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Culberson EJ, Shields KC, Glynn RA, Allyn BM, Hayer KE, Bassing CH. The Cyclin D3 Protein Enforces Monogenic TCRβ Expression by Mediating TCRβ Protein-Signaled Feedback Inhibition of Vβ Recombination. J Immunol 2024; 212:534-540. [PMID: 38117277 PMCID: PMC10872516 DOI: 10.4049/jimmunol.2300623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
In jawed vertebrates, adaptive immunity depends on the process of V(D)J recombination creating vast numbers of T and B lymphocytes that each expresses unique Ag receptors of uniform specificity. The asynchronous initiation of V-to-(D)J rearrangement between alleles and the resulting protein from one allele signaling feedback inhibition of V recombination on the other allele ensures homogeneous receptor specificity of individual cells. Upon productive Vβ-to-DβJβ rearrangements in noncycling double-negative thymocytes, TCRβ protein signals induction of the cyclin D3 protein to accelerate cell cycle entry, thereby driving proliferative expansion of developing αβ T cells. Through undetermined mechanisms, the inactivation of cyclin D3 in mice causes an increased frequency of αβ T cells that express TCRβ proteins from both alleles, producing lymphocytes of heterogeneous specificities. To determine how cyclin D3 enforces monogenic TCRβ expression, we used our mouse lines with enhanced rearrangement of specific Vβ segments due to replacement of their poor-quality recombination signal sequence (RSS) DNA elements with a better RSS. We show that cyclin D3 inactivation in these mice elevates the frequencies of αβ T cells that display proteins from RSS-augmented Vβ segments on both alleles. By assaying mature αβ T cells, we find that cyclin D3 deficiency increases the levels of Vβ rearrangements that occur within developing thymocytes. Our data demonstrate that a component of the cell cycle machinery mediates TCRβ protein-signaled feedback inhibition in thymocytes to achieve monogenic TCRβ expression and resulting uniform specificity of individual αβ T cells.
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Affiliation(s)
- Erica J. Culberson
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Kymberle C. Shields
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Rebecca A. Glynn
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Brittney M. Allyn
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Katharina E. Hayer
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA 19104
| | - Craig H. Bassing
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Allyn BM, Hayer KE, Oyeniran C, Nganga V, Lee K, Mishra B, Sacan A, Oltz EM, Bassing CH. Locus folding mechanisms determine modes of antigen receptor gene assembly. J Exp Med 2024; 221:e20230985. [PMID: 38189780 PMCID: PMC10772921 DOI: 10.1084/jem.20230985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
The dynamic folding of genomes regulates numerous biological processes, including antigen receptor (AgR) gene assembly. We show that, unlike other AgR loci, homotypic chromatin interactions and bidirectional chromosome looping both contribute to structuring Tcrb for efficient long-range V(D)J recombination. Inactivation of the CTCF binding element (CBE) or promoter at the most 5'Vβ segment (Trbv1) impaired loop extrusion originating locally and extending to DβJβ CBEs at the opposite end of Tcrb. Promoter or CBE mutation nearly eliminated Trbv1 contacts and decreased RAG endonuclease-mediated Trbv1 recombination. Importantly, Trbv1 rearrangement can proceed independent of substrate orientation, ruling out scanning by DβJβ-bound RAG as the sole mechanism of Vβ recombination, distinguishing it from Igh. Our data indicate that CBE-dependent generation of loops cooperates with promoter-mediated activation of chromatin to juxtapose Vβ and DβJβ segments for recombination through diffusion-based synapsis. Thus, the mechanisms that fold a genomic region can influence molecular processes occurring in that space, which may include recombination, repair, and transcriptional programming.
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Affiliation(s)
- Brittney M. Allyn
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E. Hayer
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Perelman School of Medicine, Philadelphia, PA, USA
| | - Clement Oyeniran
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Vincent Nganga
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Kyutae Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bikash Mishra
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Ahmet Sacan
- Biomedical Engineering Doctoral Degree Program, School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eugene M. Oltz
- Department of Microbial Infection and Immunity, Ohio State College of Medicine, Ohio State University, Columbus, OH, USA
| | - Craig H. Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Danan CH, Naughton KE, Hayer KE, Vellappan S, McMillan EA, Zhou Y, Matsuda R, Nettleford SK, Katada K, Parham LR, Ma X, Chowdhury A, Wilkins BJ, Shah P, Weitzman MD, Hamilton KE. Intestinal transit-amplifying cells require METTL3 for growth factor signaling and cell survival. JCI Insight 2023; 8:e171657. [PMID: 37883185 PMCID: PMC10795831 DOI: 10.1172/jci.insight.171657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023] Open
Abstract
Intestinal epithelial transit-amplifying cells are essential stem progenitors required for intestinal homeostasis, but their rapid proliferation renders them vulnerable to DNA damage from radiation and chemotherapy. Despite these cells' critical roles in intestinal homeostasis and disease, few studies have described genes that are essential to transit-amplifying cell function. We report that RNA methyltransferase-like 3 (METTL3) is required for survival of transit-amplifying cells in the murine small intestine. Transit-amplifying cell death after METTL3 deletion was associated with crypt and villus atrophy, loss of absorptive enterocytes, and uniform wasting and death in METTL3-depleted mice. Sequencing of polysome-bound and methylated RNAs in enteroids and in vivo demonstrated decreased translation of hundreds of methylated transcripts after METTL3 deletion, particularly transcripts involved in growth factor signal transduction such as Kras. Further investigation verified a relationship between METTL3 and Kras methylation and protein levels in vivo. Our study identifies METTL3 as an essential factor supporting the homeostasis of small intestinal tissue via direct maintenance of transit-amplifying cell survival. We highlight the crucial role of RNA modifications in regulating growth factor signaling in the intestine with important implications for both homeostatic tissue renewal and epithelial regeneration.
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Affiliation(s)
- Charles H. Danan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Medical Scientist Training Program, Perelman School of Medicine; and
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kaitlyn E. Naughton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sangeevan Vellappan
- Waksman Institute of Microbiology and
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
| | - Emily A. McMillan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rina Matsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathobiology, School of Veterinary Medicine, and
| | - Shaneice K. Nettleford
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louis R. Parham
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Afrah Chowdhury
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
- Human Genetics Institute of New Jersey, Piscataway, New Jersey, USA
| | - Matthew D. Weitzman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Ang Z, Paruzzo L, Hayer KE, Schmidt C, Torres Diz M, Xu F, Zankharia U, Zhang Y, Soldan S, Zheng S, Falkenstein CD, Loftus JP, Yang SY, Asnani M, King Sainos P, Pillai V, Chong E, Li MM, Tasian SK, Barash Y, Lieberman PM, Ruella M, Schuster SJ, Thomas-Tikhonenko A. Alternative splicing of its 5'-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies. Blood 2023; 142:1724-1739. [PMID: 37683180 PMCID: PMC10667349 DOI: 10.1182/blood.2023020400] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/04/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Aberrant skipping of coding exons in CD19 and CD22 compromises the response to immunotherapy in B-cell malignancies. Here, we showed that the MS4A1 gene encoding human CD20 also produces several messenger RNA (mRNA) isoforms with distinct 5' untranslated regions. Four variants (V1-4) were detected using RNA sequencing (RNA-seq) at distinct stages of normal B-cell differentiation and B-lymphoid malignancies, with V1 and V3 being the most abundant. During B-cell activation and Epstein-Barr virus infection, redirection of splicing from V1 to V3 coincided with increased CD20 positivity. Similarly, in diffuse large B-cell lymphoma, only V3, but not V1, correlated with CD20 protein levels, suggesting that V1 might be translation-deficient. Indeed, the longer V1 isoform contained upstream open reading frames and a stem-loop structure, which cooperatively inhibited polysome recruitment. By modulating CD20 isoforms with splice-switching morpholino oligomers, we enhanced CD20 expression and anti-CD20 antibody rituximab-mediated cytotoxicity in a panel of B-cell lines. Furthermore, reconstitution of CD20-knockout cells with V3 mRNA led to the recovery of CD20 positivity, whereas V1-reconstituted cells had undetectable levels of CD20 protein. Surprisingly, in vitro CD20-directed chimeric antigen receptor T cells were able to kill both V3- and V1-expressing cells, but the bispecific T-cell engager mosunetuzumab was only effective against V3-expressing cells. To determine whether CD20 splicing is involved in immunotherapy resistance, we performed RNA-seq on 4 postmosunetuzumab follicular lymphoma relapses and discovered that in 2 of them, the downregulation of CD20 was accompanied by a V3-to-V1 shift. Thus, splicing-mediated mechanisms of epitope loss extend to CD20-directed immunotherapies.
