bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Evaluation of a Custom Genome Wide 44K Oligoarray for Copy Number Changes in Acute Myeloid Leukemia
Authors: Patel Ankita , Wang Rui-Yu , Hixson Patricia , Li Jian , Milosavljevic Aleksandar , Kantarjian Hagop M , Cheung Sau w , Andreeff Michael 
Published: April 2020

Abstract
Oligonucleotide-based array CGH (aCGH) technique enables detection of submicroscopic copy number changes in cancer. This technique offers the flexibility to
increase robustness by selecting best performing probes maximize the gene coverage while excluding repetitive sequences through a combination of bioinformatics and computation and increased resolution that allows for detection of smaller region of change. We designed a high resolution (44,000 probes) custom array using an Agilent platform and specifically targeted ~500 genes implicated in leukemogenesis.
The disease gene regions have an average spatial resolution of ~1 oligo per 7.5 kb whereas the backbone regions have an average resolution of 1 oligo per 78 kb. A total of 13 samples from patients with AML have been studied to date. aCGH was performed in a blinded fashion and the results were compared to the results from routine cytogenetic analysis. A GAIN in copy number on the long arm of chromosome 8 at band 8q22.2 encompassing 2.05 Mb was observed in one of 7 cases with normal chromosome analysis. Of the remaining 6 cases, the results from aCGH were concordant with the abnormality detected by chromosome analysis in three although the size of the copy number change was determined with greater precision by aCGH. Additional copy number changes were observed in the remaining two cases. In one case, in addition to the deletion of 5q14q34 detected by cytogenetic analysis, a loss in copy number on the long arm of 17q at band 17q11.2 encompassing 1.8 Mb including the NF-1 gene was detected by aCGH. Two additional copy number changes in 3q26.1 and 8q24.1 were observed in another case in which monosomy 7 was observed cytogenetically. aCGH failed to detect a clone (2 cells) with a deletion on 5 from band 5p13q13 in one case. In total, 30% of the patients with chromosome analysis displayed an additional cryptic change by aCGH. Our results suggest that a subset of potentially significant genomic alteration may be missed by the conventional chromosome analysis. This pilot study demonstrates that aCGH offers high sensitivity and specificity for routine screening of copy number changes in acute myeloid leukemia.
Novel Multiparametric Quantitative Immunocytomorphological Characterisation of Human Bone Marrow Precursor Differentiation and of Haematopoietic Neoplasms Using ImageStream® Cytometry
Authors: Martin Catherine Claude , Jayat-Vignoles Chantal , Faucher Jean-Luc , George Thaddeus , Venkatachalam Vidya , Morrissey Phil , Feuillard Jean 
Published: April 2020

Abstract
The ImageStream technology performs high speed acquisition of brightfield, laser scatter and up to four fluorescent images per cell for several thousands of cells in suspension, thereby enabling simultaneous immunophenotyping and morphology-based measurements. This is the only technology combining cytology and flow cytometry in one single platform.
Our aim was to study normal and tumour cells of the haematopoietic lineage with this new technology in order to improve diagnosis of haematological disorders. We have defined cytomorphological criteria of normal bone marrow (n=4) and circulating blood cells (n=40). Cells were multi-colour labelled with both DRAQ5 nuclear stain and CD45 ECD-mAb, and additionally labeled with a combination of mAbs against either CD3/CD19, CD11b/CD16, CD14/CRTH2, or CD71/CD235. Results for normal cells were compared to those obtained by classical cytometry and cytology. We then applied these criteria to samples with patients with circulating leukemic cells, including 1 myelodysplatic syndrome (MDS), 1 myeloproliferative syndrome (MPS), 3 acute lymphoblastic leukaemia (ALL), 2 follicular lymphomas (FL) and 20 chronic lymphocytic lymphomas (CLL).
We have created completely new quantitative cytomorphological criteria for classifying blood cells using parameters that measure cellular size and shape, nuclear to cytoplasmic area ratio, nuclear lobe count, SSC texture, the ratio between the size and the major axis of CD45, the ratio between the intensity and the compactness of SSC signal, and the intensity of DRAQ5 labelling, to name a few. Using these criteria, we have characterised normal bone marrow differentiation and normal circulating blood cells. We have obtained a perfect correlation with classical cytology and flow cytometry. Analysis of pathological samples showed that abnormal cells were recognized in all cases. We found an abnormal blast cell compartment and an abnormal monocytic differentiation branch in the case of MDS. We have also defined specific cytomorphological properties that distinguish ALL, FL and CLL tumour cells from normal cells. We also provide data that enumerates the proportion of large cells, of atypical CLL cells and of cells in the G2/M phase.
Altogether, these results show that a technology combining cytology and flow cytometry in a single platform leads to the discovery of completely new and quantitative cytomorphological parameters defining each stage of normal cell and each category of abnormal cells of the haematopoietic lineage, opening completely new perspectives for the diagnosis of haematopoietic neoplasms.
Functional Characterisation of a MYB-HBS1L Intergenic Region Controlling Fetal Hemoglobin Levels in Adults
Authors: Wahlberg Karin E , Jiang Jie , Rooks Helen , Best Steve , Thein Swee Lay 
Published: April 2020

