1
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Stevens CS, Carmichael J, Watkinson R, Kowdle S, Reis RA, Hamane K, Jang J, Park A, Pernet O, Khamaikawin W, Hong P, Thibault P, Gowlikar A, An DS, Lee B. A temperature-sensitive and interferon-silent Sendai virus vector for CRISPR-Cas9 delivery and gene editing in primary human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592383. [PMID: 38746439 PMCID: PMC11092779 DOI: 10.1101/2024.05.03.592383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The transformative potential of gene editing technologies hinges on the development of safe and effective delivery methods. In this study, we developed a temperature-sensitive and interferon-silent Sendai virus (ts SeV) as a novel delivery vector for CRISPR-Cas9 and for efficient gene editing in sensitive human cell types without inducing IFN responses. ts SeV demonstrates unprecedented transduction efficiency in human CD34+ hematopoietic stem and progenitor cells (HSPCs) including transduction of the CD34+/CD38-/CD45RA-/CD90+(Thy1+)/CD49fhigh stem cell enriched subpopulation. The frequency of CCR5 editing exceeded 90% and bi-allelic CCR5 editing exceeded 70% resulting in significant inhibition of HIV-1 infection in primary human CD14+ monocytes. These results demonstrate the potential of the ts SeV platform as a safe, efficient, and flexible addition to the current gene-editing tool delivery methods, which may help to further expand the possibilities in personalized medicine and the treatment of genetic disorders.
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Affiliation(s)
- Christian S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jillian Carmichael
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ruth Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Shreyas Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rebecca A Reis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kory Hamane
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Jason Jang
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Arnold Park
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Olivier Pernet
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Wannisa Khamaikawin
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Patrick Hong
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Patricia Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aditya Gowlikar
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Dong Sung An
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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2
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Mayuranathan T, Newby GA, Feng R, Yao Y, Mayberry KD, Lazzarotto CR, Li Y, Levine RM, Nimmagadda N, Dempsey E, Kang G, Porter SN, Doerfler PA, Zhang J, Jang Y, Chen J, Bell HW, Crossley M, Bhoopalan SV, Sharma A, Tisdale JF, Pruett-Miller SM, Cheng Y, Tsai SQ, Liu DR, Weiss MJ, Yen JS. Potent and uniform fetal hemoglobin induction via base editing. Nat Genet 2023; 55:1210-1220. [PMID: 37400614 PMCID: PMC10722557 DOI: 10.1038/s41588-023-01434-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/23/2023] [Indexed: 07/05/2023]
Abstract
Inducing fetal hemoglobin (HbF) in red blood cells can alleviate β-thalassemia and sickle cell disease. We compared five strategies in CD34+ hematopoietic stem and progenitor cells, using either Cas9 nuclease or adenine base editors. The most potent modification was adenine base editor generation of γ-globin -175A>G. Homozygous -175A>G edited erythroid colonies expressed 81 ± 7% HbF versus 17 ± 11% in unedited controls, whereas HbF levels were lower and more variable for two Cas9 strategies targeting a BCL11A binding motif in the γ-globin promoter or a BCL11A erythroid enhancer. The -175A>G base edit also induced HbF more potently than a Cas9 approach in red blood cells generated after transplantation of CD34+ hematopoietic stem and progenitor cells into mice. Our data suggest a strategy for potent, uniform induction of HbF and provide insights into γ-globin gene regulation. More generally, we demonstrate that diverse indels generated by Cas9 can cause unexpected phenotypic variation that can be circumvented by base editing.
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Affiliation(s)
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kalin D Mayberry
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rachel M Levine
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nikitha Nimmagadda
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Erin Dempsey
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Phillip A Doerfler
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Zhang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yoonjeong Jang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Chen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Henry W Bell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute and National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jonathan S Yen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Bou-Fakhredin R, De Franceschi L, Motta I, Cappellini MD, Taher AT. Pharmacological Induction of Fetal Hemoglobin in β-Thalassemia and Sickle Cell Disease: An Updated Perspective. Pharmaceuticals (Basel) 2022; 15:ph15060753. [PMID: 35745672 PMCID: PMC9227505 DOI: 10.3390/ph15060753] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
A significant amount of attention has recently been devoted to the mechanisms involved in hemoglobin (Hb) switching, as it has previously been established that the induction of fetal hemoglobin (HbF) production in significant amounts can reduce the severity of the clinical course in diseases such as β-thalassemia and sickle cell disease (SCD). While the induction of HbF using lentiviral and genome-editing strategies has been made possible, they present limitations. Meanwhile, progress in the use of pharmacologic agents for HbF induction and the identification of novel HbF-inducing strategies has been made possible as a result of a better understanding of γ-globin regulation. In this review, we will provide an update on all current pharmacological inducer agents of HbF in β-thalassemia and SCD in addition to the ongoing research into other novel, and potentially therapeutic, HbF-inducing agents.
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Affiliation(s)
- Rayan Bou-Fakhredin
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (R.B.-F.); (I.M.)
| | - Lucia De Franceschi
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Verona, 37128 Verona, Italy;
| | - Irene Motta
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (R.B.-F.); (I.M.)
- UOC General Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy; (R.B.-F.); (I.M.)
- UOC General Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Correspondence: (M.D.C.); (A.T.T.)
| | - Ali T. Taher
- Department of Internal Medicine, Division of Hematology-Oncology, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
- Correspondence: (M.D.C.); (A.T.T.)
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4
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Single Nucleotide Polymorphisms in XMN1-HBG2, HBS1L-MYB, and BCL11A and Their Relation to High Fetal Hemoglobin Levels That Alleviate Anemia. Diagnostics (Basel) 2022; 12:diagnostics12061374. [PMID: 35741184 PMCID: PMC9221560 DOI: 10.3390/diagnostics12061374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 02/01/2023] Open
Abstract
Anemia is a condition in which red blood cells and/or hemoglobin (Hb) concentrations are decreased below the normal range, resulting in a lack of oxygen being transported to tissues and organs. Those afflicted with this condition may feel lethargic and weak, which reduces their quality of life. The condition may be manifested in inherited blood disorders, such as thalassemia and sickle cell disease, whereas acquired disorders include aplastic anemia, chronic disease, drug toxicity, pregnancy, and nutritional deficiency. The augmentation of fetal hemoglobin (HbF) results in the reduction in clinical symptoms in beta-hemoglobinopathies. Several transcription factors as well as medications such as hydroxyurea may help red blood cells produce more HbF. HbF expression increases with the downregulation of three main quantitative trait loci, namely, the XMN1-HBG2, HBS1L-MYB, and BCL11A genes. These genes contain single nucleotide polymorphisms (SNPs) that modulate the expression of HbF differently in various populations. Allele discrimination is important in SNP genotyping and is widely applied in many assays. In conclusion, the expression of HbF with a genetic modifier is crucial in determining the severity of anemic diseases, and genetic modification of HbF expression may offer clinical benefits in diagnosis and disease management.
