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BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

Frederik Otzen Bagger, Damir Sasivarevic, Sina Hadi Sohi, Linea Gøricke Laursen, Sachin Pundhir, Casper Kaae Sønderby, Ole Winther, Nicolas Rapin, Bo T. Porse
2015 Nucleic Acids Research  
To address these shortcomings, we present BloodSpot (www.bloodspot. eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS  ...  Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation.  ...  INTRODUCTION A decade of intense studies of the genetic programs underlying normal and malignant haematopoiesis has resulted in a number of gene-expression data sets, which can potentially help answer  ... 
doi:10.1093/nar/gkv1101 pmid:26507857 pmcid:PMC4702803 fatcat:c6cdihofyneq3b3c4ynuemlgvi

Expression of the Cavin Family in Childhood Leukemia and Its Implications in Subtype Diagnosis and Prognosis Evaluation

Jing Yang, Junbin Huang, Huabin Wang, Yong Liu, Yanlai Tang, Chao Lin, Qin Zhou, Chun Chen
2022 Frontiers in Pediatrics  
leukemia.MethodsWe performed a detailed analysis of Cavin family mRNA expression levels in different cancer tissues vs. normal tissues via the ONCOMINE, Gene Expression Profiling Interactive Analysis (  ...  Interestingly, low expression of CAVIN1 and CAVIN4 is correlated with poorer outcome but low CAVIN2 expression is associated with a significantly better leukemia prognosis in leukemia.ConclusionThe Cavin  ...  ACKNOWLEDGMENTS We are grateful to the open access websites of the ONCOMINE, CCLE, GEPIA, and LinkedOmics databases for providing clinical data and gene expression information.  ... 
doi:10.3389/fped.2022.815421 pmid:35722492 pmcid:PMC9203855 fatcat:utoazgtisjcwxprcoff2f4g7oa

Survivin' Acute Myeloid Leukaemia—A Personalised Target for inv(16) Patients

Jochen Greiner, Elliott Brown, Lars Bullinger, Robert K. Hills, Vanessa Morris, Hartmut Döhner, Ken I. Mills, Barbara-ann Guinn
2021 International Journal of Molecular Sciences  
Genes and Genomes (KEGG), search tool for recurring instances of neighbouring genes (STRING), WEB-based Gene Set Analysis Toolkit, Bloodspot and performed a comprehensive literature review.  ...  To better understand its potential to act as a target for immunotherapy and a biomarker for AML survival, we examined the protein and pathways that BIRC5 interacts with using the Kyoto Encyclopedia of  ...  Materials and Methods BIRC5 Expression in Healthy Haematopoietic Cells The BloodSpot database [20] includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in  ... 
doi:10.3390/ijms221910482 pmid:34638823 fatcat:iqj4wevlo5dqhluldu46wvk2mm

Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia

Subha Saha, Krushna Chandra Murmu, Mayukh Biswas, Sohini Chakraborty, Jhinuk Basu, Swati Madhulika, Srinivasa Prasad Kolapalli, Santosh Chauhan, Amitava Sengupta, Punit Prasad
2019 Frontiers in Oncology  
Acute myeloid leukemia (AML) is a common and aggressive hematological malignancy.  ...  We identified co-expression modules of RBP genes in LSCs and among these, distinct modules of RBP genes with high and low expression.  ...  BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles.  ... 
doi:10.3389/fonc.2019.00692 pmid:31448224 pmcid:PMC6691814 fatcat:yezj6v4glngqjf2tj6lruowfsu

Autophagy-mediated degradation of Fatty Acid Synthase (FASN) facilitates ATRA-induced granulocytic differentiation of acute myeloid leukemia (AML) cells [article]

Magali Humbert, Kristina Seiler, Severin Mosimann, Vreni Rentsch, Sharon L McKenna, Mario P Tschan
2020 bioRxiv   pre-print
Decreasing FASN expression reduced mTOR activity and promoted translocation of transcription factor EB (TFEB) to the nucleus.  ...  Lysosomal biogenesis was activated, consistent with TFEB transcriptional activation of CLEAR network genes.  ...  programs for healthy and malignant haematopoiesis.  ... 
doi:10.1101/2020.01.29.924555 fatcat:7hybnzavzref7iuf25eofi4mkm

iMAC: An interactive atlas to explore phenotypic differences between in vivo, ex vivo and in vitro-derived myeloid cells in the Stemformatics platform [article]

