1
|
Hopper MA, Wenzl K, Hartert KT, Krull JE, Dropik AR, Novak JP, Manske MK, Serres MR, Sarangi V, Larson MC, Maurer MJ, Yang ZZ, Paludo J, McPhail ED, Habermann TM, Link BK, Rimsza LM, Ansell SM, Cerhan JR, Jevremovic D, Novak AJ. Molecular classification and identification of an aggressive signature in low-grade B-cell lymphomas. Hematol Oncol 2023; 41:644-654. [PMID: 37254453 PMCID: PMC10592585 DOI: 10.1002/hon.3187] [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: 01/05/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023]
Abstract
Non-follicular low-grade B-cell lymphomas (LGBCL) are biologically diverse entities that share clinical and histologic features that make definitive pathologic categorization challenging. While most patients with LGBCL have an indolent course, some experience aggressive disease, highlighting additional heterogeneity across these subtypes. To investigate the potential for shared biology across subtypes, we performed RNA sequencing and applied machine learning approaches that identified five clusters of patients that grouped independently of subtype. One cluster was characterized by inferior outcome, upregulation of cell cycle genes, and increased tumor immune cell content. Integration of whole exome sequencing identified novel LGBCL mutations and enrichment of TNFAIP3 and BCL2 alterations in the poor survival cluster. Building on this, we further refined a transcriptomic signature associated with early clinical failure in two independent cohorts. Taken together, this study identifies unique clusters of LGBCL defined by novel gene expression signatures and immune profiles associated with outcome across diagnostic subtypes.
Collapse
Affiliation(s)
| | | | | | | | | | - Joseph P. Novak
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | | | | | | | - Melissa C. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Matthew J. Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | | | - Jonas Paludo
- Division of Hematology, Mayo Clinic, Rochester, MN
| | | | | | - Brian K. Link
- Division of Hematology, Oncology, and Bone & Marrow Transplantation, University of Iowa, Iowa City, IA
| | - Lisa M. Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ
| | | | - James R. Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Dragan Jevremovic
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | |
Collapse
|
2
|
Sabharwal A, Wishman MD, Cervera RL, Serres MR, Anderson JL, Holmberg SR, Kar B, Treichel AJ, Ichino N, Liu W, Yang J, Ding Y, Deng Y, Lacey JM, Laxen WJ, Loken PR, Oglesbee D, Farber SA, Clark KJ, Xu X, Ekker SC. Genetic therapy in a mitochondrial disease model suggests a critical role for liver dysfunction in mortality. eLife 2022; 11:e65488. [PMID: 36408801 PMCID: PMC9859037 DOI: 10.7554/elife.65488] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
The clinical and largely unpredictable heterogeneity of phenotypes in patients with mitochondrial disorders demonstrates the ongoing challenges in the understanding of this semi-autonomous organelle in biology and disease. Previously, we used the gene-breaking transposon to create 1200 transgenic zebrafish strains tagging protein-coding genes (Ichino et al., 2020), including the lrpprc locus. Here, we present and characterize a new genetic revertible animal model that recapitulates components of Leigh Syndrome French Canadian Type (LSFC), a mitochondrial disorder that includes diagnostic liver dysfunction. LSFC is caused by allelic variations in the LRPPRC gene, involved in mitochondrial mRNA polyadenylation and translation. lrpprc zebrafish homozygous mutants displayed biochemical and mitochondrial phenotypes similar to clinical manifestations observed in patients, including dysfunction in lipid homeostasis. We were able to rescue these phenotypes in the disease model using a liver-specific genetic model therapy, functionally demonstrating a previously under-recognized critical role for the liver in the pathophysiology of this disease.
Collapse
Affiliation(s)
- Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Mark D Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Roberto Lopez Cervera
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - MaKayla R Serres
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for ScienceBaltimoreUnited States
| | - Shannon R Holmberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Anthony J Treichel
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Weibin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Jingchun Yang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Yun Deng
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Jean M Lacey
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - William J Laxen
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - Perry R Loken
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - Devin Oglesbee
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic College of MedicineRochesterUnited States
| | - Steven A Farber
- Department of Embryology, Carnegie Institution for ScienceBaltimoreUnited States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of MedicineRochesterUnited States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of MedicineRochesterUnited States
| |
Collapse
|
3
|
Ichino N, Serres MR, Urban RM, Urban MD, Treichel AJ, Schaefbauer KJ, Greif LE, Varshney GK, Skuster KJ, McNulty MS, Daby CL, Wang Y, Liao HK, El-Rass S, Ding Y, Liu W, Anderson JL, Wishman MD, Sabharwal A, Schimmenti LA, Sivasubbu S, Balciunas D, Hammerschmidt M, Farber SA, Wen XY, Xu X, McGrail M, Essner JJ, Burgess SM, Clark KJ, Ekker SC. Building the vertebrate codex using the gene breaking protein trap library. eLife 2020; 9:54572. [PMID: 32779569 PMCID: PMC7486118 DOI: 10.7554/elife.54572] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 12/19/2019] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b, fras1, tnnt2a, edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated genes with 40 as potential new disease models. Severely reduced skeletal muscle Ca2+ transients in GBT ryr1b homozygous animals validated the ability to explore molecular mechanisms of genetic diseases. This GBT system facilitates novel functional genome annotation towards understanding cellular and molecular underpinnings of vertebrate biology and human disease.