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5
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Dehury S, Mohanty PK, Patel S, Meher S, Das K, Purohit P, Sahoo S, Ratha J. Profiling of 35 Cases of Hb S/Hb E ( HBB: c.20A>T/ HBB: c.79G>a), Disease and Association with α-Thalassemia and β-Globin Gene Cluster Haplotypes from Odisha, India. Hemoglobin 2022; 45:380-386. [PMID: 35243949 DOI: 10.1080/03630269.2021.1965618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hb S/Hb E (HBB: c.20A>T/HBB: c.79G>A) is an uncommon variant of sickle cell disease resulting from coinheritance of Hb S and Hb E. Clinico-hematological and biochemical parameters of 35 cases of Hb S/Hb E disease were studied and compared with 70 matched cases of homozygous sickle cell disease (Hb SS) and Hb S/β-thalassemia (β-thal) with IVS-I-5 (G>C) (HBB: c.92+5G>C). The influence of α-thal and that of of β-globin gene cluster haplotypes among Hb S/Hb E disease was also studied. Statistical analysis was done using GraphPad InStat version 3.06. Of the 35 cases, 20 (57.14%) had a moderate clinical presentation. Mean lactate dehydrogenase (LDH) level, vaso-occlusive crises (VOCs) per year, and annual blood transfusion requirements were significantly lower in Hb S/Hb E cases than in the other two groups. The hemoglobin (Hb) and packed cell volume (PCV) levels were significantly high in Hb S/Hb E cases with α-thal and these cases were associated with microcytic-hypochromic anemia. α-Thalassemia did not influence clinical presentation in Hb S/Hb E cases. The β-globin gene cluster haplotypes of 70 alleles of Hb S/Hb E revealed an association of five typical haplotypes [Arab-Indian (A-I), Benin, Bantu, Cameroon and Senegal] in 95.71% cases. Hb S/Hb E disease exhibit asymptomatic to moderate phenotypic expression. However, further in-depth studies on Hb S/Hb E will help in reducing the disease burden especially in high-risk countries like India.
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Affiliation(s)
- Snehadhini Dehury
- Sickle Cell Institute, Sickle Cell Project (National Health Mission Odisha), Veer Surendra Sai Institute of Medical Science and Research (VIMSAR), Burla, Sambalpur, Odisha, India.,School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, Sambalpur, Odisha, India
| | - Pradeep K Mohanty
- Sickle Cell Institute, Sickle Cell Project (National Health Mission Odisha), Veer Surendra Sai Institute of Medical Science and Research (VIMSAR), Burla, Sambalpur, Odisha, India.,Department of Medicine, VIMSAR, Burla, Sambalpur, Odisha, India
| | - Siris Patel
- Sickle Cell Institute, Sickle Cell Project (National Health Mission Odisha), Veer Surendra Sai Institute of Medical Science and Research (VIMSAR), Burla, Sambalpur, Odisha, India
| | - Satyabrata Meher
- Sickle Cell Institute, Sickle Cell Project (National Health Mission Odisha), Veer Surendra Sai Institute of Medical Science and Research (VIMSAR), Burla, Sambalpur, Odisha, India
| | - Kishalaya Das
- Sickle Cell Institute, Sickle Cell Project (National Health Mission Odisha), Veer Surendra Sai Institute of Medical Science and Research (VIMSAR), Burla, Sambalpur, Odisha, India
| | - Prasanta Purohit
- Multi-Disciplinary Research Unit, Maharaja Krishna Chandra Gajapati (MKCG) Medical College, Berhampur, Odisha, India
| | - Sarmila Sahoo
- Sickle Cell Institute, Sickle Cell Project (National Health Mission Odisha), Veer Surendra Sai Institute of Medical Science and Research (VIMSAR), Burla, Sambalpur, Odisha, India
| | - Jagnyeswar Ratha
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Burla, Sambalpur, Odisha, India
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6
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Chen HQ, Wu LS, Jiang F, Li DZ. Dominant β-Thalassemia Phenotype Caused by Hb Dieppe ( HBB: c.383A>G): Another Case Report. Hemoglobin 2021; 45:329-331. [PMID: 34957901 DOI: 10.1080/03630269.2021.2016441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Homozygous or compound heterozygous mutations of the β-globin gene lead to β-thalassemia (β-thal) major (β-TM) or β-thal intermedia (β-TI), whereas heterozygotes usually show microcytosis with negligible or no hemolysis. Certain missense mutations in exon 3, however, produce unstable globins causing a dominant β-thal phenotype or hemolytic anemia in heterozygotes. Here we report a mutation in exon 3 of the β-globin gene, which results in an unstable globin (Hb Dieppe) [β127(H5)Gln→Arg; HBB: c.383A>G] with a dominant β-thal phenotype in two generations of a Chinese family. Physicians should be alerted to this mechanism of β-thal considering its relative rarity.
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Affiliation(s)
- Huan-Qing Chen
- Prenatal Diagnosis Center, Yunfu Women and Children's Hospital, Yunfu, Guangdong, People's Republic of China
| | - Li-Sha Wu
- Prenatal Diagnosis Center, Yunfu Women and Children's Hospital, Yunfu, Guangdong, People's Republic of China
| | - Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdon, People's Republic of China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdon, People's Republic of China
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7
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Chen PJ, Hussmann JA, Yan J, Knipping F, Ravisankar P, Chen PF, Chen C, Nelson JW, Newby GA, Sahin M, Osborn MJ, Weissman JS, Adamson B, Liu DR. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 2021; 184:5635-5652.e29. [PMID: 34653350 PMCID: PMC8584034 DOI: 10.1016/j.cell.2021.09.018] [Citation(s) in RCA: 298] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/09/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022]
Abstract
While prime editing enables precise sequence changes in DNA, cellular determinants of prime editing remain poorly understood. Using pooled CRISPRi screens, we discovered that DNA mismatch repair (MMR) impedes prime editing and promotes undesired indel byproducts. We developed PE4 and PE5 prime editing systems in which transient expression of an engineered MMR-inhibiting protein enhances the efficiency of substitution, small insertion, and small deletion prime edits by an average 7.7-fold and 2.0-fold compared to PE2 and PE3 systems, respectively, while improving edit/indel ratios by 3.4-fold in MMR-proficient cell types. Strategic installation of silent mutations near the intended edit can enhance prime editing outcomes by evading MMR. Prime editor protein optimization resulted in a PEmax architecture that enhances editing efficacy by 2.8-fold on average in HeLa cells. These findings enrich our understanding of prime editing and establish prime editing systems that show substantial improvement across 191 edits in seven mammalian cell types.