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Affiliation(s)
- Zhiwei Ang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Luca Paruzzo
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Carolin Schmidt
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Manuel Torres Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Feng Xu
- Division of Genomic Diagnostic, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Urvi Zankharia
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Yunlin Zhang
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha Soldan
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Sisi Zheng
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Joseph P. Loftus
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Scarlett Y. Yang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Vinodh Pillai
- Division of Hematopathology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Emeline Chong
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Marilyn M. Li
- Division of Genomic Diagnostic, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Hematopathology, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sarah K. Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Paul M. Lieberman
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA
| | - Marco Ruella
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephen J. Schuster
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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5
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Ang Z, Paruzzo L, Hayer KE, Schmidt C, Torres Diz M, Xu F, Zankharia U, Zhang Y, Soldan S, Zheng S, Falkenstein CD, Loftus JP, Yang SY, Asnani M, King Sainos P, Pillai V, Chong E, Li MM, Tasian SK, Barash Y, Lieberman PM, Ruella M, Schuster SJ, Thomas-Tikhonenko A. Alternative splicing of its 5'-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies. bioRxiv 2023:2023.02.19.529123. [PMID: 37645778 PMCID: PMC10461923 DOI: 10.1101/2023.02.19.529123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Aberrant skipping of coding exons in CD19 and CD22 compromises responses to immunotherapy for B-cell malignancies. Here, we show that the MS4A1 gene encoding human CD20 also produces several mRNA isoforms with distinct 5' untranslated regions (5'-UTR). Four variants (V1-4) were detectable by RNA-seq in distinct stages of normal B-cell differentiation and B-lymphoid malignancies, with V1 and V3 being the most abundant by far. During B-cell activation and Epstein-Barr virus infection, redirection of splicing from V1 to V3 coincided with increased CD20 positivity. Similarly, in diffuse large B-cell lymphoma only V3, but not V1, correlated with CD20 protein levels, suggesting that V1 might be translation-deficient. Indeed, the longer V1 isoform was found to contain upstream open reading frames (uORFs) and a stem-loop structure, which cooperatively inhibited polysome recruitment. By modulating CD20 isoforms with splice-switching Morpholino oligomers, we enhanced CD20 expression and anti-CD20 antibody rituximab-mediated cytotoxicity in a panel of B-cell lines. Furthermore, reconstitution of CD20-knockout cells with V3 mRNA led to the recovery of CD20 positivity, while V1-reconstituted cells had undetectable levels of CD20 protein. Surprisingly, in vitro CD20-directed CAR T cells were able to kill both V3- and V1-expressing cells, but the bispecific T cell engager mosunetuzumab was only effective against V3-expressing cells. To determine whether CD20 splicing is involved in immunotherapy resistance, we performed RNA-seq on four post-mosunetuzumab follicular lymphoma relapses and discovered that in two of them downregulation of CD20 was accompanied by the V3-to-V1 shift. Thus, splicing-mediated mechanisms of epitope loss extend to CD20-directed immunotherapies. Key Points In normal & malignant human B cells, CD20 mRNA is alternatively spliced into four 5'-UTR isoforms, some of which are translation-deficient.The balance between translation-deficient and -competent isoforms modulates CD20 protein levels & responses to CD20-directed immunotherapies. Explanation of Novelty We discovered that in normal and malignant B-cells, CD20 mRNA is alternatively spliced to generate four distinct 5'-UTRs, including the longer translation-deficient V1 variant. Cells predominantly expressing V1 were still sensitive to CD20-targeting chimeric antigen receptor T-cells. However, they were resistant to the bispecific anti-CD3/CD20 antibody mosunetuzumab, and the shift to V1 were observed in CD20-negative post-mosunetuzumab relapses of follicular lymphoma.
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6
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Danan CH, Naughton KE, Hayer KE, Vellappan S, McMillan EA, Zhou Y, Matsuda R, Nettleford SK, Katada K, Parham LR, Ma X, Chowdhury A, Wilkins BJ, Shah P, Weitzman MD, Hamilton KE. Intestinal transit amplifying cells require METTL3 for growth factor signaling, KRAS expression, and cell survival. bioRxiv 2023:2023.04.06.535853. [PMID: 37066277 PMCID: PMC10104132 DOI: 10.1101/2023.04.06.535853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Intestinal epithelial transit amplifying cells are essential stem progenitors required for intestinal homeostasis, but their rapid proliferation renders them vulnerable to DNA damage from radiation and chemotherapy. Despite their critical roles in intestinal homeostasis and disease, few studies have described genes that are essential to transit amplifying cell function. We report that the RNA methyltransferase, METTL3, is required for survival of transit amplifying cells in the murine small intestine. Transit amplifying cell death after METTL3 deletion was associated with crypt and villus atrophy, loss of absorptive enterocytes, and uniform wasting and death in METTL3-depleted mice. Ribosome profiling and sequencing of methylated RNAs in enteroids and in vivo demonstrated decreased translation of hundreds of unique methylated transcripts after METTL3 deletion, particularly transcripts involved in growth factor signal transduction such as Kras. Further investigation confirmed a novel relationship between METTL3 and Kras methylation and protein levels in vivo. Our study identifies METTL3 as an essential factor supporting the homeostasis of small intestinal tissue via direct maintenance of transit amplifying cell survival. We highlight the crucial role of RNA modifications in regulating growth factor signaling in the intestine, with important implications for both homeostatic tissue renewal and epithelial regeneration.
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Affiliation(s)
- Charles H. Danan
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kaitlyn E. Naughton
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sangeevan Vellappan
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ, 08854, USA
| | - Emily A. McMillan
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Rina Matsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shaneice K. Nettleford
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Louis R. Parham
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Afrah Chowdhury
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ, 08854, USA
| | - Matthew D. Weitzman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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7
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Burn TN, Miot C, Gordon SM, Culberson EJ, Diamond T, Kreiger PA, Hayer KE, Bhattacharyya A, Jones JM, Bassing CH, Behrens EM. The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCRβ and TCRα Genes and Influences Development of αβ T Cell Lineages. J Immunol 2022; 209:938-949. [PMID: 35948399 PMCID: PMC9492648 DOI: 10.4049/jimmunol.2001441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/29/2022] [Indexed: 01/04/2023]
Abstract
RAG1/RAG2 (RAG) endonuclease-mediated assembly of diverse lymphocyte Ag receptor genes by V(D)J recombination is critical for the development and immune function of T and B cells. The RAG1 protein contains a ubiquitin ligase domain that stabilizes RAG1 and stimulates RAG endonuclease activity in vitro. We report in this study that mice with a mutation that inactivates the Rag1 ubiquitin ligase in vitro exhibit decreased rearrangements and altered repertoires of TCRβ and TCRα genes in thymocytes and impaired thymocyte developmental transitions that require the assembly and selection of functional TCRβ and/or TCRα genes. These Rag1 mutant mice present diminished positive selection and superantigen-mediated negative selection of conventional αβ T cells, decreased genesis of invariant NK T lineage αβ T cells, and mature CD4+ αβ T cells with elevated autoimmune potential. Our findings reveal that the Rag1 ubiquitin ligase domain functions in vivo to stimulate TCRβ and TCRα gene recombination and influence differentiation of αβ T lineage cells, thereby establishing replete diversity of αβ TCRs and populations of αβ T cells while restraining generation of potentially autoreactive conventional αβ T cells.
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Affiliation(s)
- Thomas N Burn
- Penn Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Division of Rheumatology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Charline Miot
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Scott M Gordon
- Penn Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Division of Neonatology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Erica J Culberson
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Tamir Diamond
- Penn Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Portia A Kreiger
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Katharina E Hayer
- Department of Biomedical and Health Bioinformatics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Anamika Bhattacharyya
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC; and
| | - Jessica M Jones
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC; and
| | - Craig H Bassing
- Penn Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA;
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Edward M Behrens
- Penn Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA;
- Division of Rheumatology, The Children's Hospital of Philadelphia, Philadelphia, PA
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8
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Price AM, Steinbock RT, Lauman R, Charman M, Hayer KE, Kumar N, Halko E, Lum KK, Wei M, Wilson AC, Garcia BA, Depledge DP, Weitzman MD. Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts. PLoS Pathog 2022; 18:e1010797. [PMID: 36095031 PMCID: PMC9499273 DOI: 10.1371/journal.ppat.1010797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/22/2022] [Accepted: 08/05/2022] [Indexed: 01/07/2023] Open
Abstract
Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and RNA cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts that meet stringent criteria for expression. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORFs), six novel ORF-containing transcripts, and 15 transcripts encoding for messages that could alter protein functions through truncation or fusion of canonical ORFs. In addition, we detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking distinct gene transcription units. Among these chimeric proteins we detected an evolutionarily conserved protein containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies combined with mass spectrometry can reveal further complexity within viral transcriptomes and resulting proteomes.
