Spatiotemporal expression and control of haemoglobin in space.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
11 Jun 2024
Historique:
received: 19 06 2023
accepted: 31 05 2024
medline: 12 6 2024
pubmed: 12 6 2024
entrez: 11 6 2024
Statut: epublish

Résumé

It is now widely recognised that the environment in space activates a diverse set of genes involved in regulating fundamental cellular pathways. This includes the activation of genes associated with blood homoeostasis and erythropoiesis, with a particular emphasis on those involved in globin chain production. Haemoglobin biology provides an intriguing model for studying space omics, as it has been extensively explored at multiple -omic levels, spanning DNA, RNA, and protein analyses, in both experimental and clinical contexts. In this study, we examined the developmental expression of haemoglobin over time and space using a unique suite of multi-omic datasets available on NASA GeneLab, from the NASA Twins Study, the JAXA CFE study, and the Inspiration4 mission. Our findings reveal significant variations in globin gene expression corresponding to the distinct spatiotemporal characteristics of the collected samples. This study sheds light on the dynamic nature of globin gene regulation in response to the space environment and provides valuable insights into the broader implications of space omics research.

Identifiants

pubmed: 38862545
doi: 10.1038/s41467-024-49289-8
pii: 10.1038/s41467-024-49289-8
doi:

Substances chimiques

Hemoglobins 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

4927

Informations de copyright

© 2024. The Author(s).