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Affiliation(s)
- Peter J Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Friederike Knipping
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55108, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Pin-Fang Chen
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cidi Chen
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - James W Nelson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Mustafa Sahin
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55108, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
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8
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Rampul A, Nagel SE, Blumenthal R, Potgieter J, Pillay TS. Postmortem Hyperglycemic Dilemma. J Appl Lab Med 2021; 6:1360-1365. [PMID: 34468762 DOI: 10.1093/jalm/jfaa228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/12/2020] [Indexed: 11/14/2022]
Affiliation(s)
- Ashlin Rampul
- Department of Chemical Pathology and National Health Laboratory Service, Tshwane Academic Division, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Susanna E Nagel
- Department of Chemical Pathology and National Health Laboratory Service, Tshwane Academic Division, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Ryan Blumenthal
- Department of Forensic Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Johan Potgieter
- Department of Haematology and National Health Laboratory Service, Tshwane Academic Division, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Tahir S Pillay
- Department of Chemical Pathology and National Health Laboratory Service, Tshwane Academic Division, Faculty of Health Sciences, University of Pretoria, South Africa.,Division of Chemical Pathology, University of Cape Town, South Africa
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9
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Activation of γ-globin gene expression by GATA1 and NF-Y in hereditary persistence of fetal hemoglobin. Nat Genet 2021; 53:1177-1186. [PMID: 34341563 PMCID: PMC8610173 DOI: 10.1038/s41588-021-00904-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 06/25/2021] [Indexed: 11/30/2022]
Abstract
Hereditary persistence of fetal hemoglobin (HPFH) ameliorates β-hemoglobinopathies by inhibiting the developmental switch from γ-globin (HBG1/HBG2) to β-globin (HBB) gene expression. Some forms of HPFH are associated with γ-globin promoter variants that either disrupt binding motifs for transcriptional repressors or create new motifs for transcriptional activators. How these variants sustain γ-globin gene expression postnatally remains undefined. We mapped γ-globin promoter sequences functionally in erythroid cells harboring different HPFH variants. Those that disrupt a BCL11A repressor binding element induce γ-globin expression by facilitating the recruitment of transcription factors NF-Y to a nearby proximal CCAAT box and GATA1 to an upstream motif. The proximal CCAAT element becomes dispensable for HPFH variants that generate new binding motifs for activators NF-Y or KLF1, but GATA1 recruitment remains essential. Our findings define distinct mechanisms through which transcription factors and their cis-regulatory elements activate γ-globin expression in different forms of HPFH, some of which are being recreated by therapeutic genome editing.
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10
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High level of fetal-globin reactivation by designed transcriptional activator-like effector. Blood Adv 2021; 4:687-695. [PMID: 32084259 DOI: 10.1182/bloodadvances.2019000482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/27/2020] [Indexed: 12/15/2022] Open
Abstract
The fetal-to-adult hemoglobin switch has been a focus of a long-standing effort to potentially treat sickle cell disease and β thalassemia by induction of fetal hemoglobin. In a continuation of this effort, we designed specific transcriptional activator-like effectors (TALEs) to target both the Gγ and Aγ-globin promoters. We fused the TALEs to a LIM domain binding protein (Ldb1) dimerization domain, followed by a T2A green fluorescent protein (GFP) cassette, which were assembled into a lentiviral vector. To prevent deletions caused by the repeats of TALEs during the lentivirus packing process, we changed the TALE encoding DNA by codon optimization. Intriguingly, 5 of 14 TALEs showed forced reactivation of fetal-globin expression in human umbilical cord blood-derived erythroid progenitor (HUDEP-2) cells, with a significant increase in the γ-globin mRNA level by more than 70-fold. We also observed a more than 50% reduction of β-globin mRNA. High-performance liquid chromatography analysis revealed more than 30% fetal globin in TALE-induced cells compared with the control of 2%. Among several promoters studied, the β-globin gene promoter with the locus control region (LCR) enhancer showed the highest TALE expression during CD34 erythroid differentiation. At day 19 of differentiation, 2 TALEs increased fetal-globin expression more than 40-fold in the mRNA level and up to 70% of the total globin protein. These TALEs have potential for clinical translation.
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11
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Papizan JB, Porter SN, Sharma A, Pruett-Miller SM. Therapeutic gene editing strategies using CRISPR-Cas9 for the β-hemoglobinopathies. J Biomed Res 2021; 35:115-134. [PMID: 33349624 PMCID: PMC8038529 DOI: 10.7555/jbr.34.20200096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
With advancements in gene editing technologies, our ability to make precise and efficient modifications to the genome is increasing at a remarkable rate, paving the way for scientists and clinicians to uniquely treat a multitude of previously irremediable diseases. CRISPR-Cas9, short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9, is a gene editing platform with the ability to alter the nucleotide sequence of the genome in living cells. This technology is increasing the number and pace at which new gene editing treatments for genetic disorders are moving toward the clinic. The β-hemoglobinopathies are a group of monogenic diseases, which despite their high prevalence and chronic debilitating nature, continue to have few therapeutic options available. In this review, we will discuss our existing comprehension of the genetics and current state of treatment for β-hemoglobinopathies, consider potential genome editing therapeutic strategies, and provide an overview of the current state of clinical trials using CRISPR-Cas9 gene editing.
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Affiliation(s)
- James B Papizan
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shaina N Porter
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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12
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Venkatesan V, Srinivasan S, Babu P, Thangavel S. Manipulation of Developmental Gamma-Globin Gene Expression: an Approach for Healing Hemoglobinopathies. Mol Cell Biol 2020; 41:e00253-20. [PMID: 33077498 PMCID: PMC7849396 DOI: 10.1128/mcb.00253-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
β-Hemoglobinopathies are the most common monogenic disorders, and a century of research has provided us with a better understanding of the attributes of these diseases. Allogenic stem cell transplantation was the only potentially curative option available for these diseases until the discovery of gene therapy. The findings on the protective nature of fetal hemoglobin in sickle cell disease (SCD) and thalassemia patients carrying hereditary persistence of fetal hemoglobin (HPFH) mutations has given us the best evidence that the cure for β-hemoglobinopathies remains hidden in the hemoglobin locus. The detailed understanding of the developmental gene regulation of gamma-globin (γ-globin) and the emergence of gene manipulation strategies offer us the opportunity for developing a γ-globin gene-modified autologous stem cell transplantation therapy. In this review, we summarize different therapeutic strategies that reactivate fetal hemoglobin for the gene therapy of β-hemoglobinopathies.