Collapse
Affiliation(s)
- Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - MaKayla R Serres
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Rhianna M Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Mark D Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Anthony J Treichel
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Kyle J Schaefbauer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Lauren E Greif
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States.,Functional & Chemical Genomics Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Kimberly J Skuster
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Melissa S McNulty
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Camden L Daby
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Ying Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Hsin-Kai Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Suzan El-Rass
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Weibin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Mark D Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Lisa A Schimmenti
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Clinical Genomics, Mayo Clinic, Rochester, United States.,Department of Otorhinolaryngology, Mayo Clinic, Rochester, United States
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Darius Balciunas
- Department of Biology, Temple University, Philadelphia, United States
| | - Matthias Hammerschmidt
- Institute of Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
| | - Steven Arthur Farber
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| |
Collapse
|
4
|
Lee HB, Schwab TL, Sigafoos AN, Gauerke JL, Krug RG, Serres MR, Jacobs DC, Cotter RP, Das B, Petersen MO, Daby CL, Urban RM, Berry BC, Clark KJ. Novel zebrafish behavioral assay to identify modifiers of the rapid, nongenomic stress response. Genes Brain Behav 2019; 18:e12549. [PMID: 30588759 PMCID: PMC6446827 DOI: 10.1111/gbb.12549] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/30/2018] [Accepted: 12/18/2018] [Indexed: 12/23/2022]
Abstract
When vertebrates face acute stressors, their bodies rapidly undergo a repertoire of physiological and behavioral adaptations, which is termed the stress response. Rapid changes in heart rate and blood glucose levels occur via the interaction of glucocorticoids and their cognate receptors following hypothalamic-pituitary-adrenal axis activation. These physiological changes are observed within minutes of encountering a stressor and the rapid time domain rules out genomic responses that require gene expression changes. Although behavioral changes corresponding to physiological changes are commonly observed, it is not clearly understood to what extent hypothalamic-pituitary-adrenal axis activation dictates adaptive behavior. We hypothesized that rapid locomotor response to acute stressors in zebrafish requires hypothalamic-pituitary-interrenal (HPI) axis activation. In teleost fish, interrenal cells are functionally homologous to the adrenocortical layer. We derived eight frameshift mutants in genes involved in HPI axis function: two mutants in exon 2 of mc2r (adrenocorticotropic hormone receptor), five in exon 2 or 5 of nr3c1 (glucocorticoid receptor [GR]) and two in exon 2 of nr3c2 (mineralocorticoid receptor [MR]). Exposing larval zebrafish to mild environmental stressors, acute changes in salinity or light illumination, results in a rapid locomotor response. We show that this locomotor response requires a functioning HPI axis via the action of mc2r and the canonical GR encoded by nr3c1 gene, but not MR (nr3c2). Our rapid behavioral assay paradigm based on HPI axis biology can be used to screen for genetic and environmental modifiers of the hypothalamic-pituitary-adrenal axis and to investigate the effects of corticosteroids and their cognate receptor interactions on behavior.
Collapse
Affiliation(s)
- Han B. Lee
- Neuroscience Graduate ProgramMayo Clinic Graduate School of Biomedical SciencesRochesterMinnesota
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Ashley N. Sigafoos
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Jennifer L. Gauerke
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Randall G. Krug
- Neuroscience Graduate ProgramMayo Clinic Graduate School of Biomedical SciencesRochesterMinnesota
| | - MaKayla R. Serres
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Dakota C. Jacobs
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Ryan P. Cotter
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Biswadeep Das
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Morgan O. Petersen
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Camden L. Daby
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Rhianna M. Urban
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Bethany C. Berry
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| | - Karl J. Clark
- Neuroscience Graduate ProgramMayo Clinic Graduate School of Biomedical SciencesRochesterMinnesota
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesota
| |
Collapse
|