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Affiliation(s)
- Alexander M. Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Robert T. Steinbock
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard Lauman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew Charman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Namrata Kumar
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Edwin Halko
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Krystal K. Lum
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Monica Wei
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Matthew D. Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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9
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Zheng S, Gillespie E, Naqvi AS, Hayer KE, Ang Z, Torres-Diz M, Quesnel-Vallières M, Hottman DA, Bagashev A, Chukinas JA, Schmidt C, Asnani MM, Shraim R, Taylor DM, Rheingold SR, M. O’Brien M, Singh N, Lynch KW, Ruella M, Barash Y, Tasian SK, Thomas-Tikhonenko A. Abstract 6248: Modulation of CD22 protein expression in childhood leukemia by pervasive splicing aberrations: Implications for CD22-directed immunotherapies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Downregulation of surface epitopes causes post-immunotherapy relapses in B-lymphoblastic leukemia (B-ALL). Here we demonstrate that mRNA encoding CD22 undergoes aberrant splicing in B-ALL. We describe the plasma-membrane-bound CD22 Δex5-6 splice isoform resistant to CAR-T cells targeting the third immunoglobulin-like domain of CD22. We also describe splice variants skipping the AUG-containing exon 2 and failing to produce any identifiable protein; therefore, this event is rate-limiting for epitope presentation. Indeed, forcing exon 2 skipping with Morpholino oligonucleotides reduced CD22 protein expression and conferred resistance to the CD22-directed antibody-drug conjugate inotuzumab in vitro. Furthermore, among inotuzumab-treated pediatric B-ALL patients, we identified one non-responder in whose blasts Δex2 isoforms comprised the majority of CD22 transcripts. In a second patient, a sharp reduction in CD22 protein levels during relapse was driven entirely by increased CD22 exon 2 skipping. Thus, dysregulated CD22 splicing is a major mechanism of epitope downregulation and ensuing resistance to immunotherapy.
Citation Format: Sisi Zheng, Elisabeth Gillespie, Ammar S. Naqvi, Katharina E. Hayer, Zhiwei Ang, Manuel Torres-Diz, Mathieu Quesnel-Vallières, David A. Hottman, Asen Bagashev, John A. Chukinas, Carolin Schmidt, Mukta Mukta Asnani, Rawan Shraim, Deanne M. Taylor, Susan R. Rheingold, Maureen M. O’Brien, Nathan Singh, Kristen W. Lynch, Marco Ruella, Yoseph Barash, Sarah K. Tasian, Andrei Thomas-Tikhonenko. Modulation of CD22 protein expression in childhood leukemia by pervasive splicing aberrations: Implications for CD22-directed immunotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6248.
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Affiliation(s)
- Sisi Zheng
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | | | - Zhiwei Ang
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | | | - Asen Bagashev
- 1Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | | | - Rawan Shraim
- 1Children's Hospital of Philadelphia, Philadelphia, PA
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10
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Heard A, Landmann JH, Hansen AR, Papadopolou A, Hsu YS, Selli ME, Warrington JM, Lattin J, Chang J, Ha H, Haug-Kroeper M, Doray B, Gill S, Ruella M, Hayer KE, Weitzman MD, Green AM, Fluhrer R, Singh N. Antigen glycosylation regulates efficacy of CAR T cells targeting CD19. Nat Commun 2022; 13:3367. [PMID: 35690611 PMCID: PMC9188573 DOI: 10.1038/s41467-022-31035-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/31/2022] [Indexed: 01/16/2023] Open
Abstract
While chimeric antigen receptor (CAR) T cells targeting CD19 can cure a subset of patients with B cell malignancies, most patients treated will not achieve durable remission. Identification of the mechanisms leading to failure is essential to broadening the efficacy of this promising platform. Several studies have demonstrated that disruption of CD19 genes and transcripts can lead to disease relapse after initial response; however, few other tumor-intrinsic drivers of CAR T cell failure have been reported. Here we identify expression of the Golgi-resident intramembrane protease Signal peptide peptidase-like 3 (SPPL3) in malignant B cells as a potent regulator of resistance to CAR therapy. Loss of SPPL3 results in hyperglycosylation of CD19, an alteration that directly inhibits CAR T cell effector function and suppresses anti-tumor cytotoxicity. Alternatively, over-expression of SPPL3 drives loss of CD19 protein, also enabling resistance. In this pre-clinical model these findings identify post-translational modification of CD19 as a mechanism of antigen escape from CAR T cell therapy.
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Affiliation(s)
- Amanda Heard
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jack H Landmann
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alkmini Papadopolou
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Yu-Sung Hsu
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mehmet Emrah Selli
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John M Warrington
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John Lattin
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jufang Chang
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Helen Ha
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Martina Haug-Kroeper
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Balraj Doray
- Division of Hematology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Saar Gill
- Division of Hematology and Oncology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Marco Ruella
- Division of Hematology and Oncology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO, USA
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Nathan Singh
- Division of Oncology, Washington University School of Medicine, Saint Louis, MO, USA.
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11
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Danan CH, Hayer KE, Simon LA, Weitzman MD, Hamilton KE. N6‐Methyladenosine (m
6
A) Modifies Regenerative Transcripts in the Intestinal Epithelium. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Lee YY, Cal-Kayitmazbatir S, Francey LJ, Bahiru MS, Hayer KE, Wu G, Zeller MJ, Roberts R, Speers J, Koshalek J, Berres ME, Bittman EL, Hogenesch JB. duper is a null mutation of Cryptochrome 1 in Syrian hamsters. Proc Natl Acad Sci U S A 2022; 119:e2123560119. [PMID: 35471909 PMCID: PMC9170138 DOI: 10.1073/pnas.2123560119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
The duper mutation is a recessive mutation that shortens the period length of the circadian rhythm in Syrian hamsters. These animals show a large phase shift when responding to light pulses. Limited genetic resources for the Syrian hamster (Mesocricetus auratus) presented a major obstacle to cloning duper. This caused the duper mutation to remain unknown for over a decade. In this study, we did a de novo genome assembly of Syrian hamsters with long-read sequencing data from two different platforms, Pacific Biosciences and Oxford Nanopore Technologies. Using two distinct ecotypes and a fast homozygosity mapping strategy, we identified duper as an early nonsense allele of Cryptochrome 1 (Cry1) leading to a short, unstable protein. CRY1 is known as a highly conserved component of the repressive limb of the core circadian clock. The genome assembly and other genomic datasets generated in this study will facilitate the use of the Syrian hamster in biomedical research.
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Affiliation(s)
- Yin Yeng Lee
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Sibel Cal-Kayitmazbatir
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Lauren J. Francey
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Michael Seifu Bahiru
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003
- Program in Neuroscience & Behavior, University of Massachusetts Amherst, Amherst, MA 01003
| | - Katharina E. Hayer
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
| | - Gang Wu
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Molly J. Zeller
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Robyn Roberts
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - James Speers
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Justin Koshalek
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Mark E. Berres
- University of Wisconsin Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706
| | - Eric L. Bittman
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003
- Program in Neuroscience & Behavior, University of Massachusetts Amherst, Amherst, MA 01003
| | - John B. Hogenesch
- Divisions of Human Genetics and Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
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13
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Abebe JS, Price AM, Hayer KE, Mohr I, Weitzman MD, Wilson AC, Depledge DP. DRUMMER—Rapid detection of RNA modifications through comparative nanopore sequencing. Bioinformatics 2022; 38:3113-3115. [PMID: 35426900 PMCID: PMC9154255 DOI: 10.1093/bioinformatics/btac274] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/23/2022] Open
Abstract
Motivation The chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides. Results DRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity. Availability and implementation DRUMMER is written in Python 3 and is available as open source in the GitHub repository: https://github.com/DepledgeLab/DRUMMER. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jonathan S Abebe
- Department of Microbiology, New York University School of Medicine, New York, NY
| | - Alexander M Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, NY
| | - Matthew D Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY
| | - Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
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14
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Zheng S, Gillespie E, Naqvi AS, Hayer KE, Ang Z, Torres-Diz M, Quesnel-Vallières M, Hottman DA, Bagashev A, Chukinas J, Schmidt C, Asnani M, Shraim R, Taylor DM, Rheingold SR, O'Brien MM, Singh N, Lynch KW, Ruella M, Barash Y, Tasian SK, Thomas-Tikhonenko A. Modulation of CD22 Protein Expression in Childhood Leukemia by Pervasive Splicing Aberrations: Implications for CD22-Directed Immunotherapies. Blood Cancer Discov 2022; 3:103-115. [PMID: 35015683 PMCID: PMC9780083 DOI: 10.1158/2643-3230.bcd-21-0087] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/30/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Downregulation of surface epitopes causes postimmunotherapy relapses in B-lymphoblastic leukemia (B-ALL). Here we demonstrate that mRNA encoding CD22 undergoes aberrant splicing in B-ALL. We describe the plasma membrane-bound CD22 Δex5-6 splice isoform, which is resistant to chimeric antigen receptor (CAR) T cells targeting the third immunoglobulin-like domain of CD22. We also describe splice variants skipping the AUG-containing exon 2 and failing to produce any identifiable protein, thereby defining an event that is rate limiting for epitope presentation. Indeed, forcing exon 2 skipping with morpholino oligonucleotides reduced CD22 protein expression and conferred resistance to the CD22-directed antibody-drug conjugate inotuzumab ozogamicin in vitro. Furthermore, among inotuzumab-treated pediatric patients with B-ALL, we identified one nonresponder in whose leukemic blasts Δex2 isoforms comprised the majority of CD22 transcripts. In a second patient, a sharp reduction in CD22 protein levels during relapse was driven entirely by increased CD22 exon 2 skipping. Thus, dysregulated CD22 splicing is a major mechanism of epitope downregulation and ensuing resistance to immunotherapy. SIGNIFICANCE The mechanism(s) underlying downregulation of surface CD22 following CD22-directed immunotherapy remains underexplored. Our biochemical and correlative studies demonstrate that in B-ALL, CD22 expression levels are controlled by inclusion/skipping of CD22 exon 2. Thus, aberrant splicing of CD22 is an important driver/biomarker of de novo and acquired resistance to CD22-directed immunotherapies. See related commentary by Bourcier and Abdel-Wahab, p. 87. This article is highlighted in the In This Issue feature, p. 85.