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Affiliation(s)
- Vigneshwaran Venkatesan
- Centre for Stem Cell Research (CSCR), InStem Bengaluru, Christian Medical College, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Saranya Srinivasan
- Centre for Stem Cell Research (CSCR), InStem Bengaluru, Christian Medical College, Vellore, Tamil Nadu, India
| | - Prathibha Babu
- Centre for Stem Cell Research (CSCR), InStem Bengaluru, Christian Medical College, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (CSCR), InStem Bengaluru, Christian Medical College, Vellore, Tamil Nadu, India
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13
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Steinberg MH. Fetal Hemoglobin in Sickle Hemoglobinopathies: High HbF Genotypes and Phenotypes. J Clin Med 2020; 9:jcm9113782. [PMID: 33238542 PMCID: PMC7700170 DOI: 10.3390/jcm9113782] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/30/2022] Open
Abstract
Fetal hemoglobin (HbF) usually consists of 4 to 10% of total hemoglobin in adults of African descent with sickle cell anemia. Rarely, their HbF levels reach more than 30%. High HbF levels are sometimes a result of β-globin gene deletions or point mutations in the promoters of the HbF genes. Collectively, the phenotype caused by these mutations is called hereditary persistence of fetal hemoglobin, or HPFH. The pancellularity of HbF associated with these mutations inhibits sickle hemoglobin polymerization in most sickle erythrocytes so that these patients usually have inconsequential hemolysis and few, if any, vasoocclusive complications. Unusually high HbF can also be associated with variants of the major repressors of the HbF genes, BCL11A and MYB. Perhaps most often, we lack an explanation for very high HbF levels in sickle cell anemia.
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Affiliation(s)
- Martin H Steinberg
- Department of Medicine, Division of Hematology/Oncology, Center of Excellence for Sickle Cell Disease, Center for Regenerative Medicine, Genome Science Institute, Boston University School of Medicine and Boston Medical Center, 72 E. Concord St., Boston, MA 02118, USA
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14
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Mingoia M, Caria CA, Ye L, Asunis I, Marongiu MF, Manunza L, Sollaino MC, Wang J, Cabriolu A, Kurita R, Nakamura Y, Cucca F, Kan YW, Marini MG, Moi P. Induction of therapeutic levels of HbF in genome-edited primary β 0 39-thalassaemia haematopoietic stem and progenitor cells. Br J Haematol 2020; 192:395-404. [PMID: 33216968 DOI: 10.1111/bjh.17167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/06/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022]
Abstract
Hereditary persistence of fetal haemoglobin (HPFH) is the major modifier of the clinical severity of β-thalassaemia. The homozygous mutation c.-196 C>T in the Aγ-globin (HBG1) promoter, which causes Sardinian δβ0 -thalassaemia, is able to completely rescue the β-major thalassaemia phenotype caused by the β0 39-thalassaemia mutation, ensuring high levels of fetal haemoglobin synthesis during adulthood. Here, we describe a CRISPR/Cas9 genome-editing approach, combined with the non-homologous end joining (NHEJ) pathway repair, aimed at reproducing the effects of this naturally occurring HPFH mutation in both HBG promoters. After selecting the most efficient guide RNA in K562 cells, we edited the HBG promoters in human umbilical cord blood-derived erythroid progenitor 2 cells (HUDEP-2) and in haematopoietic stem and progenitor cells (HSPCs) from β0 -thalassaemia patients to assess the therapeutic potential of HbF induction. Our results indicate that small deletions targeting the -196-promoter region restore high levels of fetal haemoglobin (HbF) synthesis in all cell types tested. In pools of HSPCs derived from homozygous β0 39-thalassaemia patients, a 20% editing determined a parallel 20% increase of HbF compared to unedited pools. These results suggest that editing the region of HBG promoters around the -196 position has the potential to induce therapeutic levels of HbF in patients with most types of β-thalassaemia irrespective of the β-globin gene (HBB) mutations.
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Affiliation(s)
- Maura Mingoia
- Dipartimento di Scienze Mediche e Sanità Pubblica, Università degli Studi di Cagliari, Cagliari, 09124, Italy
| | - Cristian A Caria
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale Ricerche, Monserrato, 09042, Italy
| | - Lin Ye
- Department of Medicine and Institute for Human Genetics, University of California, San Francisco, CA, 93143, USA
| | - Isadora Asunis
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale Ricerche, Monserrato, 09042, Italy
| | - M Franca Marongiu
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale Ricerche, Monserrato, 09042, Italy
| | - Laura Manunza
- Dipartimento di Scienze Mediche e Sanità Pubblica, Università degli Studi di Cagliari, Cagliari, 09124, Italy
| | - M Carla Sollaino
- Ospedale Pediatrico "A. Cao" - A.O. "G. Brotzu", Cagliari, 09121, Italy
| | - Jiaming Wang
- Department of Medicine and Institute for Human Genetics, University of California, San Francisco, CA, 93143, USA
| | - Annalisa Cabriolu
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Centre, New York, NY, 10065, USA
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale Ricerche, Monserrato, 09042, Italy
| | - Yuet W Kan
- Department of Medicine and Institute for Human Genetics, University of California, San Francisco, CA, 93143, USA
| | - M Giuseppina Marini
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale Ricerche, Monserrato, 09042, Italy
| | - Paolo Moi
- Dipartimento di Scienze Mediche e Sanità Pubblica, Università degli Studi di Cagliari, Cagliari, 09124, Italy.,Ospedale Pediatrico "A. Cao" - A.O. "G. Brotzu", Cagliari, 09121, Italy
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15
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EF Bart's Disease with Coinheritance of G γ-XmnI and A γ-Globin Polymorphisms: A Case of Nontransfusion-Dependant Thalassemia. Case Rep Hematol 2020; 2020:8869335. [PMID: 33178467 PMCID: PMC7647742 DOI: 10.1155/2020/8869335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/17/2020] [Accepted: 10/21/2020] [Indexed: 11/17/2022] Open
Abstract
EF Bart's disease is a rare form of nontransfusion-dependant thalassemia (NTDT) due to the coinheritance of homozygous hemoglobin E (βE/βE) genotype with hemoglobin H disease. These individuals are routinely found to have thalassemia intermedia with moderate anemia, increased hemoglobin Bart's and hemoglobin F on electrophoresis. The contribution of hemoglobin F-inducing polymorphisms in this disease has not been described previously. Here, we describe the hematological profile in a young child with coinheritance of Gγ-XmnI and Aγ-globin gene polymorphisms in EF Bart's disease. Interestingly, in this rare form of NTDT, normal HbF and elevated HbA2 were noted.
