 ng/ml, favors Tcm over Tem cell accumulation at 7 days (CD4+: 55.80 vs 35.51% (P= 0.0074); CD8+: 56.9 vs 40.3% (P= 0.0063)). Reciprocally, the inhibition of TGF-β signaling with a TGF-β receptor kinase inhibitor (GW788388) accentuated Tem phenotype acquisition. Importantly, these effects of TGF-β on Tcm marker expression were maintained in the presence of exogenous cytokines commonly used in ex-vivo cultures for adoptive immunotherapy (IL-2, IL-7 and IL-15). The manipulation of TGF-β signaling did not increase the expression of exhaustion markers (KRLG-1, CD57) but exogenous TGF-β decreased interferon-gamma (IFN-γ) expression. No effect was noted on TNF-α and IL-2 expression as well as on the percentage of polyfunctional cells generated. We also found that modulating TGF-β signaling during the course of clinically relevant cultures capable of expanding T-cells specific for Epstein-Barr virus LMP2 protein antigens, in the presence of IL-7 and IL-15, could increase the number of CD4 Tcm cells, even 2 weeks after the withdrawal of TGF-β from the culture (38.24 vs 27.82, N=3) without compromising antigen-specific IFN-γ release. In conclusion, the modulation of TGF-β signaling can significantly alter Tcm and Tem phenotype acquisition and may therefore be used to optimize Tcm phenotype expression by ex-vivo pathogen/antigen-specific T cells expanded for adoptive immunotherapy.

Disclosures
No relevant conflicts of interest to declare.
Preliminary Report of a Multicenter Prospective Phase II Study of DA-EPOCH-R in MYC-Rearranged Aggressive B-Cell Lymphoma
Authors: Dunleavy Kieron , Fanale Michelle , LaCasce Ann , Noy Ariela , Caimi Paolo , Parekh Samir , Hayslip John W , Jagadeesh Deepa , Lord Raymond S , Lechowicz Mary J , Gaur Rakesh , Lucas Andrea , Staudt Louis M , Steinberg Seth M. , Kahl Brad , Friedberg Jonathan W. , Little Richard F , Bartlett Nancy L , Wilson Wyndham H 
Published: October 2019

Abstract
Background: In diffuse large B-cell lymphoma (DLBCL), a MYC-rearrangement (MYC-R) is present in approximately 10% of cases and has been associated with an inferior outcome following R-CHOP chemotherapy. In a previous report that retrospectively analyzed the prognostic impact of a MYC-R on survival following DA-EPOCH-R, patients with a MYC-R had a similar outcome to MYC negative cases (4 year EFS of 83% versus 76% respectively: p=0.46 Ann Oncol 2011 (22) Suppl 4 # 71). We set out to prospectively validate these results in a multicenter study.
Methods: Patients were newly diagnosed with DLBCL or B-cell lymphoma unclassifiable (BCL-U) with features intermediate between DLBCL and Burkitt lymphoma (BL). Only cases that harbored a MYC translocation by fluorescent in-situ hybridization (FISH) or conventional cytogenetic testing were included in this report. Treatment consisted of 6 cycles of DA-EPOCH-R.
R esults: 52 patients were included in this preliminary analysis. Characteristics were median (range) age 61 (29-80) years; male sex 37 (71%); stage III or IV disease 38 (73%); IPI score 0-2 in 35% versus 3-5 in 65%; HIV positive 4 (7%). Histologic diagnosis was DLBCL in 45 (86%) and BCL-U in 7 (14%). All cases had a MYC-rearrangement. BCL2 was rearranged in 14/31 (45%) and overexpressed by IHC in 24/43 (56%) cases tested. There were 3 deaths secondary to infectious complications and otherwise toxicities were similar to previous reports of the regimen. At a median follow-up time of 14 months, progression-free survival (PFS), time to progression (TTP) and overall survival (OS) were 79%, 86% and 77% respectively for all patients. PFS was 87% and 64% in cases that were FISH positive (double-hit) and IHC positive for BCL2 respectively.
Conclusions: Albeit short follow-up, DA-EPOCH-R in MYC-R DLBCL demonstrates promising activity in a multicenter prospective setting. Further analysis of this data is planned with central pathology review of cases and longer follow-up. The principal arm of this study testing the regimen in BL remains open to accrual (NCT01092182).
Figure 1 Figure 1.

