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Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia

Eleftheria Polychronidou, Ilias Kalamaras, Andreas Agathangelidis, Lesley-Ann Sutton, Xiao-Jie Yan, Vasilis Bikos, Anna Vardi, Konstantinos Mochament, Nicholas Chiorazzi, Chrysoula Belessi, Richard Rosenquist, Paolo Ghia (+7 others)
2018 BMC Bioinformatics  
Although the etiology of chronic lymphocytic leukemia (CLL), the most common type of adult leukemia, is still unclear, strong evidence implicates antigen involvement in disease ontogeny and evolution.  ...  Results: Here we propose a novel method for clustering a set of proteins based on their 3D structure focusing on 3D structures of BcR IG from a large series of patients with CLL.  ...  The current work aims to categorize chronic lymphocytic leukemia (CLL) patients based on their 3dimensional protein structures of the clonotypic B cell receptor immunoglobulin (BcR IG) amino acid (IG)  ... 
doi:10.1186/s12859-018-2381-1 fatcat:7mnozo63kbbffhyw2m2exuhfau

In vitro and in vivo study of the role of the mitochondria - shaping protein opa1 in cancer

Dijana Samardžić, Nika Danial, Luca Scorrano
2016 Biochimica et Biophysica Acta - Bioenergetics  
ACKNOWLEDGEMENTS As this exciting PhD journey is slowly coming to its end, from the first days in Geneva, over the move to Padova, I would like to take the opportunity to thank all the people whose help  ...  B-NHL: non -Hodgkin B cell lymphoma; CLL: chronic lymphocytic leukemia; DLBCL: diffuse large B cell lymphoma; DTG: double transgenic mice; n.d.: not determined.  ...  mouse B lymphocytes based on negative selection.  ... 
doi:10.1016/j.bbabio.2016.04.246 fatcat:3unxvs7akrcldjd4sgld7kh7hq

Idiopathic myelofibrosis accompanied by peritoneal extramedullary hematopoiesis presenting as refractory ascites in a dog

Yolandi Rautenbach, Amelia Goddard, Sarah J. Clift
2016 Veterinary clinical pathology  
A 2.5-year-old spayed female American Pit Bull Terrier dog presented with a primary complaint of chronic refractory ascites.  ...  Cytology of the ascitic fluid demonstrated a sterile transudate, with evidence of a chronic inflammatory reaction as well as erythroid and myeloid precursor cells, and a few megakaryocytes with occasional  ...  leukemia (AMegL), they exceed 20% of which ≥50% of the blasts are of megakaryocytic lineage, 13, 15 and in MDS they are less than 20% based upon recommendations by the World Health Organisation, 13  ... 
doi:10.1111/vcp.12430 pmid:27874969 fatcat:kueqsoyin5hhzpi55xtsklozki

Mass Cytometry for the Assessment of Immune Reconstitution After Hematopoietic Stem Cell Transplantation

Lauren Stern, Helen McGuire, Selmir Avdic, Simone Rizzetto, Barbara Fazekas de St Groth, Fabio Luciani, Barry Slobedman, Emily Blyth
2018 Frontiers in Immunology  
Reconstitution of a healthy donor-derived immune system after HSCT involves the coordinated regeneration of innate and adaptive immune cell subsets in the recipient.  ...  This review explores the current knowledge of immune reconstitution in HSCT recipients and highlights recent mass cytometry studies contributing to the field.  ...  of leukemia (162) , revealing inconsistent and abnormal shapes that formed from leukemia samples which were distinct from healthy human bone marrow. viSNE was also used to compare bone marrow samples  ... 
doi:10.3389/fimmu.2018.01672 pmid:30093901 pmcid:PMC6070614 fatcat:zxsnhfrnovga5b3yxwpv3osjse

Emodin Exerts an Antiapoptotic Effect on Human Chronic Myelocytic Leukemia K562 Cell Lines by Targeting the PTEN/PI3K-AKT Signaling Pathway and Deleting BCR-ABL

Chun-Guang Wang, Liang Zhong, Yong-Li Liu, Xue-Jun Shi, Long-Qin Shi, Li Zeng, Bei-Zhong Liu
2016 Integrative Cancer Therapies  
The BCR-ABL kinase inhibitor, imatinib mesylate, is the front-line treatment for chronic myeloid leukemia, but the emergence of imatinib resistance has led to the search for alternative drug treatments  ...  In this article, we demonstrate that emodin inhibited the growth of K562 cells harboring BCR-ABL in vitro and in vivo, and induced abundant apoptosis, which was correlated with the inhibition of PETN/PI3K  ...  The other 2 forms of BCR-ABL are 230 kDa and 185 kDa proteins that are associated with chronic neutrophilic leukemia and acute lymphocytic leukemia, respectively. 31 Various studies have established  ... 
doi:10.1177/1534735416664784 pmid:27698265 pmcid:PMC5739139 fatcat:ctoqwfueafddtjqapffj5sslsa