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17
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Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA, Thuronyi BW, Wilson C, Koblan LW, Zeng J, Bauer DE, Doudna JA, Liu DR. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat Biotechnol 2020; 38:883-891. [PMID: 32433547 PMCID: PMC7357821 DOI: 10.1038/s41587-020-0453-z] [Citation(s) in RCA: 443] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/02/2020] [Accepted: 02/07/2020] [Indexed: 12/19/2022]
Abstract
Applications of adenine base editors (ABEs) have been constrained by the limited compatibility of the deoxyadenosine deaminase component with Cas homologs other than SpCas9. We evolved the deaminase component of ABE7.10 using phage-assisted non-continuous and continuous evolution (PANCE and PACE), which resulted in ABE8e. ABE8e contains eight additional mutations that increase activity (kapp) 590-fold compared with that of ABE7.10. ABE8e offers substantially improved editing efficiencies when paired with a variety of Cas9 or Cas12 homologs. ABE8e is more processive than ABE7.10, which could benefit screening, disruption of regulatory regions and multiplex base editing applications. A modest increase in Cas9-dependent and -independent DNA off-target editing, and in transcriptome-wide RNA off-target editing can be ameliorated by the introduction of an additional mutation in the TadA-8e domain. Finally, we show that ABE8e can efficiently install natural mutations that upregulate fetal hemoglobin expression in the BCL11A enhancer or in the the HBG promoter in human cells, targets that were poorly edited with ABE7.10. ABE8e augments the effectiveness and applicability of adenine base editing.
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Affiliation(s)
- Michelle F Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kevin T Zhao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Elliot Eton
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - B W Thuronyi
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry, Williams College, Williamstown, MA, USA
| | - Christopher Wilson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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18
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Jiang F, Zuo L, Li D, Li J, Tang X, Chen G, Zhou J, Lu H, Liao C. Molecular epidemiology and hematologic characterization of δβ-thalassemia and hereditary persistence of fetal hemoglobin in 125,661 families of greater Guangzhou area, the metropolis of southern China. BMC MEDICAL GENETICS 2020; 21:43. [PMID: 32111191 PMCID: PMC7049201 DOI: 10.1186/s12881-020-0981-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/19/2020] [Indexed: 11/10/2022]
Abstract
Background Individuals with δβ-thalassemia/HPFH and β-thalassemia usually present with intermedia or thalassemia major. No large-scale survey on HPFH/δβ-thalassemia in southern China has been reported to date. The purpose of this study was to examine the molecular epidemiology and hematologic characteristics of these disorders in Guangzhou, the largest city in Southern China, to offer advice for thalassemia screening programs and genetic counseling. Methods A total of 125,661 couples participated in pregestational thalassemia screening. 654 subjects with fetal hemoglobin (HbF) level ≥ 5% were selected for further investigation. Gap-PCR combined with Multiplex ligation dependent probe amplification (MLPA) was used to screen for β-globin gene cluster deletions. Gene sequencing for the promoter region of HBG1 /HBG2 gene was performed for all those subjects. Results A total of 654 individuals had hemoglobin (HbF) levels≥5, and 0.12% of the couples were found to be heterozygous for HPFH/δβ-thalassemia, including Chinese Gγ (Aγδβ)0-thal, Southeast Asia HPFH (SEA-HPFH), Taiwanese deletion and Hb Lepore–Boston–Washington. The highest prevalence was observed in the Huadu district and the lowest in the Nansha district. Three cases were identified as carrying β-globin gene cluster deletions, which had not been previously reported. Two at-risk couples (0.0015%) were required to receive prenatal diagnosis. We also found 55cases of nondeletional-HPFH (nd-HPFH), including 54 with Italian nd-HPFH and one with the Aγ-197C-T heterozygous state. It is difficult to discriminate between Chinese Gγ (Aγδβ)0-thal and Italian nd-HPFH carriers using hemoglobin (Hb) analysis. Conclusions This study is the first to describe the familial prevalence of HPFH/δβ-thalassemia and the high-risk rate in Greater Guangzhou Area, and the findings will support the implementation of thalassemia screening for three common deletions by gap-PCR. We also presented a systematic description of genotype-phenotype relationships which will be useful for genetic counseling and prenatal diagnostic services for β-thalassemia intermedia.
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Affiliation(s)
- Fan Jiang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China.,Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Liandong Zuo
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Xuewei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Guilan Chen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Jianying Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Hang Lu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China
| | - Can Liao
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, People's Republic of China. .,Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated with Guangzhou Medical University, Guangzhou, Guangdong Province, People's Republic of China.
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19
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Turner OC, Aeffner F, Bangari DS, High W, Knight B, Forest T, Cossic B, Himmel LE, Rudmann DG, Bawa B, Muthuswamy A, Aina OH, Edmondson EF, Saravanan C, Brown DL, Sing T, Sebastian MM. Society of Toxicologic Pathology Digital Pathology and Image Analysis Special Interest Group Article*: Opinion on the Application of Artificial Intelligence and Machine Learning to Digital Toxicologic Pathology. Toxicol Pathol 2019; 48:277-294. [DOI: 10.1177/0192623319881401] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Toxicologic pathology is transitioning from analog to digital methods. This transition seems inevitable due to a host of ongoing social and medical technological forces. Of these, artificial intelligence (AI) and in particular machine learning (ML) are globally disruptive, rapidly growing sectors of technology whose impact on the long-established field of histopathology is quickly being realized. The development of increasing numbers of algorithms, peering ever deeper into the histopathological space, has demonstrated to the scientific community that AI pathology platforms are now poised to truly impact the future of precision and personalized medicine. However, as with all great technological advances, there are implementation and adoption challenges. This review aims to define common and relevant AI and ML terminology, describe data generation and interpretation, outline current and potential future business cases, discuss validation and regulatory hurdles, and most importantly, propose how overcoming the challenges of this burgeoning technology may shape toxicologic pathology for years to come, enabling pathologists to contribute even more effectively to answering scientific questions and solving global health issues. [Box: see text]
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Affiliation(s)
- Oliver C. Turner
- Novartis, Novartis Institutes for Biomedical Research, Preclinical Safety, East Hanover, NJ, USA
| | - Famke Aeffner
- Amgen Inc, Research, Comparative Biology and Safety Sciences, San Francisco, CA, USA
| | | | - Wanda High
- High Preclinical Pathology Consulting, Rochester, NY, USA
| | - Brian Knight
- Boehringer Ingelheim Pharmaceuticals Incorporated, Nonclinical Drug Safety, Ridgefield, CT, USA
| | | | - Brieuc Cossic
- Roche, Pharmaceutical Research and Early Development (pRED), Roche Innovation Center, Basel, Switzerland
| | - Lauren E. Himmel
- Division of Animal Care, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | | | - Elijah F. Edmondson
- Pathology/Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, NIH, Frederick, MD, USA
| | - Chandrassegar Saravanan
- Novartis, Novartis Institutes for Biomedical Research, Preclinical Safety, Cambridge, MA, USA
| | | | - Tobias Sing
- Novartis, Novartis Institutes for Biomedical Research, NIBR Informatics, Basel, Switzerland
| | - Manu M. Sebastian
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
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20
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Zhang J, Yang Y, Li P, Yan Y, Lv T, Zhao T, Zeng X, Li D, Zhou X, Chen H, Su J, Yang T, He J, Zhu B. Analysis of deletional hereditary persistence of fetal hemoglobin/δβ-thalassemia and δ-globin gene mutations in Southerwestern China. Mol Genet Genomic Med 2019; 7:e706. [PMID: 31044540 PMCID: PMC6565566 DOI: 10.1002/mgg3.706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 03/31/2019] [Accepted: 04/01/2019] [Indexed: 01/07/2023] Open
Abstract
Background Deletional hereditary persistence of fetal hemoglobin (HPFH)/δβ‐thalassemia and δ‐thalassemia are rare inherited disorders which may complicate the diagnosis of β‐thalassemia. The aim of this study was to reveal the frequency of these two disorders in Southwestern China. Methods A total of 33,596 subjects were enrolled for deletional HPFH/δβ‐thalassemia, and positive individuals with high fetal hemoglobin (Hb F) level were diagnosed by multiplex ligation‐dependent probe amplification (MLPA). A total of 17,834 subjects were analyzed for mutations in the δ‐globin gene. Positive samples with low Hb A2 levels were confirmed by δ‐globin gene sequencing. Furthermore, the pathogenicity and construction of a selected δ‐globin mutation were analyzed. Results A total of 92 suspected cases with Hb F ≥5.0% were further characterized by MLPA. Eight different deletional HPFH/δβ‐thalassemia were observed at a frequency of 0.024%. In addition, 195 cases suspected to have a δ‐globin gene mutation (Hb A2 ≤2.0%) were characterized by molecular analysis. δ‐Globin gene mutation was found at a frequency of 0.49% in Yunnan. The pathogenicity and construction for a selected δ‐globin mutation was predicted. Conclusion Screening of these two disorders was analyzed in Southwestern China, which could define the molecular basis of these conditions in this population.