Disclosures
LaCasce: Seattle Genetics, Inc.: Research Funding.
The Combination of Belinostat with Zidovudine for Treatment of HTLV-I Related Adult T-Cell Leukemia-Lymphoma
Authors: Toomey Ngoc , Ramos Juan Carlos 
Published: October 2019

Abstract
Adult T-cell leukemia-lymphoma (ATLL) is an aggressive malignancy with poor prognosis that is incurable by conventional drugs. Histone deacetylase (HDAC) inhibitors (HDIs) are broadly active anti-neoplastic agents that can be cautiously exploited in the treatment of ATLL. The HTLV-I provirus is clonally integrated in virtually all ATLL cells. The HTLV-I 5'LTR promoter is trans -activated by the viral protein Tax through binding of CREB and p300/CBP. Tax binding enhances p300/CBP histone acetyl transferase (HAT) activity resulting in histone acetylation, chromatin unwinding, and transcription of the viral genome. HAT activity is countered by HDACs, and also by the viral-encoded protein HTLV-I bZip factor (HBZ), which is transcribed from the negative proviral strand at the 3' end. The 5' LTR is often mutated or deleted in ATLL cells thus HBZ is the only viral gene consistently expressed in ATLL. We hypothesized that HDAC inhibitors, which can be potent anti-neoplastic drugs, would reactivate HTLV-I in ATLL tumors containing intact provirus, thus killing virus-infected cells and provoking an immune response in vivo. Supporting this notion, adding the old generation HDI valproic acid (VPA) to AZT/IFNa in one subject suffering from aggressive acute-type ATLL resulted in HTLV-I proviral load reduction, followed by a complete molecular and prolonged clinical remission that lasted several years. We recently tested other more potent HDIs on primary ATLL cells and low-passage cell lines, which are rare and difficult to establish. In general, HDIs induced dose-dependent Tax expression and apoptosis in ATLL cells. Belinostat, a pan HDI, caused H3 acetylation, blocked HBZ protein expression, and induced Tax protein expression in ATLL cells resulting in concomitant apoptosis. ATLL cells exhibit high constitutive expression of nuclear factor kappa B (NF-kB), which is known to be activated by Tax and to play a major role in HTLV-I mediated T-cell transformation and ATLL development. Paradoxically, while belinostat induced Tax, it also inhibited NF-kB nuclear activity resulting in apoptosis. Further, adding AZT to belinostat augmented ATLL cell death. By contrast, IFNα diminished apoptosis induced by belinostat in freshly isolated ATLL cells from some of our patients. Based on these preclinical data, we have developed a clinical trial using belinostat in combination with AZT as consolidation therapy for ATLL. Our primary goal using this approach is to eradicate residual ATLL cells and HTLV-I infected reservoirs that normally persist regardless of treatment.

Disclosures
No relevant conflicts of interest to declare.
Efficacy and Bleeding Risk of Newer Anticoagulants Compared to Conventional Treatment in Patients with Chronic Kidney Disease- a Meta-Analysis of Randomized Controlled Trials
Authors: Sundararajan Srinath , Poongkunran Mugilan , Poongkunran Chithra , Kannan Arun , Balamuthusamy Saravananan 
Published: October 2019