Abstract
A major ameliorating factor in sickle cell disease and beta-thalassemia is the inherent ability to produce fetal hemoglobin (HbF, a2g2), a highly heritable trait. We have previously mapped a major quantitative trait locus (QTL) controlling HbF levels to an array of single nucleotide polymorphisms (SNPs) within a 79 kb block between the gene for HBS1L (a G-protein/elongation factor) and the MYB proto-oncogene in Northern European Caucasians. These variants in chromosome 6q23.3, are referred to as HBS1L-MYB intergenic polymorphism (HMIP) and exist in three linkage disequilibrium (LD) blocks, HMIP-1, -2 and -3, of which HMIP-2 shows the strongest association. Association of HMIP with HbF has recently been replicated in two independent cohorts of patients with sickle cell disease, African-American and Brazilian, as well as in a cohort of Chinese patients with beta-thalassemia. Physiologically, MYB and HBS1L expression was simultaneously down-regulated in individuals with high HbF while over-expression of MYB inhibits gamma-globin expression. We also showed that HMIP influences erythrocyte, platelet and monocyte counts in humans. We hypothesised that the genetic variants in the MYB-HBS1L intergenic region are situated in a regulatory region and affect HbF levels by altering the expression of MYB and/or HBS1L.
Initial DNase I hypersensitivity analysis of the HMIP-2 region in K562 cells identified a number of hypersensitive sites which encouraged further functional analysis of the region. To study activity and to map potential regulatory elements in the entire MYB-HBS1L region we used chromatin immunopreciptation on microarray (ChIP–chip) of acetylated histones H3 and 4, RNA polymerase II and GATA-1. ChIP was performed on chromatin from primary human erythroid precursor cells and enrichment for specific sequences was evaluated using a high resolution Nimblegen microarray covering a large part of chromosome 6q.
Our ChIP-chip data show high levels of histone acetylation in the MYB-HBS1L intergenic region with a concentration in the HMIP-2 block, indicating that the region is transcriptionally active in erythroid precursors. Moreover, a number of potential cis-regulatory elements were identified in the same region as strong GATA-1 signals in coincidence with DNase I hypersensitive sites. These results suggest a regulatory region in the MYB-HBS1L intergenic region that could be important in erythroid development by controlling expression in the MYB locus.
Correlation Between Soluble Vascular Endothelial Growth Factor-a and Vascular Endothelial Growth Factor-Receptor 1 with Response to Chemotherapy in Childhood Acute Leukemia
Authors: Mehrazma Mitra , Rafsanjani Khadije Arjomandi , Torkamanipoor Behzad , Keyhani Manoutchehr 
Published: April 2020