Nadia Rajab, Paul Angel, Mariola Kurowska-Stolarska, Simon Milling, Chris Pacheco Rivera, Matt Rutar, Jarny Choi, Christine A Wells
2019 bioRxiv   pre-print
By assembling a large transcriptional atlas of human myeloid biology representing ~1000 samples, we address the question of how well laboratory models, including pluripotent-derived cells, represent macrophage  ...  biology, and particularly whether these can model resident tissue macrophage specialisation.  ...  ., and Porse, B.T. (2016). BloodSpot: A database of gene expression profiles and 374 transcriptional programs for healthy and malignant haematopoiesis.  ... 
doi:10.1101/719237 fatcat:oakh4a3cajeo7oizl6d5n2q3ke

SETDB1 mediated histone H3 lysine 9 methylation suppresses MLL-fusion target expression and leukemic transformation

James Ropa, Nirmalya Saha, Hsiangyu Hu, Luke F. Peterson, Moshe Talpaz, Andrew G. Muntean
2019 Haematologica  
Epigenetic regulators play a critical role in normal and malignant hematopoiesis.  ...  These data reveal novel targets of SETDB1 in leukemia that point to a role for SETDB1 in negatively regulating pro-leukemic target genes and suppressing acute myeloid leukemia.  ...  Jianyong Shou for a SETDB1 expression construct and Dr. Schahram Akbarian for Setdb1fl/fl mice. We also thank Dr. Russell Ryan, Dr. Emmalee Adelman, Dr. Maria Figueroa, and Dr.  ... 
doi:10.3324/haematol.2019.223883 pmid:31558673 pmcid:PMC7556517 fatcat:7lqxim5w5jdodgikdpzhjjluyy

A comprehensive single-cell expression atlas of human AML leukemia-initiating cells unravels the contribution of HIF pathway and its therapeutic potential [article]

Talia Velasco-Hernandez, Juan L. Trincado, Meritxell Vinyoles, Adria Closa, Francisco Gutiérrez-Agüera, Oscar Molina, Virginia C Rodríguez-Cortez, Paolo Petazzi, Sergi Beneyto-Calabuig, Lars Velten, Paola Romecin, Raquel Casquero (+13 others)
2022 bioRxiv   pre-print
Here, we provide a comprehensive single-cell expression atlas (119,000 cells) of AML cells and AML-LSCs in paired diagnostic-relapse samples from risk-stratified patients with AML.  ...  These findings support the HIF pathway as a stem cell regulator in human AML, and reveal avenues for combinatorial targeted and chemotherapy-based approaches to specifically eliminate AML-LSCs.  ...  Aleix Prat for technical help and Dr. Fernando Anjos-Afonso for technical discussions and advices.  ... 
doi:10.1101/2022.03.02.482638 fatcat:xmoo4fgstfcqnc3bxngizyst6q

Characterization and evolutionary origin of novel C2H2 zinc finger protein (ZNF648) required for both erythroid and megakaryocyte differentiation in humans

Daniel C. J. Ferguson, Juraidah Haji Mokim, Marjolein Meinders, Edmund R. R. Moody, Tom A. Williams, Sarah Cooke, Kongtana Trakarnsanga, Deborah E. Daniels, Ivan Ferrer-Vicens, Deborah Shoemark, Chartsiam Tipgomut, Katherine A. Macinnes (+3 others)
2020 Haematologica  
Orthologues of ZNF648 were detected across Mammals, Reptilia, Actinopterygii, in some Aves, Amphibia and Coelacanthiformes suggesting the gene originated in the common ancestor of Osteichthyes (Euteleostomi  ...  As for other such transcription factors, the N-terminus likely carries out regulatory functions, but showed no sequence similarity to any known domains.  ...  Dr Lee Carpenter, Oxford for providing the iPSCs, Profs Yukio Nakamura and Ryo Kurita, RIKEN BioResource Research Center, Japan for the HiDEP-1 cells.  ... 
doi:10.3324/haematol.2020.256347 pmid:33054117 pmcid:PMC8561289 fatcat:efxgycqkgjhghcjv2gdf2gul7a

A gain-of-function p53 mutant oncogene promotes cell fate plasticity and myeloid leukemia through the pluripotency factor Foxh1

Evangelia Loizou, Ana Banito, Geulah Livshits, Yu-Jui Ho, Richard P. Koche, Francisco J Sanchez-Rivera, Allison Mayle, Chi-Chao Chen, Savvas Kinalis, Frederik Otzen Bagger, Edward R Kastenhuber, Benjamin H. Durham (+1 others)
2019 Cancer Discovery  
We identify FOXH1 as a critical mediator of mutant p53 function that binds to and regulates stem cell-associated genes and transcriptional programs.  ...  Our results identify a context where mutant p53 acts as a bona fide oncogene that contributes to the pathogenesis of CK-AML and suggests a common biological theme for TP53 GOF in cancer.  ...  BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles. Nucleic Acids Res 2019;47(D1):D881-D5 doi 10.1093/nar/gky1076. 32.  ... 
doi:10.1158/2159-8290.cd-18-1391 pmid:31068365 pmcid:PMC6606372 fatcat:etbjr4elujbrrgr2flr27qhl7q