Abstract

Background
Multiple newer oral anticoagulants (NOAC) are currently approved for the prevention, treatment of venous thromboembolism (VTE) and prevention of stoke in atrial fibrillation (AF). Most of the clinical trials with NOAC have excluded patients with severe renal insufficiency. There is a paucity of safety and efficacy data of NOAC in comparison with conventional treatment (CT) in patients with mild or moderate renal impairment. We performed a meta-analysis of the randomized control trials (RCTs) comparing NOAC to CT in patients with renal insufficiency to understand the safety and efficacy of NACs.
Methods
Medline, PubMed, EMBASE, EBSCO, CINAHL and Cochrane databases were queried with the keywords - "newer anticoagulants", "renal insufficiency", "dabigatran", "rivaroxaban", "apixaban", and "edoxaban". RCTs comparing NOAC to CT (warfarin, low molecular weight heparin, heparin, aspirin or placebo) were included. Non-randomized single arm trials were excluded. Authors of RCTs with missing pertinent data were contacted through electronic mail. The safety end point analyzed was clinically significant or major bleeding risk. The efficacy end points analyzed were incidence of arterial embolism in AF studies and venous thromboembolism in VTE studies. European Medical Agency classification of renal insufficiency was used, with mild renal insufficiency defined as estimated glomerular filtration rate (eGFR) from 50 to 79 and moderate renal insufficiency defined as eGFR of 30 to 49 and severe renal insufficiency defined as eGFR< 30.
Results
Sixteen RCTs with 115,147 patients fulfilled our inclusion criteria. Rivoroxaban, apixaban, edoxaban and dabigatran were the newer anticoagulants used in these 16 RCTs. Among these, 48,403 patients had either mild or moderate renal insufficiency. Patients with mild renal insufficiency treated with NAOC had lower bleeding risk [Odds ratio 0.81(CI 0.72-0.90) p<0.0001], lower incidence of arterial thromboembolism [Odds ratio 0.74(CI 0.64-0.85) p<0.0001] compared to conventional treatment. Patients with moderate renal insufficiency treated with NAOC had lower incidence of arterial thromboembolism [Odds ratio 0.74(CI 0.62-0.89) p=0.001] and a trend towards lower bleeding risk [Odds ratio 0.89(CI 0.66-1.18) p=0.41], compared to conventional treatment. Also, a trend of lowered VTE incidence was observed with NOAC compared to conventional treatment in patients with mild [Odds ratio 0.70(CI 0.46 to 1.070) p=0.1] as well moderate [Odds ratio 0.69(CI 0.34 to 1.41) p=0.31] renal insufficiency.
Conclusion:
Newer anticoagulants have decreased odds for VTE, arterial embolism and bleeding in patients with mild to moderate renal insufficiency compared to conventional treatment.

Disclosures
No relevant conflicts of interest to declare.
Involvement of the EGF Domain in the Formation of the Human Platelet Alloantigen, HPA-1a
Authors: Zhi Huiying , Lertkiatmongkol Panida , Curtis Brian R , Newman Peter J. 
Published: October 2019

Abstract
The human platelet alloantigen, HPA-1a (also known as PlA1), is most frequently responsible for several clinically important alloimmune platelet disorders, including neonatal alloimmune thrombocytopenia (NAIT), post-transfusion purpura, and less frequently, platelet transfusion refractoriness. A single C29523T nucleotide substitution, resulting in a Leu33Pro amino acid polymorphism within PSI domain of the integrin β3 subunit, controls the expression of the HPA-1a/HPA-1b alloantigenic epitopes. Small linear or cyclic synthetic peptides encompassing amino acid 33, however, fail to bind human anti-HPA-1a alloantibodies, leading to the notion that the HPA-1a antigenic determinant is conformationally dependent, and may require noncontiguous regions of the polypeptide chain that are linearly distal to polymorphic residue 33. This concept is supported by the finding that antibodies from some alloimmunized women fail to recognize a Cys435Ala mutant form of β3, and by the observation that the PSI domain of β3 is immediately adjacent in the crystal structure of β3 to the first epidermal growth factor (EGF1 - residues 436-472) domain of the molecule. The purpose of the present investigation, therefore, was to localize the amino acid(s) within EGF1 that contribute to the HPA-1a alloantibody binding interface. Two complementary approaches were employed. In the first, site-directed mutagenesis was used to introduce four amino acid substitutions (T30A, S32P, Q33L, and N39D) into mouse β3 cDNA that have previously been shown to be necessary for reconstituting the human anti-HPA-1a epitope into the murine protein. The resulting mouse β3 integrin subunit containing this "humanized" PSI domain (termed APLDmβ3) was able to bind both the murine HPA-1a-selective monoclonal antibody, SZ21, as well as human maternal anti-HPA-1a antisera. Structural analysis indicates that S469 and Q470 at the C-terminus of EGF1 are immediately adjacent to Leu33 in human β3. Ser469 is conserved in the mouse, however residue 470 is a methionine in the murine protein. Based on these observations, we introduced an additional M470Q amino acid substitution within APLDmβ3 to produce APLDQmβ3. As predicted, binding of mAb SZ21 and human anti-HPA-1a alloantisera toHEK293 cells expressing an aIIb/APLDQmβ3 complex was increased ~30% over that which bound to cells expressing similar levels of aIIb/APLDmβ3. Conversely, substitution of M for Q at position 470 within human β3 resulted in a marked reduction in the ability of SZ21 and human anti-HPA-1a alloantisera to bind. Taken together, ourresults demonstrate that this region of the conformationally close EGF1 domain contributes importantly to the expression of the HPA-1a alloantigenic determinant. These findings may have important implications for diagnostic and therapeutic use of synthetic or recombinant HPA-1a mimetics.