Abstract
Objective: Vascular endothelial growth factor (VEGF) and its receptors (VEGF-R1 and R2) are major regulators of angiogenesis, which plays a key role in the growth and dissemination of solid tumors and hematological neoplasms.
Materials and methods: To assess serum levels of VEGF and VEGF-R1 and their prognostic significance in newly diagnosed childhood acute leukemia, we used an Enzyme linked Immuno-Sorbant Assay (ELISA) to quantify their levels in stored samples obtained before treatment. Demographic data were recorded. Bone marrow blast percentage was counted at day of diagnosis and 2 weeks after induction therapy. The data entered and analyzed with SPSS11 software. P value under 0.05 assumed significant.
Results: Fifty-three children (22boys and 31girls) with newly diagnosed ALL with median age of 6.4±3.72 years were enrolled into the study. Most cases (56.6%) were pre B cell ALL. Mean value of VEFG-A in good responders was 55.13±24.96 pg/ml and in poor responders was 94.46±15.75 (P&lt;0.0001). Mean valve of VEGF-R1 in good and poor responders were 0.132±0.0653 and 0.1665±0.0857 pg/ml, respectively (P&gt;0.05). By using ROC curve, we found cut off point 76 pg/ml with sensitivity 99 % and specificity 81 % to discriminate poor response to chemotherapy.
Conclusion: Soluble VEGF-A is an independent factor of response to therapy in childhood leukemia and leukemic patients with sVEGF-A level over 76pg/ml, will have poor response to treatment.
Monosodium Urate Crystals Bind with Idiotype Protein and Promote Dendritic Cells to Induce Cytotoxic T Cells in Vitro
Authors: Sakamaki Ippei , Inai Kunihiro , Ueda Takanori , Tsutani Hiroshi 
Published: April 2020

Abstract
Monosodium urate (MSU) crystals have been studied to act as a key substance in local immunoreactions. MSU released from damaged cells works as an endogenous danger signal to antigen-presenting cells. MSU crystals evoke specific cell immunity and work as an adjuvant in a mouse model. The crystals also have another unique characteristic to bind with positively charged proteins, which could help to deliver some antigens into human dendritic cells (DCs). We focused on the application of MSU crystals as a not only an adjuvant but also as a carrier of positively charged antigenic protein to induce human cytotoxic T cells (CTLs) efficiently in vitro. We confirmed that MSU crystals facilitated human DCs to express the maturation marker, CD83, deliver (Fab′)2 attaching to the crystals. In order to determine whether MSU crystals facilitate the T-cell proliferation activity of DCs, the proliferative effects of DCs on allogeneic CD4+ cells were investigated. DCs pulsed with MSU crystals significantly facilitated the proliferation of allogeneic CD4+ cells when compared to DCs alone. The stimulation index (SI) was 2.5 ± 0.1 and 1.7 ± 0.1, respectively. When using DCs pulsed with the Fab attached to MSU crystals, the proliferation of CD4+ cells was significantly greater than when using DCs pulsed with Fab alone. The SI was 2.6 ± 0.2 and 1.9 ± 0.1, respectively. No significant differences were seen in the proliferation of allogeneic CD4+ cells between DCs pulsed with the Fab attached to MSU and DCs pulsed with MSU alone. We selected the multiple myeloma IM-9 cell line and its product idiotype (Id) protein as an ideal pair of target cells and positively charged tumor-specific antigen, respectively. After sensitizing DCs derived from HLA-A matched volunteers pulsed with tumor-specific monoclonal IgG-Fab fragments (IM-9 Fab) attached to MSU crystals, the CD8+ T cells stimulated by the DCs killed significantly more target cells (38.5 ± 3.5%, n=4) than those stimulated by DCs pulsed with IM-9 Fab alone (3.5 ± 7.5%). These cytotoxic effects of CD8+ cells stimulated by the DCs pulsed with IM-9 Fab attached to MSU crystals were reduced (3.6 ± 1.7%) when MSU crystals were pre-coated with fetal bovine serum to block to bind with IM-9 Fab. For efficient induction of CTLs, it is necessary for Id proteins to attach to MSU crystals. MSU crystals have some advantages of a protein carrier binding with positively charged proteins and delivering antigenic protein into DCs, as well as an adjuvant promoting DC maturation and inducing CTLs.
Innate Immunity in Idiopathic Thrombocytopenic Purpura (ITP)
Authors: Saito Akio , Yokohama Akihiko , Nakahashi Hirotaka , Toyama Kohtaro , Mitsui Takeki , Hashimoto Yoko , Koiso Hiromi , Saitoh Takayuki , Uchiumi Hideki , Handa Hiroshi , Sawamura Morio , Karasawa Masamitsu , Murakami Hirokazu , Nojima Yoshihisa , Tsukamoto Norifumi 
Published: April 2020