Références

De Santo, N. G. et al. Anemia and erythropoietin in space flights. In: Seminars in Nephrology. Vol. 25, 379–387 (Elsevier, 2005).
Trudel, G., Shafer, J., Laneuville, O. & Ramsay, T. Characterizing the effect of exposure to microgravity on anemia: more space is worse. Am. J. Hematol. 95, 267–273 (2020).
pubmed: 31816115 doi: 10.1002/ajh.25699
Borg, J., Patrinos, G. P., Felice, A. E. & Philipsen, S. Erythroid phenotypes associated with klf1 mutations. Haematologica 96, 635 (2011).
pubmed: 21531944 pmcid: 3084906 doi: 10.3324/haematol.2011.043265
Atweh, G. F. et al. Hemoglobinopathies. ASH Educ. Program Book 2003, 14–39 (2003).
Dzierzak, E. & Philipsen, S. Erythropoiesis: development and differentiation. Cold Spring Harb. Perspect. Med. 3, 011601 (2013).
doi: 10.1101/cshperspect.a011601
Borg, J. et al. Haploinsufficiency for the erythroid transcription factor klf1 causes hereditary persistence of fetal hemoglobin. Nat. Genet. 42, 801–805 (2010).
pubmed: 20676099 pmcid: 2930131 doi: 10.1038/ng.630
Giardine, B. et al. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nat. Genet. 43, 295–301 (2011).
pubmed: 21423179 doi: 10.1038/ng.785
Ray, S. et al. Genelab: Omics database for spaceflight experiments. Bioinformatics 35, 1753–1759 (2019).
pubmed: 30329036 doi: 10.1093/bioinformatics/bty884
Garrett-Bakelman, F. E. et al. The NASA twins study: a multidimensional analysis of a year-long human spaceflight. Science 364, 8650 (2019).
doi: 10.1126/science.aau8650
Gertz, M. L. et al. Multi-omic, single-cell, and biochemical profiles of astronauts guide pharmacological strategies for returning to gravity. Cell Rep. 33, 108429 (2020).
pubmed: 33242408 pmcid: 9444344 doi: 10.1016/j.celrep.2020.108429
Trudel, G., Shahin, N., Ramsay, T., Laneuville, O. & Louati, H. Hemolysis contributes to anemia during long-duration space flight. Nat. Med. 28, 59–62 (2022).
pubmed: 35031790 pmcid: 8799460 doi: 10.1038/s41591-021-01637-7
Valderrábano, R. J. et al. Bone density loss is associated with blood cell counts. J. Bone Miner. Res. 32, 212–220 (2017).
pubmed: 27653240 doi: 10.1002/jbmr.3000
Polineni, S. et al. Red and white blood cell counts are associated with bone marrow adipose tissue, bone mineral density, and bone microarchitecture in premenopausal women. J. Bone Miner. Res. 35, 1031–1039 (2020).
pubmed: 32078187 doi: 10.1002/jbmr.3986
Galanello, R. & Cao, A. Alpha-thalassemia. Genet. Med. 13, 83–88 (2011).
pubmed: 21381239 doi: 10.1097/GIM.0b013e3181fcb468
Piel, F. B. & Weatherall, D. J. The α-thalassemias. N. Engl. J. Med. 371, 1908–1916 (2014).
pubmed: 25390741 doi: 10.1056/NEJMra1404415
Stelzer, G. et al. The genecards suite: from gene data mining to disease genome sequence analyses. Curr. Protoc. Bioinforma. 54, 1–30 (2016).
doi: 10.1002/cpbi.5
Safran, M. et al. The GeneCards Suite. Practical Guide to Life Science Databases. 27–56 (Current Protocols in Bioinformatics, 2021).
Fujiwara, T. et al. Effect of 5-aminolevulinic acid on erythropoiesis: a preclinical in vitro characterization for the treatment of congenital sideroblastic anemia. Biochem. Biophys. Res. Commun. 454, 102–108 (2014).
pubmed: 25450364 doi: 10.1016/j.bbrc.2014.10.050
Tanimura, N. et al. Mechanism governing heme synthesis reveals a gata factor/heme circuit that controls differentiation. EMBO Rep. 17, 249–265 (2016).
pubmed: 26698166 doi: 10.15252/embr.201541465
Laranjeira, P. et al. Expression of cd44 and cd35 during normal and myelodysplastic erythropoiesis. Leuk. Res. 39, 361–370 (2015).
pubmed: 25582385 doi: 10.1016/j.leukres.2014.12.009
Mercurio, S. et al. The heme exporter flvcr1 regulates expansion and differentiation of committed erythroid progenitors by controlling intracellular heme accumulation. Haematologica 100, 720 (2015).
pubmed: 25795718 pmcid: 4450617 doi: 10.3324/haematol.2014.114488
Rey, M. A. et al. Enhanced alternative splicing of the flvcr1 gene in diamond blackfan anemia disrupts flvcr1 expression and function that are critical for erythropoiesis. Haematologica 93, 1617–1626 (2008).
pubmed: 18815190 doi: 10.3324/haematol.13359
Kim, M. Y. et al. Mbd2-cp2c loop drives adult-type globin gene expression and definitive erythropoiesis. Nucleic Acids Res. 46, 4933–4949 (2018).
pubmed: 29547954 pmcid: 6007553 doi: 10.1093/nar/gky193
Sankaran, V. G. et al. Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor bcl11a. Science 322, 1839–1842 (2008).
pubmed: 19056937 doi: 10.1126/science.1165409