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Affiliation(s)
- Sisi Zheng
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elisabeth Gillespie
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ammar S. Naqvi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katharina E. Hayer
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Zhiwei Ang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - David A. Hottman
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Asen Bagashev
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - John Chukinas
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Carolin Schmidt
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rawan Shraim
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Deanne M. Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Susan R. Rheingold
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maureen M. O'Brien
- Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Nathan Singh
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristen W. Lynch
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marco Ruella
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sarah K. Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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15
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Sehgal P, Lanauze C, Wang X, Hayer KE, Torres-Diz M, Leu NA, Sela Y, Stanger BZ, Lengner CJ, Thomas-Tikhonenko A. MYC Hyperactivates Wnt Signaling in APC/ CTNNB1-Mutated Colorectal Cancer Cells through miR-92a-Dependent Repression of DKK3. Mol Cancer Res 2021; 19:2003-2014. [PMID: 34593610 PMCID: PMC8642317 DOI: 10.1158/1541-7786.mcr-21-0666] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022]
Abstract
Activation of Wnt signaling is among the earliest events in colon cancer development. It is achieved either via activating mutations in the CTNNB1 gene encoding β-catenin, the key transcription factor in the Wnt pathway, or most commonly by inactivating mutations affecting APC, a major β-catenin binding partner and negative regulator. However, our analysis of recent Pan Cancer Atlas data revealed that CTNNB1 mutations significantly co-occur with those affecting Wnt receptor complex components (e.g., Frizzled and LRP6), underscoring the importance of additional regulatory events even in the presence of common APC/CTNNB1 mutations. In our effort to identify non-mutational hyperactivating events, we determined that KRAS-transformed murine colonocytes overexpressing direct β-catenin target MYC show significant upregulation of the Wnt signaling pathway and reduced expression of Dickkopf 3 (DKK3), a reported ligand for Wnt co-receptors. We demonstrate that MYC suppresses DKK3 transcription through one of miR-17-92 cluster miRNAs, miR-92a. We further examined the role of DKK3 by overexpression and knockdown and discovered that DKK3 suppresses Wnt signaling in Apc-null murine colonic organoids and human colon cancer cells despite the presence of downstream activating mutations in the Wnt pathway. Conversely, MYC overexpression in the same cell lines resulted in hyperactive Wnt signaling, acquisition of epithelial-to-mesenchymal transition markers, and enhanced migration/invasion in vitro and metastasis in a syngeneic orthotopic mouse colon cancer model. IMPLICATIONS: Our results suggest that the MYC→miR-92a-|DKK3 axis hyperactivates Wnt signaling, forming a feed-forward oncogenic loop.
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Affiliation(s)
- Priyanka Sehgal
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Claudia Lanauze
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xin Wang
- Department of Biomedical Sciences, School of Veterinary Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Katharina E Hayer
- The Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - N Adrian Leu
- Department of Biomedical Sciences, School of Veterinary Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yogev Sela
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ben Z Stanger
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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16
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Price AM, Steinbock RT, Di C, Hayer KE, Li Y, Herrmann C, Parenti NA, Whelan JN, Weiss SR, Weitzman MD. Adenovirus prevents dsRNA formation by promoting efficient splicing of viral RNA. Nucleic Acids Res 2021; 50:1201-1220. [PMID: 34671803 PMCID: PMC8860579 DOI: 10.1093/nar/gkab896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/10/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells recognize intracellular pathogens through pattern recognition receptors, including sensors of aberrant nucleic acid structures. Sensors of double-stranded RNA (dsRNA) are known to detect replication intermediates of RNA viruses. It has long been suggested that annealing of mRNA from symmetrical transcription of both top and bottom strands of DNA virus genomes can produce dsRNA during infection. Supporting this hypothesis, nearly all DNA viruses encode inhibitors of dsRNA-recognition pathways. However, direct evidence that DNA viruses produce dsRNA is lacking. Contrary to dogma, we show that the nuclear-replicating DNA virus adenovirus (AdV) does not produce detectable levels of dsRNA during infection. In contrast, abundant dsRNA is detected within the nucleus of cells infected with AdV mutants defective for viral RNA processing. In the presence of nuclear dsRNA, the cytoplasmic dsRNA sensor PKR is relocalized and activated within the nucleus. Accumulation of viral dsRNA occurs in the late phase of infection, when unspliced viral transcripts form intron/exon base pairs between top and bottom strand transcripts. We propose that DNA viruses actively limit dsRNA formation by promoting efficient splicing and mRNA processing, thus avoiding detection and restriction by host innate immune sensors of pathogenic nucleic acids.
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Affiliation(s)
- Alexander M Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert T Steinbock
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Chao Di
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christin Herrmann
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas A Parenti
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jillian N Whelan
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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17
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Green AM, DeWeerd RA, O'Leary DR, Hansen AR, Hayer KE, Kulej K, Dineen AS, Szeto JH, Garcia BA, Weitzman MD. Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. EMBO Rep 2021; 22:e52145. [PMID: 34347354 DOI: 10.15252/embr.202052145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The APOBEC3 cytidine deaminases are implicated as the cause of a prevalent somatic mutation pattern found in cancer genomes. The APOBEC3 enzymes act as viral restriction factors by mutating viral genomes. Mutation of the cellular genome is presumed to be an off-target activity of the enzymes, although the regulatory measures for APOBEC3 expression and activity remain undefined. It is therefore difficult to predict circumstances that enable APOBEC3 interaction with cellular DNA that leads to mutagenesis. The APOBEC3A (A3A) enzyme is the most potent deaminase of the family. Using proteomics, we evaluate protein interactors of A3A to identify potential regulators. We find that A3A interacts with the chaperonin-containing TCP-1 (CCT) complex, a cellular machine that assists in protein folding and function. Importantly, depletion of CCT results in A3A-induced DNA damage and cytotoxicity. Evaluation of cancer genomes demonstrates an enrichment of A3A mutational signatures in cancers with silencing mutations in CCT subunit genes. Together, these data suggest that the CCT complex interacts with A3A, and that disruption of CCT function results in increased A3A mutational activity.