Abstract
Background: Dendritic cells (DCs), natural killer (NK) cells, and invariant NKT (iNKT) cells play important roles in innate immune systems. These cells have recently been shown to be involved in immunoregulation, and some studies have suggested associations with various kinds of autoimmune disease. Conversely, regulatory T cells (Tregs) that are important for peripheral tolerance and Th17 cells that play a central role in maintenance of chronic inflammation are also associated with the pathogenesis of several autoimmune diseases. Idiopathic thrombocytopenic purpura (ITP) is an autoimmune disease mediated by anti-platelet autoantibodies, but relationships to innate immunity are unclear. In addition, the pathogenesis of ITP associated with Helicobacter pylori remains obscure. In particular, the regulation of immune responses by these cells in patients infected with H. pylori has not been investigated. This study analyzed DCs, NK cells, iNKT cells, Tregs and Th17 cells in patients with ITP.
Methods: Subjects comprised 31 patients with ITP and 22 healthy donors. Study protocols were approved by the Institutional Review Board of Gunma University Hospital, and written informed consent was obtained from all subjects. Flow cytometry was used to investigate amounts of circulating plasmacytoid DCs (pDCs) (CD123+ HLA−DR+) and myeloid DCs (mDCs) (CD11c+ HLA−DR+) from whole white blood cells, and NK cells (CD3− CD56+), iNKT cells (Vα24+ Vβ11+), Tregs (CD4+ CD25+ Foxp3+) and Th17 cells (CD4+ IL−17A+) from mononuclear cells. The intracellular interleukin (IL)-17A production in CD4+ T-cells activated by phorbol 12-myristate 13-acetate (PMA) and ionomycin was assessed to detect Th17 cells.
Results: Both the percentage and numbers of pDCs were significantly reduced in patients compared to healthy controls (p&lt;0.001), while those of mDCs tended to be lower in patients than in controls, but with no significant differences. NK cell counts tended to be higher in patients than in controls and counts of iNKT cells tended to be lower in patients than in controls, but again no significant differences were demonstrated. Notably, Treg levels were comparable between patients and controls, while Th17 cells were significantly increased in patients compared with controls (p&lt;0.002). In all cases, no significant differences were demonstrated between patients with H. pylori-positive and -negative results.
Conclusion: These results suggest that alterations in innate immunity as a reduction of pDCs could be associated with the pathogenesis of ITP. Furthermore, as in some autoimmune diseases that have been considered as Th1 diseases, Th17 cells may play an important role in ITP.
Inhibition of T-Cell Activation by a CEACAM1 (CD66a) Peptide
Authors: Skubitz Keith M. , Skubitz Amy P.N. , Kammerer Robert 
Published: April 2020

Abstract
Carcinoembryonic antigen family (CEACAM) members are widely expressed, and depending on the tissue, capable of regulating diverse functions, including tumor promotion, tumor suppression, angiogenesis, neutrophil activation, and T-cell activation. CEACAM1, a member of the carcinoembryonic antigen family, is expressed on human T-cells and is recognized by CD66a mAb. CD66a mAb binding to the T-cell surface inhibits T-cell activation. To identify active sites on CEACAM1, molecular modeling was performed using IgG and CD4 as models, and 28 peptides of 14 amino acids in length were synthesized that were predicted to be present at loops and turns between beta-sheets. The peptides were tested for their ability to alter T-cell activation by anti-CD3 and IL-2. One peptide from the internal domain inhibited T-cell activation. Scrambled versions of this peptide had no effect on T-cell activation. The data suggest that a peptide motif from the internal domain of CEACAM1 is involved in the interaction of CEACAM1 with other ligands and can alter signal transduction in T-cells. This peptide may serve as a template for the development of structurally related compounds that can regulate T-cell activation.
In Vitro Study of the Function of Dendritic Cells on Stimulating T Lymphocytes Proliferation in Severe Aplastic Anemia
Authors: Shao Zonghong , Wang Jun , Fu Rong , Li Lijuan , Liu Hui , Qu Wen , Rua Erbao , Liang Yong , Liu Hong , Wu Yuhong , Wang Guojin , Song Jia , Wang Huaquan , Xing Limin , Guan Jing , Wang Xiaoming 
Published: April 2020