Zhou, D., Liu, K., Sun, C.-W., Pawlik, K. M. & Townes, T. M. Klf1 regulates bcl11a expression and γ-to β-globin gene switching. Nat. Genet. 42, 742–744 (2010).
pubmed: 20676097 doi: 10.1038/ng.637
Wilber, A., Nienhuis, A. W. & Persons, D. A. Transcriptional regulation of fetal to adult hemoglobin switching: new therapeutic opportunities. Blood 117, 3945–3953 (2011).
pubmed: 21321359 pmcid: 3087525 doi: 10.1182/blood-2010-11-316893
Xu, J. et al. Transcriptional silencing of γ-globin by bcl11a involves long-range interactions and cooperation with sox6. Genes Dev. 24, 783–798 (2010).
pubmed: 20395365 pmcid: 2854393 doi: 10.1101/gad.1897310
Masuda, T. et al. Transcription factors lrf and bcl11a independently repress expression of fetal hemoglobin. Science 351, 285–289 (2016).
pubmed: 26816381 pmcid: 4778394 doi: 10.1126/science.aad3312
Martyn, G. E. et al. Natural regulatory mutations elevate the fetal globin gene via disruption of bcl11a or zbtb7a binding. Nat. Genet. 50, 498–503 (2018).
pubmed: 29610478 doi: 10.1038/s41588-018-0085-0
Lee, Y. T. et al. Lin28b-mediated expression of fetal hemoglobin and production of fetal-like erythrocytes from adult human erythroblasts ex vivo. Blood 122, 1034–1041 (2013).
pubmed: 23798711 pmcid: 3739030 doi: 10.1182/blood-2012-12-472308
Gravia, A. et al. Correlation of sin3a genomic variants with β-hemoglobinopathies disease severity and hydroxyurea treatment efficacy. Pharmacogenomics 17, 1785–1793 (2016).
pubmed: 27767389 doi: 10.2217/pgs-2016-0076
Elalfy, M. S., El Sherif, N. H., Kamal, T. M. & Aly, N. H. Klf10 gene, a secondary modifier and a pharmacogenomic biomarker of hydroxyurea treatment among patients with hemoglobinopathies. J. Pediatr. Hematol./Oncol. 39, 155–162 (2017).
doi: 10.1097/MPH.0000000000000762
Wang, G., Xu, G. & Wang, W. Long noncoding rna cdkn2b-as1 facilitates lung cancer development through regulating mir-378b/nr2c2. OncoTargets Ther. 13, 10641 (2020).
doi: 10.2147/OTT.S261973
Tanabe, O. et al. Embryonic and fetal β-globin gene repression by the orphan nuclear receptors, tr2 and tr4. EMBO J. 26, 2295–2306 (2007).
pubmed: 17431400 pmcid: 1864974 doi: 10.1038/sj.emboj.7601676
Tanabe, O. et al. An embryonic/fetal β-type globin gene repressor contains a nuclear receptor tr2/tr4 heterodimer. EMBO J. 21, 3434–3442 (2002).
pubmed: 12093744 pmcid: 126089 doi: 10.1093/emboj/cdf340
Amaya, M. et al. Mi2β-mediated silencing of the fetal γ-globin gene in adult erythroid cells. Blood 121, 3493–3501 (2013).
pubmed: 23444401 pmcid: 3637018 doi: 10.1182/blood-2012-11-466227
Bianchi, E. et al. c-myb supports erythropoiesis through the transactivation of klf1 and lmo2 expression. Blood 116, 99–110 (2010).
doi: 10.1182/blood-2009-08-238311
Stockmann, C. & Fandrey, J. Hypoxia-induced erythropoietin production: a paradigm for oxygen-regulated gene expression. Clin. Exp. Pharmacol. Physiol. 33, 968–979 (2006).
pubmed: 17002676 doi: 10.1111/j.1440-1681.2006.04474.x
Darling, R. J. et al. Glycosylation of erythropoietin affects receptor binding kinetics: role of electrostatic interactions. Biochemistry 41, 14524–14531 (2002).
pubmed: 12463751 doi: 10.1021/bi0265022
Suragani, R. N. et al. Heme-regulated eIF2α kinase activated Atf4 signaling pathway in oxidative stress and erythropoiesis. Blood 119, 5276–5284 (2012).
pubmed: 22498744 pmcid: 3369616 doi: 10.1182/blood-2011-10-388132
Azad, P. et al. Arid1b, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge’s disease. Exp. Mol. Med. 54, 777–787 (2022).
pubmed: 35672450 pmcid: 9256584 doi: 10.1038/s12276-022-00769-1
Pevny, L. et al. Erythroid differentiation in chimaeric mice blocked by a targeted mutation in the gene for transcription factor gata-1. Nature 349, 257–260 (1991).
pubmed: 1987478 doi: 10.1038/349257a0
Weiss, M. J., Keller, G. & Orkin, S. H. Novel insights into erythroid development revealed through in vitro differentiation of gata-1 embryonic stem cells. Genes Dev. 8, 1184–1197 (1994).
pubmed: 7926723 doi: 10.1101/gad.8.10.1184
Love, P. E., Warzecha, C. & Li, L. Ldb1 complexes: the new master regulators of erythroid gene transcription. Trends Genet. 30, 1–9 (2014).
pubmed: 24290192 doi: 10.1016/j.tig.2013.10.001
Robb, L. & Begley, C. G. The scl/tal1 gene: roles in normal and malignant haematopoiesis. Bioessays 19, 607–613 (1997).
pubmed: 9230693 doi: 10.1002/bies.950190711
Shivdasani, R. A., Mayer, E. L. & Orkin, S. H. Absence of blood formation in mice lacking the t-cell leukaemia oncoprotein tal-1/scl. Nature 373, 432–434 (1995).
pubmed: 7830794 doi: 10.1038/373432a0