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Affiliation(s)
- Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ariel S Dineen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julia H Szeto
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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18
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Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A. Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biol 2021; 22:190. [PMID: 34183059 PMCID: PMC8240250 DOI: 10.1186/s13059-021-02411-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While "exitrons" are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed "falsitrons," that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
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MESH Headings
- Alternative Splicing
- Antibodies, Bispecific/pharmacology
- Antineoplastic Agents, Immunological/pharmacology
- Artifacts
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Base Pairing
- Base Sequence
- Cell Line, Tumor
- Datasets as Topic
- Exons
- High-Throughput Nucleotide Sequencing
- Humans
- Immunotherapy/methods
- Introns
- Models, Biological
- Nucleic Acid Conformation
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Reverse Transcription
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Affiliation(s)
- Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | - Katharina E Hayer
- The Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sarah K Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Present address: Stanford Cancer Institute, 265 Campus Dr., Stanford, CA, 94305, USA
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) and Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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19
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Wu GS, Yang-Iott KS, Klink MA, Hayer KE, Lee KD, Bassing CH. Poor quality Vβ recombination signal sequences stochastically enforce TCRβ allelic exclusion. J Exp Med 2021; 217:151853. [PMID: 32526772 PMCID: PMC7478721 DOI: 10.1084/jem.20200412] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022] Open
Abstract
The monoallelic expression of antigen receptor (AgR) genes, called allelic exclusion, is fundamental for highly specific immune responses to pathogens. This cardinal feature of adaptive immunity is achieved by the assembly of a functional AgR gene on one allele, with subsequent feedback inhibition of V(D)J recombination on the other allele. A range of epigenetic mechanisms have been implicated in sequential recombination of AgR alleles; however, we now demonstrate that a genetic mechanism controls this process for Tcrb. Replacement of V(D)J recombinase targets at two different mouse Vβ gene segments with a higher quality target elevates Vβ rearrangement frequency before feedback inhibition, dramatically increasing the frequency of T cells with TCRβ chains derived from both Tcrb alleles. Thus, TCRβ allelic exclusion is enforced genetically by the low quality of Vβ recombinase targets that stochastically restrict the production of two functional rearrangements before feedback inhibition silences one allele.
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Affiliation(s)
- Glendon S Wu
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Katherine S Yang-Iott
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Morgann A Klink
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kyutae D Lee
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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20
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Price AM, Hayer KE, McIntyre ABR, Gokhale NS, Abebe JS, Della Fera AN, Mason CE, Horner SM, Wilson AC, Depledge DP, Weitzman MD. Direct RNA sequencing reveals m 6A modifications on adenovirus RNA are necessary for efficient splicing. Nat Commun 2020; 11:6016. [PMID: 33243990 PMCID: PMC7691994 DOI: 10.1038/s41467-020-19787-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022] Open
Abstract
Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we profile m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.
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Affiliation(s)
- Alexander M Price
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, 10065, USA
- Department of Molecular Life Sciences, University of Zurich, 8006, Zurich, Switzerland
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Immunology, University of Washington, Seattle, WA, 98115, USA
| | - Jonathan S Abebe
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA
| | - Ashley N Della Fera
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Biological Sciences Graduate Group, University of Maryland, College Park, MD, 20742, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- The World Quant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, 10017, USA
| | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA.
| | - Matthew D Weitzman
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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21
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Herrmann C, Dybas JM, Liddle JC, Price AM, Hayer KE, Lauman R, Purman CE, Charman M, Kim ET, Garcia BA, Weitzman MD. Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing. Nat Microbiol 2020; 5:1217-1231. [PMID: 32661314 PMCID: PMC7529849 DOI: 10.1038/s41564-020-0750-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 06/04/2020] [Indexed: 01/06/2023]
Abstract
Viruses promote infection by hijacking the ubiquitin machinery of the host to counteract or redirect cellular processes. Adenovirus encodes two early proteins, E1B55K and E4orf6, that together co-opt a cellular ubiquitin ligase complex to overcome host defences and promote virus production. Adenovirus mutants lacking E1B55K or E4orf6 display defects in viral RNA processing and protein production, but previously identified substrates of the redirected ligase do not explain these phenotypes. Here, we used a quantitative proteomics approach to identify substrates of E1B55K/E4orf6-mediated ubiquitination that facilitate RNA processing. While all currently known cellular substrates of E1B55K and E4orf6 are degraded by the proteasome, we uncovered RNA-binding proteins as high-confidence substrates that are not decreased in overall abundance. We focused on two RNA-binding proteins, RALY and hnRNP-C, which we confirm are ubiquitinated without degradation. Knockdown of RALY and hnRNP-C increased levels of viral RNA splicing, protein abundance and progeny production during infection with E1B55K-deleted virus. Furthermore, infection with E1B55K-deleted virus resulted in an increased interaction of hnRNP-C with viral RNA and attenuation of viral RNA processing. These data suggest that viral-mediated ubiquitination of RALY and hnRNP-C relieves a restriction on viral RNA processing and reveal an unexpected role for non-degradative ubiquitination in the manipulation of cellular processes during virus infection.
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Affiliation(s)
- Christin Herrmann
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph M Dybas
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer C Liddle
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander M Price
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Richard Lauman
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Caitlin E Purman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew Charman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eui Tae Kim
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Division of Protective Immunity and Division of Cancer Pathobiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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22
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Paris AJ, Hayer KE, Oved JH, Avgousti DC, Toulmin SA, Zepp JA, Zacharias WJ, Katzen JB, Basil MC, Kremp MM, Slamowitz AR, Jayachandran S, Sivakumar A, Dai N, Wang P, Frank DB, Eisenlohr LC, Cantu E, Beers MF, Weitzman MD, Morrisey EE, Worthen GS. STAT3-BDNF-TrkB signalling promotes alveolar epithelial regeneration after lung injury. Nat Cell Biol 2020; 22:1197-1210. [PMID: 32989251 PMCID: PMC8167437 DOI: 10.1038/s41556-020-0569-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/03/2020] [Indexed: 01/13/2023]
Abstract
Alveolar epithelial regeneration is essential for recovery from devastating lung diseases. This process occurs when type II alveolar pneumocytes (AT2 cells) proliferate and transdifferentiate into type I alveolar pneumocytes (AT1 cells). We used genome-wide analysis of chromatin accessibility and gene expression following acute lung injury to elucidate repair mechanisms. AT2 chromatin accessibility changed substantially following injury to reveal STAT3 binding motifs adjacent to genes that regulate essential regenerative pathways. Single-cell transcriptome analysis identified brain-derived neurotrophic factor (Bdnf) as a STAT3 target gene with newly accessible chromatin in a unique population of regenerating AT2 cells. Furthermore, the BDNF receptor tropomyosin receptor kinase B (TrkB) was enriched on mesenchymal alveolar niche cells (MANCs). Loss or blockade of AT2-specific Stat3, Bdnf or mesenchyme-specific TrkB compromised repair and reduced Fgf7 expression by niche cells. A TrkB agonist improved outcomes in vivo following lung injury. These data highlight the biological and therapeutic importance of the STAT3-BDNF-TrkB axis in orchestrating alveolar epithelial regeneration.
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Affiliation(s)
- Andrew J Paris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph H Oved
- Division of Hematology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daphne C Avgousti
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sushila A Toulmin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jarod A Zepp
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William J Zacharias
- Division of Pulmonary Biology, Perinatal Institute, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeremy B Katzen
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria C Basil
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Madison M Kremp
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Sowmya Jayachandran
- Division of Cardiology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aravind Sivakumar
- Division of Cardiology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ning Dai
- Division of Neonatology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ping Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David B Frank
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Cardiology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laurence C Eisenlohr
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edward Cantu
- Division of Cardiovascular Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael F Beers
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edward E Morrisey
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Regenerative Medicine, Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - G Scott Worthen
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Neonatology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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23
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Asnani M, Hayer KE, Naqvi AS, Zheng S, Yang SY, Oldridge D, Ibrahim F, Maragkakis M, Gazzara MR, Black KL, Bagashev A, Taylor D, Mourelatos Z, Grupp SA, Barrett D, Maris JM, Sotillo E, Barash Y, Thomas-Tikhonenko A. Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19. Leukemia 2020; 34:1202-1207. [PMID: 31591467 PMCID: PMC7214268 DOI: 10.1038/s41375-019-0580-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/04/2019] [Accepted: 09/17/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Katharina E Hayer
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- DBHi Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Ammar S Naqvi
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- DBHi Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sisi Zheng
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Scarlett Y Yang
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Derek Oldridge
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Fadia Ibrahim
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Manolis Maragkakis
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn L Black
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Lonza Biologics, Portsmouth, NH, USA
| | - Asen Bagashev
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Deanne Taylor
- DBHi Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zissimos Mourelatos
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephan A Grupp
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David Barrett
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John M Maris
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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24
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Singh N, Lee YG, Shestova O, Ravikumar P, Hayer KE, Hong SJ, Lu XM, Pajarillo R, Agarwal S, Kuramitsu S, Orlando EJ, Mueller KT, Good CR, Berger SL, Shalem O, Weitzman MD, Frey NV, Maude SL, Grupp SA, June CH, Gill S, Ruella M. Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction. Cancer Discov 2020. [PMID: 32001516 DOI: 10.13039/100000054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Primary resistance to CD19-directed chimeric antigen receptor T-cell therapy (CART19) occurs in 10% to 20% of patients with acute lymphoblastic leukemia (ALL); however, the mechanisms of this resistance remain elusive. Using a genome-wide loss-of-function screen, we identified that impaired death receptor signaling in ALL led to rapidly progressive disease despite CART19 treatment. This was mediated by an inherent resistance to T-cell cytotoxicity that permitted antigen persistence and was subsequently magnified by the induction of CAR T-cell functional impairment. These findings were validated using samples from two CAR T-cell clinical trials in ALL, where we found that reduced expression of death receptor genes was associated with worse overall survival and reduced T-cell fitness. Our findings suggest that inherent dysregulation of death receptor signaling in ALL directly leads to CAR T-cell failure by impairing T-cell cytotoxicity and promoting progressive CAR T-cell dysfunction. SIGNIFICANCE: Resistance to CART19 is a significant barrier to efficacy in the treatment of B-cell malignancies. This work demonstrates that impaired death receptor signaling in tumor cells causes failed CART19 cytotoxicity and drives CART19 dysfunction, identifying a novel mechanism of antigen-independent resistance to CAR therapy.See related commentary by Green and Neelapu, p. 492.