Abstract
Objective To investigate the function of dendritic cells (DCs) in severe aplastic anemia (SAA).
Methods Fifteen untreated patients, 10 recovered patients with SAA and 12 normal controls were enrolled in this study. Their mDCs were induced from their bone marrow mononuclear cells with rhIL-4, rhGM-CSF and rhTNF in vitro. Then mDCs were co-cultured with allogenic lymphocytes (mixture lymphocyte reaction, MLR). The growth rate of lymphocyte was measured by MTT colorimetry and the concentrations of IL-12 and IFNγ in MLR supernatant were measured by ELISA. The correlation between the growth rate and the concentration of IL-12 or IFNγ was analyzed.
Results When mDCs and lymphocytes were co-cultured at the ratio of 1:50, the growth rate of lymphocytes stimulated with the mDCs from untreated cases was (322.13±171.07)%, which was higher than those stimulated with the mDCs from recovered and controls [(180.90±79.12)%, (192.25±91.93)%] (P&lt;0.05). There was no statistical significance between the growth rates of lymphocytes stimulated with the mDCs from the recovered and controls (P&gt;0.05). The mDCs of 8 recovered cases and 4 controls were co-cultured with allogenic lymphocytes at the ratio of 1:100, 1:50, 1:20 and 1:10, but no statistical significance was found between two groups at each ratio (P&gt;0.05). Cross MLR showed only untreated cases versus normal had statistical significance (P&lt;0.05). The concentrations of IL-12 and IFNγ in MLR supernatant of untreated cases were higher than those of the recovered or controls (P&lt;0.05), but there was no statistical significance between the recovered and controls (P&gt;0.05). The concentration of IL-12 in MLR supernatant correlated positively with the growth rate of lymphocyte (r = 0.529,P=0.001), which was also positively correlated with the concentration of IFNγ (r = 0.381,P=0.024).
Conclusion The function of mDCs to stimulate T lymphocytes proliferation by secretingt IL-12 in SAA was enhanced, which might play an important role in the immunopathogenesis of SAA.
Multicenter Trial of Photopheresis in Early Stage Mycosis Fungoides
Authors: Duvic Madeleine , Talpur Rakhshandra , Baron Elma D , Geskin Larisa J. , Demierre Marie-France , Zic John , Bohjanan Kimberly 
Published: April 2020

Abstract
Extracorporeal photopheresis (ECP) has been approved for 20 years for patients with erythrodermic MF or Sézary syndrome (SS) with circulating atypical T-cells. The response rate of 54% was based on 25% improvement in erythema. ECP has not widely been used to treat patients with early stage MF. The objective of this multicenter single-arm open-label study was to determine the efficacy of UVAR® XTSÔ Photopheresis System in early stage MF with measurable skin lesions. Patients were eligible at stage IA if there was with minor blood involvement (B1), or at IB- IIA MF with or without minor blood involvement (B1). Patients had to be refractory to at least one treatment for early MF such as PUVA, electron beam, oral or topical high potency steroids, topical mustragen, oral methotrexate, alpha interferon, or bexarotene. Two photopheresis treatments were given on successive days every 4 weeks for six months. There were 13 evaluable patients treated with ECP (4 males/9 females; 12 Caucasians, 1 African-American) whose median age was 61 yrs (range 46–85). Their stages were IA (n=3), IB (n=8) and IIA (n=2). Patients received a median of 12 ECP sessions (range 4–42+) over a median of 6 months (range 5–22). The overall response rate of 54% (7 of 13) required a ≥50% improvement in the baseline body surface area involved with patches or plaques. The median time to response was 6 months (range 3–8 months) and median duration of response was 6 mos (range 2–30 mos). The protocol allowed additional therapy if patients failed to improve by month 3. ECP alone was effective in four of ten patients (40%) and the other three patients had partial response with combined therapy: two with low dose bexarotene (150 mg) added at 4 or 6 mos and a third with bexarotene, interferon, and PUVA at 6 mos. Only 2 of 13 patients progressed and four had stable disease. There were no photopheresis related adverse events other than mild post-ECP erythema in one patient. One patient developed central right arterial occlusion with left eye visual defect unrelated to the ECP. In conclusion, photopheresis had a 54% response rate for all 13 patients and a 40% response rate to ECP alone in 10 early stage MF patients without adverse side effects suggesting it could be successfully used to treat early MF patients.