Indoleamine 2,3-Dioxygenase [chapter]

Kazuhiko Ino, Fumitaka Kikkawa
2011 Encyclopedia of Cancer  
The database is meant to be a resource for a broad range of scientists and clinicians who work in different research areas: basic research, to study the structural and functional aspects of the ▶ p53 protein  ...  Definition The ▶ IARC ▶ TP53 mutation database is a public web-based resource for the analysis and interpretation of the biological and clinical impacts of TP53 gene variations in human cancers (http:/  ...  the 3D structure of p53 DNA-binding domain, and predicted or observed effect on protein (function patterns).  ... 
doi:10.1007/978-3-642-16483-5_3037 fatcat:ruhceyprszcm5d6te5rrm74bfq

Recurrent XPO1 mutations alter pathogenesis of chronic lymphocytic leukemia

Janek S. Walker, Zachary A. Hing, Bonnie Harrington, Jordan Baumhardt, Hatice Gulcin Ozer, Amy Lehman, Brian Giacopelli, Larry Beaver, Katie Williams, Jordan N. Skinner, Casey B. Cempre, Qingxiang Sun (+15 others)
2021 Journal of Hematology & Oncology  
Background Exportin 1 (XPO1/CRM1) is a key mediator of nuclear export with relevance to multiple cancers, including chronic lymphocytic leukemia (CLL).  ...  Conclusions These findings indicate that mutations in XPO1 at E571 can drive leukemogenesis by priming the pre-neoplastic lymphocytes for acquisition of additional genetic and epigenetic abnormalities  ...  Funding bodies played no role in the design of the study, collection, analysis, and interpretation of data and in writing the manuscript.  ... 
doi:10.1186/s13045-021-01032-2 pmid:33451349 pmcid:PMC7809770 fatcat:e75fpiu26jhglkx2a5ykmdbrq4

Dissecting intratumor heterogeneity of nodal B cell lymphomas on the transcriptional, genetic, and drug response level [article]

Tobias Roider, Julian Seufert, Alexey Uvarovskii, Felix Frauhammer, Marie Bordas, Nima Abedpour, Marta Stolarczyk, Jan-Philipp Mallm, Sophie Rabe, Peter-Martin Bruch, Hyatt Balke-Want, Michael Hundemer (+14 others)
2019 bioRxiv   pre-print
Malignant subclones of the same patient responded strikingly different to anti-cancer drugs ex vivo, which recapitulated subclone-specific drug sensitivity during in vivo treatment.  ...  Our data provide new insights into the heterogeneity of B-NHL and highlight the relevance of intratumor heterogeneity for personalized cancer therapies.  ...  DLBCL: Diffuse large B cell lymphoma, CLL: Chronic lymphocytic leukemia.  ... 
doi:10.1101/850438 fatcat:trf7kqccvzdzdcwz6olmzersgm

Multi-Omics factor analysis - a framework for unsupervised integration of multi-omic data sets [article]

Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C. Marioni, Wolfgang Huber, Florian Buettner, Oliver Stegle
2017 bioRxiv   pre-print
We applied MOFA to a cohort of 200 patient samples of chronic lymphocytic leukaemia, profiled for somatic mutations, RNA expression, DNA methylation and ex-vivo drug responses.  ...  MOFA identified major dimensions of disease heterogeneity, including immunoglobulin heavy chain variable region status, trisomy of chromosome 12 and previously underappreciated drivers, such as response  ...  disease progression and the sphingolipid metabolism as a potential novel metabolism in chronic lymphocytic leukemia.  ... 
doi:10.1101/217554 fatcat:zccskmtkdbb2xfflk6nzsuyviu

ICL670A [chapter]

2017 Encyclopedia of Cancer  
the 3D structure of p53 DNA-binding domain and predicted or observed effect on protein (function patterns).  ...  (BTLA; CD272), T-cell immunoglobulin (Ig) and ITIM domain (TIGIT), and killer inhibitory receptors, which can be divided into two classes based on structure, killer cell immunoglobulin-like receptors  ...  Mechanisms Their potential to exert estrogen-like actions lies in their chemical structure, which resembles the planar shape of endogenous estrogen 17b-estradiol (see Fig. 1 ).  ... 
doi:10.1007/978-3-662-46875-3_101180 fatcat:66hbagjkhzalvc3i2pzbhoe7aa