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Affiliation(s)
- Nathan Singh
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Yong Gu Lee
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Olga Shestova
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Pranali Ravikumar
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Seok Jae Hong
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Xueqing Maggie Lu
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Raymone Pajarillo
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sangya Agarwal
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shunichiro Kuramitsu
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Elena J Orlando
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Charly R Good
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ophir Shalem
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Cell and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Noelle V Frey
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shannon L Maude
- Divison of Oncology, Children's Hospital of Philadelphia; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Stephan A Grupp
- Divison of Oncology, Children's Hospital of Philadelphia; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Carl H June
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Saar Gill
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Marco Ruella
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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25
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Singh N, Lee YG, Shestova O, Ravikumar P, Hayer KE, Hong SJ, Lu XM, Pajarillo R, Agarwal S, Kuramitsu S, Orlando EJ, Mueller KT, Good CR, Berger SL, Shalem O, Weitzman MD, Frey NV, Maude SL, Grupp SA, June CH, Gill S, Ruella M. Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction. Cancer Discov 2020; 10:552-567. [PMID: 32001516 PMCID: PMC7416790 DOI: 10.1158/2159-8290.cd-19-0813] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/27/2019] [Accepted: 01/10/2020] [Indexed: 12/26/2022]
Abstract
Primary resistance to CD19-directed chimeric antigen receptor T-cell therapy (CART19) occurs in 10% to 20% of patients with acute lymphoblastic leukemia (ALL); however, the mechanisms of this resistance remain elusive. Using a genome-wide loss-of-function screen, we identified that impaired death receptor signaling in ALL led to rapidly progressive disease despite CART19 treatment. This was mediated by an inherent resistance to T-cell cytotoxicity that permitted antigen persistence and was subsequently magnified by the induction of CAR T-cell functional impairment. These findings were validated using samples from two CAR T-cell clinical trials in ALL, where we found that reduced expression of death receptor genes was associated with worse overall survival and reduced T-cell fitness. Our findings suggest that inherent dysregulation of death receptor signaling in ALL directly leads to CAR T-cell failure by impairing T-cell cytotoxicity and promoting progressive CAR T-cell dysfunction. SIGNIFICANCE: Resistance to CART19 is a significant barrier to efficacy in the treatment of B-cell malignancies. This work demonstrates that impaired death receptor signaling in tumor cells causes failed CART19 cytotoxicity and drives CART19 dysfunction, identifying a novel mechanism of antigen-independent resistance to CAR therapy.See related commentary by Green and Neelapu, p. 492.
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Affiliation(s)
- Nathan Singh
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Yong Gu Lee
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Olga Shestova
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Pranali Ravikumar
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Seok Jae Hong
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Xueqing Maggie Lu
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Raymone Pajarillo
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sangya Agarwal
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shunichiro Kuramitsu
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Elena J Orlando
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - Charly R Good
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Ophir Shalem
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Cell and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Noelle V Frey
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Shannon L Maude
- Divison of Oncology, Children's Hospital of Philadelphia; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Stephan A Grupp
- Divison of Oncology, Children's Hospital of Philadelphia; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Carl H June
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Saar Gill
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Marco Ruella
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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26
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Harrington CT, Sotillo E, Robert A, Hayer KE, Bogusz AM, Psathas J, Yu D, Taylor D, Dang CV, Klein PS, Hogarty MD, Geoerger B, El-Deiry WS, Wiels J, Thomas-Tikhonenko A. Correction: Transient stabilization, rather than inhibition, of MYC amplifies extrinsic apoptosis and therapeutic responses in refractory B-cell lymphoma. Leukemia 2019; 34:1485. [PMID: 31758088 DOI: 10.1038/s41375-019-0650-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Colleen T Harrington
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Stanford Cancer Institute, 265 Campus Dr., Stanford, CA, 94305, USA
| | - Aude Robert
- CNRS UMR 8126, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Agata M Bogusz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James Psathas
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,The Janssen Pharmaceutical Companies of Johnson & Johnson, 200 Great Valley Parkway, Malvern, PA, 19355, USA
| | - Duonan Yu
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Noncoding RNA Center, Yangzhou University, Yangzhou, 225001, China
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chi V Dang
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Peter S Klein
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael D Hogarty
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Birgit Geoerger
- CNRS UMR 8203, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France.,Department of Pediatric and Adolescent Oncology, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France
| | - Wafik S El-Deiry
- Department of Pathology and Laboratory Medicine, Brown University Medical School, Providence, RI, 02912, USA
| | - Joëlle Wiels
- CNRS UMR 8126, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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27
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Harrington CT, Sotillo E, Robert A, Hayer KE, Bogusz AM, Psathas J, Yu D, Taylor D, Dang CV, Klein PS, Hogarty MD, Geoerger B, El-Deiry WS, Wiels J, Thomas-Tikhonenko A. Transient stabilization, rather than inhibition, of MYC amplifies extrinsic apoptosis and therapeutic responses in refractory B-cell lymphoma. Leukemia 2019; 33:2429-2441. [PMID: 30914792 PMCID: PMC6884148 DOI: 10.1038/s41375-019-0454-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 02/07/2023]
Abstract
Therapeutic targeting of initiating oncogenes is the mainstay of precision medicine. Considerable efforts have been expended toward silencing MYC, which drives many human cancers including Burkitt lymphomas (BL). Yet, the effects of MYC silencing on standard-of-care therapies are poorly understood. Here we found that inhibition of MYC transcription renders B-lymphoblastoid cells refractory to chemotherapeutic agents. This suggested that in the context of chemotherapy, stabilization of Myc protein could be more beneficial than its inactivation. We tested this hypothesis by pharmacologically inhibiting glycogen synthase kinase 3β (GSK-3β), which normally targets Myc for proteasomal degradation. We discovered that chemorefractory BL cell lines responded better to doxorubicin and other anti-cancer drugs when Myc was transiently stabilized. In vivo, GSK3 inhibitors (GSK3i) enhanced doxorubicin-induced apoptosis in BL patient-derived xenografts (BL-PDX), as well as in murine MYC-driven lymphoma allografts. This enhancement was accompanied by and required deregulation of several key genes acting in the extrinsic, death-receptor-mediated apoptotic pathway. Consistent with this mechanism of action, GSK3i also facilitated lymphoma cell killing by a death ligand TRAIL and by a death receptor agonist mapatumumab. Thus, GSK3i synergizes with both standard chemotherapeutics and direct engagers of death receptors and could improve outcomes in patients with refractory lymphomas.