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Affiliation(s)
- Jie Zhang
- Department of Obstetrics and GynecologyThe First People’s Hospital of Yunnan ProvinceKunmingChina
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- Department of HematologyThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Yang Yang
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
| | - Peng Li
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
| | - Yuanlong Yan
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Tao Lv
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Tingting Zhao
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Xiaohong Zeng
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Dongmei Li
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Xiaoyan Zhou
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Hong Chen
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Jie Su
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Tonghua Yang
- Department of HematologyThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Jing He
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
| | - Baosheng Zhu
- Department of Obstetrics and GynecologyThe First People’s Hospital of Yunnan ProvinceKunmingChina
- Genetic Diagnosis Center, Yunnan Provincial Key Laboratory for Birth Defects and Genetic DiseasesThe First People’s Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
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21
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Roy K, Mahendru S, Kukreti R, Kukreti S. Unusual stability exhibited by (AT) XN 12(AT) Y motif associated with high fetal hemoglobin levels. J Biomol Struct Dyn 2019; 37:3848-3857. [PMID: 30295130 DOI: 10.1080/07391102.2018.1532320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Quasi-palindromic sequences (AT)XN12(AT)Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults arise due to pathological conditions such as sickle cell disease and β-thalassemia. However, elevated levels of HbF are also associated with a reducing morbidity and mortality in patients with β-thalassemia and thus ameliorate the severity of the disease. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation, and circular dichroism (CD) techniques, we demonstrated that it exhibits a hairpin-duplex equilibrium. Intramolecular species (hairpin) were observed in both low and high salt concentrations in gel assay studies displaying the unusual stability of intramolecular species even at the high counter-ion concentration. The unusual stability of hairpin secondary structures was also demonstrated by the monophasic nature of the melting profiles for the oligonucleotides which persisted at low as well as high salt and oligomer concentrations. Change in CD spectra as a function of oligomer concentration indicates that the bimolecular duplex formation is selectively favored over monomolecular hairpin formation at and above 9 µM oligomer concentration. Thus, we hypothesize that imperfect inverted repeat sequence (AT)XN12(AT)Y of HS2 of β-globin gene LCR forms the unusually stable hairpins which may result in the formation of a cruciform structure that may be recruited for binding by various nuclear proteins that could result in elevated HbF levels. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kapil Roy
- a Department of Chemistry , Nucleic Acids Research Lab, University of Delhi (North Campus) , Delhi , India
| | - Swati Mahendru
- a Department of Chemistry , Nucleic Acids Research Lab, University of Delhi (North Campus) , Delhi , India
| | - Ritushree Kukreti
- b Genomics and Molecular Medicine Unit , Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research , Delhi , India
| | - Shrikant Kukreti
- a Department of Chemistry , Nucleic Acids Research Lab, University of Delhi (North Campus) , Delhi , India
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22
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Mandal PK, Kartthik S. Autoimmune hemolytic anemia: an uncommon cause of elevated fetal hemoglobin. J Hematop 2019. [DOI: 10.1007/s12308-018-00339-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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23
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A natural regulatory mutation in the proximal promoter elevates fetal globin expression by creating a de novo GATA1 site. Blood 2019; 133:852-856. [PMID: 30617196 DOI: 10.1182/blood-2018-07-863951] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022] Open
Abstract
β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, result from mutations in the adult β-globin gene. Reactivating the developmentally silenced fetal γ-globin gene elevates fetal hemoglobin levels and ameliorates symptoms of β-hemoglobinopathies. The continued expression of fetal γ-globin into adulthood occurs naturally in a genetic condition termed hereditary persistence of fetal hemoglobin (HPFH). Point mutations in the fetal γ-globin proximal promoter can cause HPFH. The -113A>G HPFH mutation falls within the -115 cluster of HPFH mutations, a binding site for the fetal globin repressor BCL11A. We demonstrate that the -113A>G HPFH mutation, unlike other mutations in the cluster, does not disrupt BCL11A binding but rather creates a de novo binding site for the transcriptional activator GATA1. Introduction of the -113A>G HPFH mutation into erythroid cells using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system increases GATA1 binding and elevates fetal globin levels. These results reveal the mechanism by which the -113A>G HPFH mutation elevates fetal globin and demonstrate the sensitivity of the fetal globin promoter to point mutations that often disrupt repressor binding sites but here create a de novo site for an erythroid activator.
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Koblan LW, Doman JL, Wilson C, Levy JM, Tay T, Newby GA, Maianti JP, Raguram A, Liu DR. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotechnol 2018; 36:843-846. [PMID: 29813047 PMCID: PMC6126947 DOI: 10.1038/nbt.4172] [Citation(s) in RCA: 550] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 05/21/2018] [Indexed: 12/16/2022]
Abstract
Base editors enable targeted single-nucleotide conversions in genomic DNA. Here we show that expression levels are a bottleneck in base-editing efficiency. We optimize cytidine (BE4) and adenine (ABE7.10) base editors by modification of nuclear localization signals (NLS) and codon usage, and ancestral reconstruction of the deaminase component. The resulting BE4max, AncBE4max, and ABEmax editors correct pathogenic SNPs with substantially increased efficiency in a variety of mammalian cell types.