Disclosures
No relevant conflicts of interest to declare.
Selective Deletion of ATG5 in Bone Marrow Leptin-Receptor-Expressing Perivascular Stromal Cells Causes Leukopenia
Authors: Arsiwala Shabnam , Ding Wei , Wang Hong-Gang 
Published: October 2019

Abstract
Bone marrow niche cells, specifically the Leptin-receptor-expressing perivascular stromal cells (LepR+), CXCL12-abundant reticular cells (CAR), and endothelial cells play an important role in the maintenance and self-renewal functions of hematopoietic stem cells (HSCs). This maintenance function provided by the niche cells is mediated by a number of secretory-related molecules such as stem cell factor (SCF), CXCL12 and Angiopoietin. In addition, functional autophagy within HSCs is known to play a critical role for maintaining HSC homeostasis, as the loss of ATG7 in HSCs leads to loss of normal HSC functions and severe myeloproliferation. However, it remains unclear as to how hematopoiesis will be affected if autophagy is selectively blocked in bone marrow niche cells. To investigate the effect of autophagy deficiency within bone marrow niche cells on hematopoiesis, we generated a knockout mouse model allowing for a selective ablation of an autophagy-essential protein, ATG5, in LepR+ perivascular stromal cells. We have confirmed that the deletion of Atg5 is indeed restricted to LepR+ cells, and that the loss of ATG5 is sufficient to block autophagic function, as evident through the accumulation of p62 protein. We found that the white blood cell count (WBC) is significantly reduced in 16-week old male ATG5 KO mice compare to wild type (wt) littermate control mice (p<0.05). Further, the myeloid population (CD11b+ Ly6G+) in both bone marrow and peripheral blood is significantly decreased in ATG5 KO mice (p value < 0.05, ATG KO vs. wt control). WBC count continues to decline in 24-week old ATG5 KO male mice (p=0.02) but not in female mice (p=0.58). Both LSK (Lin- Sca-1+ c-Kit+) and long term HSC (LT-HSCs, CD150+ CD48- LSK) populations are decreased in both 16-week and 24-week old male mice; however, this trend did not reach statistical significance (p>0.05). Although the absolute cell count of lymphocytes, including B and T cells (CD19+ and CD3+, respectively) in peripheral blood, is significantly dropped in ATG5 KO mice compared to wt controls, there is no significant change of mature B and T cells in bone marrow. These preliminary results suggest that deletion of a key autophagy regulator in LepR+ bone marrow niche cells will cause leukopenia. The underlying mechanism is currently under investigation and it will help us to better understand the role of autophagy in hematopoiesis within the bone marrow microenvironment.

Disclosures
No relevant conflicts of interest to declare.