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Affiliation(s)
- Colleen T Harrington
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Stanford Cancer Institute, 265 Campus Dr., Stanford, CA, 94305, USA
| | - Aude Robert
- CNRS UMR 8126, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Agata M Bogusz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James Psathas
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Janssen Pharmaceutical Companies of Johnson & Johnson, 200 Great Valley Parkway, Malvern, PA, 19355, USA
| | - Duonan Yu
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Noncoding RNA Center, Yangzhou University, 225001, Yangzhou, China
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chi V Dang
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Peter S Klein
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael D Hogarty
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Birgit Geoerger
- CNRS UMR 8203, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France
| | - Wafik S El-Deiry
- Department of Pathology and Laboratory Medicine, Brown University Medical School, Providence, RI, 02912, USA
| | - Joëlle Wiels
- CNRS UMR 8126, Univ Paris-Sud - Université Paris-Saclay, Institut Gustave Roussy, 94805, Villejuif, France
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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28
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Marsden KC, Jain RA, Wolman MA, Echeverry FA, Nelson JC, Hayer KE, Miltenberg B, Pereda AE, Granato M. A Cyfip2-Dependent Excitatory Interneuron Pathway Establishes the Innate Startle Threshold. Cell Rep 2019; 23:878-887. [PMID: 29669291 PMCID: PMC6642828 DOI: 10.1016/j.celrep.2018.03.095] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/13/2017] [Accepted: 03/20/2018] [Indexed: 11/18/2022] Open
Abstract
Sensory experiences dynamically modify whether animals respond to a given stimulus, but it is unclear how innate behavioral thresholds are established. Here, we identify molecular and circuit-level mechanisms underlying the innate threshold of the zebrafish startle response. From a forward genetic screen, we isolated five mutant lines with reduced innate startle thresholds. Using whole-genome sequencing, we identify the causative mutation for one line to be in the fragile X mental retardation protein (FMRP)-interacting protein cyfip2. We show that cyfip2 acts independently of FMRP and that reactivation of cyfip2 restores the baseline threshold after phenotype onset. Finally, we show that cyfip2 regulates the innate startle threshold by reducing neural activity in a small group of excitatory hindbrain interneurons. Thus, we identify a selective set of genes critical to establishing an innate behavioral threshold and uncover a circuit-level role for cyfip2 in this process. Using forward genetics, electrophysiology, and combined behavior and Ca2+ imaging in zebrafish, Marsden et al. show that cyfip2 regulates the acoustic startle threshold by controlling the activity of excitatory spiral fiber interneurons.
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Affiliation(s)
- Kurt C Marsden
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104, USA; Department of Biological Sciences, W.M. Keck Center for Behavioral Biology, North Carolina State University, 127 David Clark Labs, 100 Brooks Ave., Raleigh, NC 27607, USA
| | - Roshan A Jain
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104, USA; Department of Biology, Haverford College, S108 Sharpless Hall, 370 Lancaster Ave., Haverford, PA 19041, USA
| | - Marc A Wolman
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104, USA; Department of Zoology, 213 Zoology Research Building, 1117 West Johnson St., University of Wisconsin, Madison, WI 53706, USA
| | - Fabio A Echeverry
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 431 Rose F. Kennedy Center, 1410 Pelham Parkway South, Bronx, NY 10461, USA
| | - Jessica C Nelson
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ben Miltenberg
- Department of Biology, Haverford College, S108 Sharpless Hall, 370 Lancaster Ave., Haverford, PA 19041, USA
| | - Alberto E Pereda
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 431 Rose F. Kennedy Center, 1410 Pelham Parkway South, Bronx, NY 10461, USA
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Blvd., Philadelphia, PA 19104, USA.
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29
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Black KL, Naqvi AS, Asnani M, Hayer KE, Yang SY, Gillespie E, Bagashev A, Pillai V, Tasian SK, Gazzara MR, Carroll M, Taylor D, Lynch KW, Barash Y, Thomas-Tikhonenko A. Aberrant splicing in B-cell acute lymphoblastic leukemia. Nucleic Acids Res 2019; 46:11357-11369. [PMID: 30357359 PMCID: PMC6277088 DOI: 10.1093/nar/gky946] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. Here we investigated its prevalence in pediatric B-cell acute lymphoblastic leukemias (B-ALL), where SFs are not mutated. By comparing these samples to normal pro-B cells, we found thousands of aberrant local splice variations (LSVs) per sample, with 279 LSVs in 241 genes present in every comparison. These genes were enriched in RNA processing pathways and encoded ∼100 SFs, e.g. hnRNPA1. HNRNPA1 3'UTR was most pervasively mis-spliced, yielding the transcript subject to nonsense-mediated decay. To mimic this event, we knocked it down in B-lymphoblastoid cells and identified 213 hnRNPA1-regulated exon usage events comprising the hnRNPA1 splicing signature in pediatric leukemia. Some of its elements were LSVs in DICER1 and NT5C2, known cancer drivers. We searched for LSVs in other leukemia and lymphoma drivers and discovered 81 LSVs in 41 additional genes. Seventy-seven LSVs out of 81 were confirmed using two large independent B-ALL RNA-seq datasets, and the twenty most common B-ALL drivers, including NT5C2, showed higher prevalence of aberrant splicing than of somatic mutations. Thus, post-transcriptional deregulation of SF can drive widespread changes in B-ALL splicing and likely contributes to disease pathogenesis.
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Affiliation(s)
- Kathryn L Black
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ammar S Naqvi
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Biomedical & Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mukta Asnani
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Katharina E Hayer
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Biomedical & Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Scarlett Y Yang
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elisabeth Gillespie
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Asen Bagashev
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Vinodh Pillai
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah K Tasian
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin Carroll
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deanne Taylor
- Department of Biomedical & Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrei Thomas-Tikhonenko
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Black KL, Naqvi AS, Asnani M, Hayer KE, Yang SY, Gillespie E, Bagashev A, Pillai V, Tasian SK, Gazzara MR, Carroll M, Taylor D, Lynch KW, Barash Y, Thomas-Tikhonenko A. Aberrant splicing in B-cell acute lymphoblastic leukemia. Nucleic Acids Res 2018; 47:1043. [PMID: 30517739 PMCID: PMC6344847 DOI: 10.1093/nar/gky1231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kathryn L Black
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ammar S Naqvi
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Biomedical & Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mukta Asnani
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Katharina E Hayer
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Biomedical & Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Scarlett Y Yang
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elisabeth Gillespie
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Asen Bagashev
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Vinodh Pillai
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah K Tasian
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew R Gazzara
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin Carroll
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deanne Taylor
- Department of Biomedical & Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristen W Lynch
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrei Thomas-Tikhonenko
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Immunology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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31
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Green AM, Hayer KE, Szeto JH, Shalem O, Weitzman MD. Abstract 3206: Synthetic lethal interactions with APOBEC3A identified by functional genomic screening. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The APOBEC3 (A3) family of cytosine deaminase enzymes is integral to innate defenses by editing viral genomes to limit infectivity. However, several members of the A3 enzyme family (A3A-A3H) have also been implicated in mutational signatures observed in human cancers. The A3 mutational signature has emerged as the most prevalent across all cancers, implicating A3 enzymes as powerful mutators of the human genome. While few prospective studies have addressed the potential for A3 enzymes to induce specific mutational patterns in human genomes, the possibility of exploiting the mutagenic activity of A3 for cancer therapy is beginning to be explored. We recently showed that A3A is highly expressed in human acute myeloid leukemia (AML), and that deamination activates the replication checkpoint via ATR kinase signaling. In an AML model, we showed that inhibition of ATR or downstream Chk1 resulted in accumulated DNA damage by A3A and ultimately death of leukemia cells. In search of additional cellular pathways that may be manipulated to take advantage of A3 activity for therapeutic effect, we performed a functional genomics screen using a genome-wide CRISPR knock-out approach in a model of human leukemia with inducible A3A expression. We introduced Cas9 and the Brunello guide RNA lentivirus library into the human AML cell line, THP1, which we engineered to express doxycycline-inducible A3A. The Brunello library consists of 4 guide RNAs targeting each human gene. Transduction was performed to enable one lentivirus integration per cell, thus resulting in a single gene disruption per cell. Cells were treated with doxycycline and genomic DNA was harvested from treated and untreated cells every week. Guide RNAs were amplified by PCR from genomic DNA and identified by next-generation sequencing. We applied the MaGECK algorithm to identify the quantity of each guide RNA remaining in treated samples and compared to untreated samples. In THP1 cells induced to express A3A, knockout of genes in cell cycle and DNA repair pathways resulted in synthetic lethality. Specifically, expression of A3A synergized with genes essential for cell cycle checkpoints and DNA damage responses to cause leukemia cell death. Clinical-grade inhibitors are available for protein products of many of the genes identified; thus these represent feasible targets for therapeutic intervention in AML that has elevated A3A activity. In addition to leukemia, A3A and the closely related enzyme A3B have been implicated in several malignant processes including breast, bladder, and ovarian cancers. We show that functional genomic screening is a powerful tool for identification of synthetic lethal interactions, which can provide therapeutic opportunities for additional cancers in which A3 enzymes are active.
Citation Format: Abby M. Green, Katharina E. Hayer, Julia H. Szeto, Ophir Shalem, Matthew D. Weitzman. Synthetic lethal interactions with APOBEC3A identified by functional genomic screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3206.