Supplementum 237: Swiss Hematology & Oncology Congress (SOHC)

2019 Swiss Medical Weekly  
myeloid leukemia (CML) patients in chronic phase (CP).  ...  with chronic myeloid leukemia transplanted with HLA-identical sibling donor and partial T-cell depletion.  ...  NSABP Foundation and Orlando Health University of Florida Health Cancer Center, Orlando, FL, USA; 2 NSABP Foundation and Virginia Commonwealth University Massey Cancer Center, Richmond, VA USA; 3 National  ... 
doi:10.4414/smw.2019.20439 fatcat:6w5t4xkolndjxkgxmru3isexxq

2019 CIS Annual Meeting: Immune Deficiency & Dysregulation North American Conference

2019 Journal of Clinical Immunology  
1 Genetic Counselor, Co-Director of Personalized Medicine, Division of Hematology/Oncology/BMT and the Institute for Genomic Medicine, Nationwide Childrens Hospital 2 Genetic Counselor, Division of Hematology  ...  BMBF 01 EO003 (Freiburg) The authors would like to thank the Director General of Health of Malaysia for permission to publish this scientific presentation.  ...  DOCK8 protein function was assessed by evaluating the morphology of patient lymphocytes when migrating in a 3D collagen matrix.  ... 
doi:10.1007/s10875-019-00597-5 pmid:30809743 fatcat:ophhlkvazzhjxl4t4eoct3tfna

Comprehensive multi-omics analysis of G6PC3 deficiency related congenital neutropenia with inflammatory bowel disease

Majed Dasouki, Ayodeele Alaiya, Tanziel ElAmin, Zakia Shinwari, Dorota Monies, Mohamed Abouelhoda, Amjad Jabaan, Feras Almourfi, Zuhair Rahbeeni, Fahad Alsohaibani, Fahad Almohareb, Hazzaa Al-Zahrani (+4 others)
2021 iScience  
Structural analysis of variant G6PC3 and MPL proteins suggests a damaging effect. A distinct molecular cytokine profile (cytokinome) in the affected proband with IBD was detected.  ...  Liquid chromatography-mass spectrometry-based proteomics analysis of the G6PC3-deficient plasma samples identified 460 distinct proteins including 75 upregulated and 73 downregulated proteins.  ...  Prediction of the 3D protein structure based on different threading templates such as the crystal structure of the transmembrane PAP2 type phosphatidylglycerol phosphate phosphatase from Bacillus subtilis  ... 
doi:10.1016/j.isci.2021.102214 pmid:33748703 pmcid:PMC7960940 fatcat:3nl4mlihmfanrj7rxecjuyjn6a

Hematopathology

2016 Laboratory Investigation  
Leukemic cells from whole peripheral blood samples from patients with acute myeloid leukemia (AML) or chronic lymphocytic leukemia (CLL) were enriched using density centrifugation and antibody-conjugated  ...  Exclusion criteria were: A) superficial biopsies where the base was not seen and B) CIS/SD within 1 mm of an invasive carcinoma, in continuity with a tonsil or base of tongue invasive carcinoma, or arising  ...  Risk Stratification of Additional Chromosomal Changes in Chronic Myelogenous Leukemia in Era of Tyrosine Kinase Inhibitor Therapy Integration of Multi-Locus DNA Methylation and Genetic Alterations Outperforms  ... 
doi:10.1038/labinvest.2016.13 pmid:26813175 fatcat:fcylb3wwpvdn7kqq4hrjo2m7ly

pp. 88–154

2004 Oncology Research and Treatment  
monoclonal antibody in single-agent use for B-cell chronic lymphocytic leukemias (B-CLL).  ...  P578 Protein Expression Analysis of Candidate Genes in Chronic Lymphocytic Leukemia with Trisomy 12 Winkler D. 1 The pathogenic role of candidate genes involved in CLL with trisomy 12, one of the  ...  P591 The mRNA Expression of Tumor Associated Antigens (TAAs) in CLL Patients Giannopoulos K. 1, 3 , Greiner J. 1 Purpose: B-cell chronic lymphocyte leukemia (B-CLL) is the most common leukemia in  ... 
doi:10.1159/000081406 fatcat:tujojku3nfdzvbjef27xlflfae
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