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Affiliation(s)
- Luke W. Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jordan L. Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Christopher Wilson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan M. Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Tristan Tay
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Greg A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Juan Pablo Maianti
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
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25
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Wienert B, Martyn GE, Funnell APW, Quinlan KGR, Crossley M. Wake-up Sleepy Gene: Reactivating Fetal Globin for β-Hemoglobinopathies. Trends Genet 2018; 34:927-940. [PMID: 30287096 DOI: 10.1016/j.tig.2018.09.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/23/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022]
Abstract
Disorders in hemoglobin (hemoglobinopathies) were the first monogenic diseases to be characterized and remain among the most common and best understood genetic conditions. Moreover, the study of the β-globin locus provides a textbook example of developmental gene regulation. The fetal γ-globin genes (HBG1/HBG2) are ordinarily silenced around birth, whereupon their expression is replaced by the adult β-globin genes (HBB primarily and HBD). Over 50 years ago it was recognized that mutations that cause lifelong persistence of fetal γ-globin expression ameliorate the debilitating effects of mutations in β-globin. Since then, research has focused on therapeutically reactivating the fetal γ-globin genes. Here, we summarize recent discoveries, focusing on the influence of genome editing technologies, including CRISPR-Cas9, and emerging gene therapy approaches.
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Affiliation(s)
- Beeke Wienert
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Present address: Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia; Present address: Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia.
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26
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Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction. Nat Biotechnol 2018. [PMID: 29813047 DOI: 10.1038/nbt.4172.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Base editors enable targeted single-nucleotide conversions in genomic DNA. Here we show that expression levels are a bottleneck in base-editing efficiency. We optimize cytidine (BE4) and adenine (ABE7.10) base editors by modification of nuclear localization signals (NLS) and codon usage, and ancestral reconstruction of the deaminase component. The resulting BE4max, AncBE4max, and ABEmax editors correct pathogenic SNPs with substantially increased efficiency in a variety of mammalian cell types.
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27
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Martyn GE, Wienert B, Yang L, Shah M, Norton LJ, Burdach J, Kurita R, Nakamura Y, Pearson RCM, Funnell APW, Quinlan KGR, Crossley M. Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding. Nat Genet 2018; 50:498-503. [PMID: 29610478 DOI: 10.1038/s41588-018-0085-0] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/02/2018] [Indexed: 01/26/2023]
Abstract
β-hemoglobinopathies such as sickle cell disease (SCD) and β-thalassemia result from mutations in the adult HBB (β-globin) gene. Reactivating the developmentally silenced fetal HBG1 and HBG2 (γ-globin) genes is a therapeutic goal for treating SCD and β-thalassemia 1 . Some forms of hereditary persistence of fetal hemoglobin (HPFH), a rare benign condition in which individuals express the γ-globin gene throughout adulthood, are caused by point mutations in the γ-globin gene promoter at regions residing ~115 and 200 bp upstream of the transcription start site. We found that the major fetal globin gene repressors BCL11A and ZBTB7A (also known as LRF) directly bound to the sites at -115 and -200 bp, respectively. Furthermore, introduction of naturally occurring HPFH-associated mutations into erythroid cells by CRISPR-Cas9 disrupted repressor binding and raised γ-globin gene expression. These findings clarify how these HPFH-associated mutations operate and demonstrate that BCL11A and ZBTB7A are major direct repressors of the fetal globin gene.
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Affiliation(s)
- Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Beeke Wienert
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Lu Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Manan Shah
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Laura J Norton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Jon Burdach
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Richard C M Pearson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Alister P W Funnell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW) Sydney, Sydney, New South Wales, Australia.
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28
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Hariharan P, Gorivale M, Colah R, Ghosh K, Nadkarni A. Does the Novel KLF1
Gene Mutation Lead to a Delay in Fetal Hemoglobin Switch? Ann Hum Genet 2017; 81:125-128. [DOI: 10.1111/ahg.12191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 02/28/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Priya Hariharan
- Department of Haematogenetics; National Institute of Immunohaematology (ICMR); Parel Mumbai India
| | - Manju Gorivale
- Department of Haematogenetics; National Institute of Immunohaematology (ICMR); Parel Mumbai India
| | - Roshan Colah
- Department of Haematogenetics; National Institute of Immunohaematology (ICMR); Parel Mumbai India
| | - Kanjaksha Ghosh
- Blood Bank; Surat Raktadan Kendra & Research Centre; Surat Gujarat India
| | - Anita Nadkarni
- Department of Haematogenetics; National Institute of Immunohaematology (ICMR); Parel Mumbai India
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29
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Martyn GE, Quinlan KGR, Crossley M. The regulation of human globin promoters by CCAAT box elements and the recruitment of NF-Y. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:525-536. [PMID: 27718361 DOI: 10.1016/j.bbagrm.2016.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 01/01/2023]
Abstract
CCAAT boxes are motifs found within the proximal promoter of many genes, including the human globin genes. The highly conserved nature of CCAAT box motifs within the promoter region of both α-like and β-like globin genes emphasises the functional importance of the CCAAT sequence in globin gene regulation. Mutations within the β-globin CCAAT box result in β-thalassaemia, while mutations within the distal γ-globin CCAAT box cause the Hereditary Persistence of Foetal Haemoglobin, a benign condition which results in continued γ-globin expression during adult life. Understanding the transcriptional regulation of the globin genes is of particular interest, as reactivating the foetal γ-globin gene alleviates the symptoms of β-thalassaemia and sickle cell anaemia. NF-Y is considered to be the primary activating transcription factor which binds to globin CCAAT box motifs. Here we review recruitment of NF-Y to globin CCAAT boxes and the role NF-Y plays in regulating globin gene expression. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Gabriella E Martyn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Kate G R Quinlan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia.