Wadman, I. A. et al. The lim-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins. EMBO J. 16, 3145–3157 (1997).
pubmed: 9214632 pmcid: 1169933 doi: 10.1093/emboj/16.11.3145
Ingley, E., Tilbrook, P. A. & Klinken, S. P. New insights into the regulation of erythroid cells. IUBMB Life 56, 177–184 (2004).
pubmed: 15230344 doi: 10.1080/15216540410001703956
Mignotte, V., Eleouet, J. F., Raich, N. & Romeo, P.-H. Cis-and trans-acting elements involved in the regulation of the erythroid promoter of the human porphobilinogen deaminase gene. Proc. Natl Acad. Sci. USA 86, 6548–6552 (1989).
pubmed: 2771941 pmcid: 297881 doi: 10.1073/pnas.86.17.6548
Tugores, A., Magness, S. T. & Brenner, D. A. A single promoter directs both housekeeping and erythroid preferential expression of the human ferrochelatase gene. J. Biol. Chem. 269, 30789–30797 (1994).
pubmed: 7983009 doi: 10.1016/S0021-9258(18)47351-6
Saki, N. et al. Microrna expression in β-thalassemia and sickle cell disease: a role in the induction of fetal hemoglobin. Cell J. (Yakhteh) 17, 583 (2016).
Sankaran, V. G. et al. Microrna-15a and-16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13. Proc. Natl Acad. Sci. USA 108, 1519–1524 (2011).
pubmed: 21205891 pmcid: 3029749 doi: 10.1073/pnas.1018384108
Malkani, S. et al. Circulating miRNA spaceflight signature reveals targets for countermeasure development. Cell Rep. 33, 108448 (2020).
pubmed: 33242410 pmcid: 8441986 doi: 10.1016/j.celrep.2020.108448
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
pubmed: 31178118 pmcid: 6687398 doi: 10.1016/j.cell.2019.05.031
Finak, G. et al. Mast: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 1–13 (2015).
doi: 10.1186/s13059-015-0844-5
Kang, W. et al. miRTrace reveals the organismal origins of microRNA sequencing data. Genome Biol. 19, 1–15 (2018).
doi: 10.1186/s13059-018-1588-9
Fromm, B. et al. Mirgenedb 2.0: the metazoan microrna complement. Nucleic Acids Res. 48, 132–141 (2020).
doi: 10.1093/nar/gkz885
Friedländer, M. R., Mackowiak, S. D., Li, N., Chen, W. & Rajewsky, N. mirdeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 40, 37–52 (2012).
pubmed: 21911355 doi: 10.1093/nar/gkr688
Muratani, M. Cell-free RNA analysis of plasma samples collected from six astronauts in JAXA cell-free epigenome (CFE) study. NASA Open Science Data Repository, Version 2, 10, 2–714 (2022).
Overbey, E. G. et al. Collection of biospecimens from the inspiration4 mission establishes the standards for the space omics and medical atlas (SOMA). Nat. Commun. https://doi.org/10.1038/s41467-024-48806-z (2024).

Auteurs

Josef Borg (J)

Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta.

Conor Loy (C)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

JangKeun Kim (J)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Alfred Buhagiar (A)

Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta.

Christopher Chin (C)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Namita Damle (N)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Iwijn De Vlaminck (I)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Alex Felice (A)

Department of Surgery, Faculty of Medicine and Surgery, University of Malta, Msida, MSD2080, Malta.

Tammy Liu (T)

Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada.

Irina Matei (I)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Cem Meydan (C)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Masafumi Muratani (M)

Department of Genome Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan.

Omary Mzava (O)

Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.

Eliah Overbey (E)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Krista A Ryon (KA)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Scott M Smith (SM)

Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA.

Braden T Tierney (BT)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Guy Trudel (G)

Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada.

Sara R Zwart (SR)

Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA.
University of Texas Medical Branch, Galveston, TX, USA.

Afshin Beheshti (A)

Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA. afshin.beheshti@nasa.gov.
Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. afshin.beheshti@nasa.gov.

Christopher E Mason (CE)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA. chm2042@med.cornell.edu.

Joseph Borg (J)

Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta. joseph.j.borg@um.edu.mt.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH