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Walsh C, Jin S. Induced Pluripotent Stem Cells and CRISPR-Cas9 Innovations for Treating Alpha-1 Antitrypsin Deficiency and Glycogen Storage Diseases. Cells 2024; 13:1052. [PMID: 38920680 PMCID: PMC11201389 DOI: 10.3390/cells13121052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Human induced pluripotent stem cell (iPSC) and CRISPR-Cas9 gene-editing technologies have become powerful tools in disease modeling and treatment. By harnessing recent biotechnological advancements, this review aims to equip researchers and clinicians with a comprehensive and updated understanding of the evolving treatment landscape for metabolic and genetic disorders, highlighting how iPSCs provide a unique platform for detailed pathological modeling and pharmacological testing, driving forward precision medicine and drug discovery. Concurrently, CRISPR-Cas9 offers unprecedented precision in gene correction, presenting potential curative therapies that move beyond symptomatic treatment. Therefore, this review examines the transformative role of iPSC technology and CRISPR-Cas9 gene editing in addressing metabolic and genetic disorders such as alpha-1 antitrypsin deficiency (A1AD) and glycogen storage disease (GSD), which significantly impact liver and pulmonary health and pose substantial challenges in clinical management. In addition, this review discusses significant achievements alongside persistent challenges such as technical limitations, ethical concerns, and regulatory hurdles. Future directions, including innovations in gene-editing accuracy and therapeutic delivery systems, are emphasized for next-generation therapies that leverage the full potential of iPSC and CRISPR-Cas9 technologies.
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Affiliation(s)
| | - Sha Jin
- Department of Biomedical Engineering, Thomas J. Watson College of Engineering and Applied Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
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2
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Afonso MB, Marques V, van Mil SW, Rodrigues CM. Human liver organoids: From generation to applications. Hepatology 2024; 79:1432-1451. [PMID: 36815360 PMCID: PMC11095893 DOI: 10.1097/hep.0000000000000343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 02/24/2023]
Abstract
In the last decade, research into human hepatology has been revolutionized by the development of mini human livers in a dish. These liver organoids are formed by self-organizing stem cells and resemble their native counterparts in cellular content, multicellular architecture, and functional features. Liver organoids can be derived from the liver tissue or pluripotent stem cells generated from a skin biopsy, blood cells, or renal epithelial cells present in urine. With the development of liver organoids, a large part of previous hurdles in modeling the human liver is likely to be solved, enabling possibilities to better model liver disease, improve (personalized) drug testing, and advance bioengineering options. In this review, we address strategies to generate and use organoids in human liver disease modeling, followed by a discussion of their potential application in drug development and therapeutics, as well as their strengths and limitations.
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Affiliation(s)
- Marta B. Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Vanda Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Saskia W.C. van Mil
- Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, The Netherlands
| | - Cecilia M.P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
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3
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Gruntman AM, Xue W, Flotte TR. Approaches to Therapeutic Gene Editing in Alpha-1 Antitrypsin Deficiency. Methods Mol Biol 2024; 2750:11-17. [PMID: 38108963 DOI: 10.1007/978-1-0716-3605-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Five distinct gene therapy approaches have been developed for treating AATD. These approaches include knockout of the mutant (PiZ) allele by introduction of double-strand breaks (DSBs) and subsequent creation of insertions and deletions (indels) by DSB repair, homology-directed repair (HDR) targeted to the mutation site, base editing, prime editing, and alternatively targeted knock-in techniques. Each approach will be discussed and a brief summary of a standard CRISPR-Cas9 targeting method will be presented.
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Affiliation(s)
- Alisha M Gruntman
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Terence R Flotte
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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4
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Shreya S, Grosset CF, Jain BP. Unfolded Protein Response Signaling in Liver Disorders: A 2023 Updated Review. Int J Mol Sci 2023; 24:14066. [PMID: 37762367 PMCID: PMC10531763 DOI: 10.3390/ijms241814066] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Endoplasmic reticulum (ER) is the site for synthesis and folding of secreted and transmembrane proteins. Disturbance in the functioning of ER leads to the accumulation of unfolded and misfolded proteins, which finally activate the unfolded protein response (UPR) signaling. The three branches of UPR-IRE1 (Inositol requiring enzyme 1), PERK (Protein kinase RNA-activated (PKR)-like ER kinase), and ATF6 (Activating transcription factor 6)-modulate the gene expression pattern through increased expression of chaperones and restore ER homeostasis by enhancing ER protein folding capacity. The liver is a central organ which performs a variety of functions which help in maintaining the overall well-being of our body. The liver plays many roles in cellular physiology, blood homeostasis, and detoxification, and is the main site at which protein synthesis occurs. Disturbance in ER homeostasis is triggered by calcium level imbalance, change in redox status, viral infection, and so on. ER dysfunction and subsequent UPR signaling participate in various hepatic disorders like metabolic (dysfunction) associated fatty liver disease, liver cancer, viral hepatitis, and cholestasis. The exact role of ER stress and UPR signaling in various liver diseases is not fully understood and needs further investigation. Targeting UPR signaling with drugs is the subject of intensive research for therapeutic use in liver diseases. The present review summarizes the role of UPR signaling in liver disorders and describes why UPR regulators are promising therapeutic targets.
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Affiliation(s)
- Smriti Shreya
- Gene Expression and Signaling Lab, Department of Zoology, Mahatma Gandhi Central University, Motihari 845401, Bihar, India;
| | - Christophe F. Grosset
- MIRCADE Team, U1312, Bordeaux Institute in Oncology, BRIC, Université de Bordeaux, 146 Rue Léo Saignat, F-33000 Bordeaux, France
| | - Buddhi Prakash Jain
- Gene Expression and Signaling Lab, Department of Zoology, Mahatma Gandhi Central University, Motihari 845401, Bihar, India;
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5
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Adlat S, Vázquez Salgado AM, Lee M, Yin D, Wangensteen KJ. Emerging and potential use of CRISPR in human liver disease. Hepatology 2023:01515467-990000000-00538. [PMID: 37607734 PMCID: PMC10881897 DOI: 10.1097/hep.0000000000000578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
CRISPR is a gene editing tool adapted from naturally occurring defense systems from bacteria. It is a technology that is revolutionizing the interrogation of gene functions in driving liver disease, especially through genetic screens and by facilitating animal knockout and knockin models. It is being used in models of liver disease to identify which genes are critical for liver pathology, especially in genetic liver disease, hepatitis, and in cancer initiation and progression. It holds tremendous promise in treating human diseases directly by editing DNA. It could disable gene function in the case of expression of a maladaptive protein, such as blocking transthyretin as a therapy for amyloidosis, or to correct gene defects, such as restoring the normal functions of liver enzymes fumarylacetoacetate hydrolase or alpha-1 antitrypsin. It is also being studied for treatment of hepatitis B infection. CRISPR is an exciting, evolving technology that is facilitating gene characterization and discovery in liver disease and holds the potential to treat liver diseases safely and permanently.
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Affiliation(s)
- Salah Adlat
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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6
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Kaserman JE, Werder RB, Wang F, Matte T, Higgins MI, Dodge M, Lindstrom-Vautrin J, Bawa P, Hinds A, Bullitt E, Caballero IS, Shi X, Gerszten RE, Brunetti-Pierri N, Liesa M, Villacorta-Martin C, Hollenberg AN, Kotton DN, Wilson AA. Human iPSC-hepatocyte modeling of alpha-1 antitrypsin heterozygosity reveals metabolic dysregulation and cellular heterogeneity. Cell Rep 2022; 41:111775. [PMID: 36476855 PMCID: PMC9780780 DOI: 10.1016/j.celrep.2022.111775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/28/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Individuals homozygous for the "Z" mutation in alpha-1 antitrypsin deficiency are known to be at increased risk for liver disease. It has also become clear that some degree of risk is similarly conferred by the heterozygous state. A lack of model systems that recapitulate heterozygosity in human hepatocytes has limited the ability to study the impact of a single Z alpha-1 antitrypsin (ZAAT) allele on hepatocyte biology. Here, we describe the derivation of syngeneic induced pluripotent stem cells (iPSCs) engineered to determine the effects of ZAAT heterozygosity in iPSC-hepatocytes (iHeps). We find that heterozygous MZ iHeps exhibit an intermediate disease phenotype and share with ZZ iHeps alterations in AAT protein processing and downstream perturbations including altered endoplasmic reticulum (ER) and mitochondrial morphology, reduced mitochondrial respiration, and branch-specific activation of the unfolded protein response in cell subpopulations. Our model of MZ heterozygosity thus provides evidence that a single Z allele is sufficient to disrupt hepatocyte homeostatic function.
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Affiliation(s)
- Joseph E. Kaserman
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Rhiannon B. Werder
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Taylor Matte
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Michelle I. Higgins
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Mark Dodge
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Jonathan Lindstrom-Vautrin
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Anne Hinds
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University, Boston, MA 02118, USA
| | - Ignacio S. Caballero
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Hospital, Boston, MA 02118, USA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Hospital, Boston, MA 02118, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Naples, Italy,Department of Translational Medicine, Federico II University, 80131 Naples, Italy
| | - Marc Liesa
- Departments of Medicine, Endocrinology, and Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA,Institut de Biologia Molecular de Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Anthony N. Hollenberg
- Joan and Sanford I. Weill Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrew A. Wilson
- Center for Regenerative Medicine (CReM) of Boston University and Boston Medical Center, Boston, MA 02118, USA,The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA,Lead contact,Correspondence:
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7
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Novel Gene-Correction-Based Therapeutic Modalities for Monogenic Liver Disorders. Bioengineering (Basel) 2022; 9:bioengineering9080392. [PMID: 36004917 PMCID: PMC9404740 DOI: 10.3390/bioengineering9080392] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
The majority of monogenic liver diseases are autosomal recessive disorders, with few being sex-related or co-dominant. Although orthotopic liver transplantation (LT) is currently the sole therapeutic option for end-stage patients, such an invasive surgical approach is severely restricted by the lack of donors and post-transplant complications, mainly associated with life-long immunosuppressive regimens. Therefore, the last decade has witnessed efforts for innovative cellular or gene-based therapeutic strategies. Gene therapy is a promising approach for treatment of many hereditary disorders, such as monogenic inborn errors. The liver is an organ characterized by unique features, making it an attractive target for in vivo and ex vivo gene transfer. The current genetic approaches for hereditary liver diseases are mediated by viral or non-viral vectors, with promising results generated by gene-editing tools, such as CRISPR-Cas9 technology. Despite massive progress in experimental gene-correction technologies, limitations in validated approaches for monogenic liver disorders have encouraged researchers to refine promising gene therapy protocols. Herein, we highlighted the most common monogenetic liver disorders, followed by proposed genetic engineering approaches, offered as promising therapeutic modalities.
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Packer MS, Chowdhary V, Lung G, Cheng LI, Aratyn-Schaus Y, Leboeuf D, Smith S, Shah A, Chen D, Zieger M, Cafferty BJ, Yan B, Ciaramella G, Gregoire FM, Mueller C. Evaluation of cytosine base editing and adenine base editing as a potential treatment for alpha-1 antitrypsin deficiency. Mol Ther 2022; 30:1396-1406. [PMID: 35121111 PMCID: PMC9077367 DOI: 10.1016/j.ymthe.2022.01.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/06/2021] [Accepted: 01/28/2022] [Indexed: 11/16/2022] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is a rare autosomal codominant disease caused by mutations within the SERPINA1 gene. The most prevalent variant in patients is PiZ SERPINA1, containing a single G > A transition mutation. PiZ alpha-1 antitrypsin (AAT) is prone to misfolding, leading to the accumulation of toxic aggregates within hepatocytes. In addition, the abnormally low level of AAT secreted into circulation provides insufficient inhibition of neutrophil elastase within the lungs, eventually causing emphysema. Cytosine and adenine base editors enable the programmable conversion of C⋅G to T⋅A and A⋅T to G⋅C base pairs, respectively. In this study, two different base editing approaches were developed: use of a cytosine base editor to install a compensatory mutation (p.Met374Ile) and use of an adenine base editor to mediate the correction of the pathogenic PiZ mutation. After treatment with lipid nanoparticles formulated with base editing reagents, PiZ-transgenic mice exhibited durable editing of SERPINA1 in the liver, increased serum AAT, and improved liver histology. These results indicate that base editing has the potential to address both lung and liver disease in AATD.
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Affiliation(s)
| | - Vivek Chowdhary
- Gene Therapy Department, UMass Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Genesis Lung
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Lo-I Cheng
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | | | | | - Sarah Smith
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Aalok Shah
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Delai Chen
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | - Marina Zieger
- Gene Therapy Department, UMass Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | | | - Bo Yan
- Beam Therapeutics, 238 Main Street, Cambridge, MA 02142, USA
| | | | | | - Christian Mueller
- Gene Therapy Department, UMass Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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9
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Endogenous ADAR-mediated RNA editing in non-human primates using stereopure chemically modified oligonucleotides. Nat Biotechnol 2022; 40:1093-1102. [DOI: 10.1038/s41587-022-01225-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/17/2022] [Indexed: 12/18/2022]
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10
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Graffmann N, Scherer B, Adjaye J. In vitro differentiation of pluripotent stem cells into hepatocyte like cells - basic principles and current progress. Stem Cell Res 2022; 61:102763. [DOI: 10.1016/j.scr.2022.102763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 12/11/2022] Open
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11
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Ghosh AJ, Hobbs BD. Recent advancements in understanding the genetic involvement of alpha-1 antitrypsin deficiency associated lung disease: a look at future precision medicine approaches. Expert Rev Respir Med 2022; 16:173-182. [PMID: 35025710 PMCID: PMC8983484 DOI: 10.1080/17476348.2022.2027755] [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: 02/03/2023]
Abstract
INTRODUCTION Alpha-1 antitrypsin deficiency occurs in individuals with deleterious genetic mutations on both chromosomes (maternal and paternal) in SERPINA1, the gene encoding the alpha-1 antitrypsin protein. There has been substantial progress in understanding the genetic variation that underlies the heterogeneous penetrance of lung disease in alpha-1 antitrypsin deficiency. AREAS COVERED This review will cover SERPINA1 gene structure and genetic variation, population genetics, genome-wide genetic modifiers of lung disease, alternative mechanisms of disease, and emerging therapeutics - including gene and cell therapy - related to alpha-1 antitrypsin deficiency-associated lung disease. EXPERT OPINION There remains ample opportunity to employ precision medicine in the diagnosis, prognosis, and therapy of alpha-1 antitrypsin deficiency-associated lung disease. In particular, a genome-wide association study and subsequent polygenic risk score is an important first step in identifying genome-wide genetic modifiers contributing to the variability of lung disease in severe alpha-1 antitrypsin deficiency.
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Affiliation(s)
- Auyon J. Ghosh
- Assistant Professor of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, SUNY Upstate Medical University, 750 E. Adams St, Syracuse, NY, 13210
| | - Brian D. Hobbs
- Assistant Professor of Medicine, Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Boston, MA, 02115,Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital,Harvard Medical School
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