Combinatorial molecule screening identifies a novel diterpene and the BET inhibitor CPI-203 as differentiation inducers of primary acute myeloid leukemia cells

Simon Hultmark, Aurélie Baudet, Ludwig Schmiderer, Pavan Prabhala, Sara Palma-Tortosa, Carl Sandén, Thoas Fioretos, Rajkumar Sasidharan, Christer Larsson, Sören Lehmann, Gunnar Juliusson, Fredrik Ek (+1 others)
2020 Haematologica  
The responding samples to H4, displayed increased expression of myeloid markers, a clear decrease in the nuclear-cytoplasmic ratio and the potential of re-activation of the monocytic transcriptional program  ...  Combination treatment has proven effective for patients with acute promyelocytic leukemia, exemplifying the importance of therapy targeting multiple components of oncogenic regulation for a successful  ...  Acknowledgement The authors would like to thank the staff at the Lund Stem Cell FACS Core Facilities for assistance with cell sorting. We thank Sofia Bengtsson for helping with primary samples. We  ... 
doi:10.3324/haematol.2020.249177 pmid:32855276 pmcid:PMC8485661 fatcat:xqx6gixwyjhgtcx3w3sotyg4du

Chemotherapy-Resistant Human Acute Myeloid Leukemia Cells Are Not Enriched for Leukemic Stem Cells but Require Oxidative Metabolism

Thomas Farge, Estelle Saland, Fabienne de Toni, Nesrine Aroua, Mohsen Hosseini, Robin Perry, Claudie Bosc, Mayumi Sugita, Lucille Stuani, Marine Fraisse, Sarah Scotland, Clément Larrue (+31 others)
2017 Cancer Discovery  
Pyronin Y was then added to a final concentration of 1 µg/ml, and incubation continued for another 20 minutes.  ...  (R)-(+)-Etomoxir was supplied by Medchem Express.  ...  BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. Nucleic Acids Res, 44(D1), D917-24.  ... 
doi:10.1158/2159-8290.cd-16-0441 pmid:28416471 pmcid:PMC5501738 fatcat:5m2kvyjx4fhanha7dkjhlukpte

RUNX3 levels in human hematopoietic progenitors are regulated by aging and dictate erythroid-myeloid balance

Peter Balogh, Emmalee R. Adelman, John V. Pluvinage, Brian J. Capaldo, Katie C. Freeman, Sandeep Singh, Kamaleldin E. Elagib, Yukio Nakamura, Ryo Kurita, Goro Sashida, Eli R. Zunder, Hui Li (+7 others)
2019 Haematologica  
Transcriptome profiling indicated control by RUNX3 of key erythroid transcription factors, including KLF1 and GATA1.  ...  Healthy bone marrow progenitors yield a coordinated balance of hematopoietic lineages.  ...  ACKNOWLEDGEMENTS Thank you to Nicole Brimer for providing the packaging plasmids for production of retroviral particles.  ... 
doi:10.3324/haematol.2018.208918 pmid:31171641 pmcid:PMC7109730 fatcat:nrlep46vbzeftgjefxnplyv4dq

Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE)

S. Téletchéa, H. Santuz, S. Léonard, C. Etchebest, Björn Wallner
2019 PLoS ONE  
To provide a more compendious view of erythrocytes and of their protein content, we developed a dedicated database called RESPIRE that aims at gathering a comprehensive and coherent ensemble of information  ...  Browsing the database is available through text search for reference gene names or protein identifiers, through pre-defined queries or via hyperlinks.  ...  Patrick Mayeux and Emilie-Fleur Gautier for fruitful discussions and their valuable support.  ... 
doi:10.1371/journal.pone.0211043 pmid:30794542 pmcid:PMC6386447 fatcat:jcuyqyndufc3bc3nypn4lcblei

A Single Cell Resolution Map of Mouse Haematopoietic Stem and Progenitor Cell Differentiation

Sonia Shaw, Fiona Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola Wilson, David Kent, Berthold Gottgens, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
2016
Finally, we report the development of an intuitive Web interface as a new community resource to permit visualization of gene expression in HSPCs at single-cell resolution for any gene of choice.  ...  The latter two trajectories were characterized by common upregulation of cell cycle and oxidative phosphorylation transcriptional programs.  ...  Cell Stem Cell. 6. profiles and transcriptional programs for healthy and malignant haematopoiesis. 2013;12(1):62-74. 2011;102:533-556. doi:10.1016/B978-0-12-374912-3.00021-3. 10.  ... 
doi:10.17863/cam.4534 fatcat:gyuauznlszerjlyflbo4dnsxda
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