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30
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Zang T, Broszczak DA, Cuttle L, Broadbent JA, Tanzer C, Parker TJ. The blister fluid proteome of paediatric burns. J Proteomics 2016; 146:122-32. [PMID: 27345418 DOI: 10.1016/j.jprot.2016.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/28/2016] [Accepted: 06/17/2016] [Indexed: 01/03/2023]
Abstract
UNLABELLED Burn injury is highly traumatic for paediatric patients, with the severity of the burn often dictating the extent of scar formation. The diagnosis of burn wound severity is largely determined by the attending clinician's experience. Thus, a greater understanding of the biochemistry at burn wound site environment and the biology of burns of different severities at an earlier stage may reduce the reliance on subjective diagnoses. In this study, blister fluid was collected from superficial thickness, deep-partial thickness, and full-thickness paediatric burn wounds. Samples were combined together based on burn depth classification and then subjected to four different fractionation methods followed by trypsin digestion. Peptides were analysed by liquid chromatography tandem mass spectrometry in order to measure the proteome of each fraction. In total, 811 individual proteins were identified, including 107, 84, and 146 proteins unique to superficial, deep-partial thickness and full-thickness burn wounds, respectively. The differences in the protein inventory and the associated gene ontologies represented within each burn depth category demonstrated that there are subtle, yet significant, variations in the biochemistry of burn wounds according to severity. Importantly, this study has produced the most comprehensive catalogue of proteins from the paediatric burn wound microenvironment to date. SIGNIFICANCE To our knowledge, this study has been the first to comprehensively measure the paediatric burn blister fluid proteome and has provided insight into the proteomic response to burn injury. The study contributes to the knowledge of blister fluid biochemistry of burn injury and provides clinically relevant knowledge through the qualitative evaluation of biochemical differences between burns of different depths. A better understanding of the burn wound environment will ultimately assist with more accurate clinical decision making and improved wound healing and scar reduction procedures.
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Affiliation(s)
- Tuo Zang
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Wound Management Innovation Co-operative Research Centre, Brisbane, Australia
| | - Daniel A Broszczak
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Wound Management Innovation Co-operative Research Centre, Brisbane, Australia
| | - Leila Cuttle
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Centre for Children's Burns and Trauma Research, Queensland University of Technology, Institute of Health and Biomedical Innovation at the Centre for Children's Health Research, South Brisbane, Australia
| | - James A Broadbent
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Wound Management Innovation Co-operative Research Centre, Brisbane, Australia
| | - Catherine Tanzer
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia; Wound Management Innovation Co-operative Research Centre, Brisbane, Australia; Centre for Children's Burns and Trauma Research, Queensland University of Technology, Institute of Health and Biomedical Innovation at the Centre for Children's Health Research, South Brisbane, Australia
| | - Tony J Parker
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
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31
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Eridani S, Avemaria F, Mosca A. Reactivation of Fetal Hemoglobin in Thalassemia and Sickle Cell Disease. THALASSEMIA REPORTS 2014. [DOI: 10.4081/thal.2014.2196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Considerable attention has been recently devoted to mechanisms involved in the perinatal hemoglobin switch, as it was long ago established that the survival of fetal hemoglobin (HbF) production in significant amount can reduce the severity of the clinical course in severe disorders like β-thalassemia and sickle cell disease (SCD). For instance, when β-thalassemia is associated with hereditary persistence of fetal hemoglobin (HPFH) the disease takes a mild course, labeled as thalassemia intermedia. The same clinical amelioration occurs for the association between HPFH and SCD. As for the mechanism of this effect, some information has been obtained from the study of natural mutations at the human β-globin locus in patients with increased HbF, like the Corfu thalassemia mutations. Important evidence came from the discovery that drugs capable of improving the clinical picture of SCD, like decitabine ad hydroxycarbamide, are acting through the reactivation, to some extent, of HbF synthesis. The study of the mechanism of action of these compounds was followed by the identification of some genetic determinants, which promote this event. In particular, among a few genetic factors involved in this process, the most relevant appears the BCL11A gene, which is now credited to be able to silence γ-globin genes in the perinatal period by interaction with several erythroid-specific transcription factors and is actually considered as a barrier to HbF reactivation by known HbF inducing agents. Epigenetics is also a player in the process, mainly through DNA demethylation. This is certified by the recent demonstration that hypomethylating agents such as 5-azacytidine and decitabine, the first compounds used for HbF induction by pharmacology, act as irreversible inhibitors of demethyltransferase enzymes. Great interest has also been raised by the finding that several micro-RNAs, which act as negative regulators of gene expression, have been implicated in the progression of globin gene expression and, particularly, in the reactivation of γ-globin gene expression associated with increased HbF synthesis. Probably, this reactivation is achieved by post-transcriptional inhibition of BCL11A expression. Finally, attention is presently focused on a recently discovered BCL11A enhancer, essential for erythroid expression of BCL11A, which might become a therapeutic target for genome engineering in the β-hemoglobinopathies as its disruption affects only the erythropoietic lineage, without hurting other cell or tissue compartments.
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Najjari A, Asouri M, Gouhari LH, Niaki HA, Nejad ASM, Eslami SM, Abolghasemi H, Ataee R, Ebrahimi AA, Moshaei MR, Ahmadi AA. α:Non-α and Gγ:Aγ globin chain ratios in thalassemia intermedia patients treated with hydroxyurea. Asian Pac J Trop Biomed 2014; 4:S177-85. [PMID: 25183077 DOI: 10.12980/apjtb.4.2014c1161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/23/2014] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES To elucidate the possible ways by which hydroxyurea molecules affect globin chain (α or β-like) synthesis. METHODS A total of 23 thalassemia intermedia patients (13 male and 10 female) aged between 5 and 26 years were treated for five months with 15 mg/(kg·day) of hydroxyurea. Hemoglobins electrophoresis and globin chain electrophoresis was performed on each sample at different time points before and during the treatment. RESULTS Fetal hemoglobin increased significantly in most patients and average episodes of transfusion decreased. Both Gγ and Aγ-globin chains increased significantly and α-globin:Nonα-globin chain as well as Gγ-globin:Aγ globin chains ratios decreased. CONCLUSIONS Improvement in α:non-α ratio and consequent decrease of free α-globin chain might be the cause of beneficial effects of hydroxyurea therapy. Two patients who felt better didn't show significant increase in their fetal hemoglobin level, and this is in contradiction with the hypothesis claiming that the HbF level increase is the cause of such therapeutic effect. In spite of the unclear mechanism of action of this drug, hydroxyurea therapy had noticeable impacts on thalassemia intermedia and also sickle cell disease and even patients suffering from thalassemia major.
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Affiliation(s)
- Abbas Najjari
- Centre for collective, reflection & implementation of ideas, Undersecretary for Research and Technology, Ministry of Health and Medical Education, Tehran, Iran
| | - Mohsen Asouri
- North Research Center, Pasteur Institute of Iran, Amol, Iran ; 17th Shahrivar Hospital, Mazandaran University of Medical Sciences, Amol, Iran
| | - Ladan Hosseini Gouhari
- Iran University of Medical Sciences, School of Paramedicine, Cellular and Molecular Research Center, Tehran, Iran
| | - Haleh Akhavan Niaki
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran
| | | | | | | | - Ramin Ataee
- Pharmaceutical Sciences Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Masoumeh Rezaei Moshaei
- Department of Plant Breeding and Biotechnology, Agricultural sciences & Natural Resources University of Sari, Iran
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