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Affiliation(s)
- Abby M. Green
- Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Ophir Shalem
- Children's Hospital of Philadelphia, Philadelphia, PA
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Lahens NF, Ricciotti E, Smirnova O, Toorens E, Kim EJ, Baruzzo G, Hayer KE, Ganguly T, Schug J, Grant GR. A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. BMC Genomics 2017; 18:602. [PMID: 28797240 PMCID: PMC5553782 DOI: 10.1186/s12864-017-4011-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case. Results Here we employ a standard treatment/control experimental design, which enables us to evaluate these platforms in the context of the expression differences common in differential gene expression experiments. Specifically, we assessed the hepatic inflammatory response of mice by assaying liver RNA from control and IL-1β treated animals with both the Illumina HiSeq and the Ion Torrent Proton sequencing platforms. We found the greatest difference between the platforms at the level of read alignment, a moderate level of concordance at the level of DGE analysis, and nearly identical results at the level of differentially affected pathways. Interestingly, we also observed a strong interaction between sequencing platform and choice of aligner. By aligning both real and simulated Illumina and Ion Torrent data with the twelve most commonly-cited aligners in the literature, we observed that different aligner and platform combinations were better suited to probing different genomic features; for example, disentangling the source of expression in gene-pseudogene pairs. Conclusions Taken together, our results indicate that while Illumina and Ion Torrent have similar capacities to detect changes in biology from a treatment/control experiment, these platforms may be tailored to interrogate different transcriptional phenomena through careful selection of alignment software. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4011-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas F Lahens
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Emanuela Ricciotti
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Olga Smirnova
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erik Toorens
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eun Ji Kim
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Giacomo Baruzzo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Tapan Ganguly
- Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jonathan Schug
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gregory R Grant
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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33
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Green AM, Budagyan K, Hayer KE, Reed MA, Savani MR, Wertheim GB, Weitzman MD. Cytosine Deaminase APOBEC3A Sensitizes Leukemia Cells to Inhibition of the DNA Replication Checkpoint. Cancer Res 2017; 77:4579-4588. [PMID: 28655787 DOI: 10.1158/0008-5472.can-16-3394] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/18/2017] [Accepted: 06/22/2017] [Indexed: 12/27/2022]
Abstract
Mutational signatures in cancer genomes have implicated the APOBEC3 cytosine deaminases in oncogenesis, possibly offering a therapeutic vulnerability. Elevated APOBEC3B expression has been detected in solid tumors, but expression of APOBEC3A (A3A) in cancer has not been described to date. Here, we report that A3A is highly expressed in subsets of pediatric and adult acute myelogenous leukemia (AML). We modeled A3A expression in the THP1 AML cell line by introducing an inducible A3A gene. A3A expression caused ATR-dependent phosphorylation of Chk1 and cell-cycle arrest, consistent with replication checkpoint activation. Further, replication checkpoint blockade via small-molecule inhibition of ATR kinase in cells expressing A3A led to apoptosis and cell death. Although DNA damage checkpoints are broadly activated in response to A3A activity, synthetic lethality was specific to ATR signaling via Chk1 and did not occur with ATM inhibition. Our findings identify elevation of A3A expression in AML cells, enabling apoptotic sensitivity to inhibitors of the DNA replication checkpoint and suggesting it as a candidate biomarker for ATR inhibitor therapy. Cancer Res; 77(17); 4579-88. ©2017 AACR.
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Affiliation(s)
- Abby M Green
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Konstantin Budagyan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katharina E Hayer
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Morgann A Reed
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Milan R Savani
- University of Pennsylvania College of Arts and Sciences, Philadelphia, Pennsylvania
| | - Gerald B Wertheim
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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34
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Kim E, Cheng Y, Bolton-Gillespie E, Cai X, Ma C, Tarangelo A, Le L, Jambhekar M, Raman P, Hayer KE, Wertheim G, Speck NA, Tong W, Viatour P. Rb family proteins enforce the homeostasis of quiescent hematopoietic stem cells by repressing Socs3 expression. J Exp Med 2017; 214:1901-1912. [PMID: 28550162 PMCID: PMC5502420 DOI: 10.1084/jem.20160719] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 01/30/2017] [Accepted: 05/01/2017] [Indexed: 12/31/2022] Open
Abstract
The mechanisms regulating the homeostasis of HSCs remain poorly understood. Here, Kim et al. identify the Rb/E2f module as a central molecular hub in the regulation of cell cycle and homeostasis in HSCs. This mechanism drives the enforced differentiation of proliferative HSCs to avoid their unnecessary accumulation. Prolonged exit from quiescence by hematopoietic stem cells (HSCs) progressively impairs their homeostasis in the bone marrow through an unidentified mechanism. We show that Rb proteins, which are major enforcers of quiescence, maintain HSC homeostasis by positively regulating thrombopoietin (Tpo)-mediated Jak2 signaling. Rb family protein inactivation triggers the progressive E2f-mediated transactivation of Socs3, a potent inhibitor of Jak2 signaling, in cycling HSCs. Aberrant activation of Socs3 impairs Tpo signaling and leads to impaired HSC homeostasis. Therefore, Rb proteins act as a central hub of quiescence and homeostasis by coordinating the regulation of both cell cycle and Jak2 signaling in HSCs.
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Affiliation(s)
- Eunsun Kim
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ying Cheng
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Xiongwei Cai
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Connie Ma
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy Tarangelo
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Linh Le
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Madhumita Jambhekar
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Pichai Raman
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Gerald Wertheim
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Nancy A Speck
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Wei Tong
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Patrick Viatour
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics 2015; 31:3938-45. [PMID: 26338770 PMCID: PMC4673975 DOI: 10.1093/bioinformatics/btv488] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/17/2015] [Indexed: 01/26/2023] Open
Abstract
MOTIVATION Because of the advantages of RNA sequencing (RNA-Seq) over microarrays, it is gaining widespread popularity for highly parallel gene expression analysis. For example, RNA-Seq is expected to be able to provide accurate identification and quantification of full-length splice forms. A number of informatics packages have been developed for this purpose, but short reads make it a difficult problem in principle. Sequencing error and polymorphisms add further complications. It has become necessary to perform studies to determine which algorithms perform best and which if any algorithms perform adequately. However, there is a dearth of independent and unbiased benchmarking studies. Here we take an approach using both simulated and experimental benchmark data to evaluate their accuracy. RESULTS We conclude that most methods are inaccurate even using idealized data, and that no method is highly accurate once multiple splice forms, polymorphisms, intron signal, sequencing errors, alignment errors, annotation errors and other complicating factors are present. These results point to the pressing need for further algorithm development. AVAILABILITY AND IMPLEMENTATION Simulated datasets and other supporting information can be found at http://bioinf.itmat.upenn.edu/BEERS/bp2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Katharina E Hayer
- University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104
| | - Angel Pizarro
- Scientific Computing at Amazon Web Services, Seattle, WA 98108
| | | | | | - Gregory R Grant
- University of Pennsylvania, Institute for Translational Medicine and Therapeutics, Philadelphia, PA 19104, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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36
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Wolman MA, Jain RA, Marsden KC, Bell H, Skinner J, Hayer KE, Hogenesch JB, Granato M. A genome-wide screen identifies PAPP-AA-mediated IGFR signaling as a novel regulator of habituation learning. Neuron 2015; 85:1200-11. [PMID: 25754827 DOI: 10.1016/j.neuron.2015.02.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/06/2015] [Accepted: 02/12/2015] [Indexed: 01/15/2023]
Abstract
Habituation represents a fundamental form of learning, yet the underlying molecular genetic mechanisms are not well defined. Here we report on a genome-wide genetic screen, coupled with whole-genome sequencing, that identified 14 zebrafish startle habituation mutants including mutants of the vertebrate-specific gene pregnancy-associated plasma protein-aa (pappaa). PAPP-AA encodes an extracellular metalloprotease known to increase IGF bioavailability, thereby enhancing IGF receptor signaling. We find that pappaa is expressed by startle circuit neurons, and expression of wild-type but not a metalloprotease-inactive version of pappaa restores habituation in pappaa mutants. Furthermore, acutely inhibiting IGF1R function in wild-type reduces habituation, while activation of IGF1R downstream effectors in pappaa mutants restores habituation, demonstrating that pappaa promotes learning by acutely and locally increasing IGF bioavailability. In sum, our results define the first functional gene set for habituation learning in a vertebrate and identify PAPPAA-regulated IGF signaling as a novel mechanism regulating habituation learning.
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Affiliation(s)
- Marc A Wolman
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA; Department of Zoology, University of Wisconsin; 213 Zoology Research Building, 1117 West Johnson Street, Madison, WI 53706, USA
| | - Roshan A Jain
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Kurt C Marsden
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Hannah Bell
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Julianne Skinner
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Katharina E Hayer
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, 829 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - John B Hogenesch
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, 829 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - Michael Granato
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 1157 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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