1
|
Czerminski JT, King OD, Lawrence JB. Large-scale organoid study suggests effects of trisomy 21 on early fetal neurodevelopment are more subtle than variability between isogenic lines and experiments. Front Neurosci 2023; 16:972201. [PMID: 36817096 PMCID: PMC9935940 DOI: 10.3389/fnins.2022.972201] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/08/2022] [Indexed: 02/05/2023] Open
Abstract
This study examines cortical organoids generated from a panel of isogenic trisomic and disomic iPSC lines (subclones) as a model of early fetal brain development in Down syndrome (DS). An initial experiment comparing organoids from one trisomic and one disomic line showed many genome-wide transcriptomic differences and modest differences in cell-type proportions, suggesting there may be a neurodevelopmental phenotype that is due to trisomy of chr21. To better control for multiple sources of variation, we undertook a highly robust study of ∼1,200 organoids using an expanded panel of six all-isogenic lines, three disomic, and three trisomic. The power of this experimental design was indicated by strong detection of the ∼1.5-fold difference in chr21 genes. However, the numerous expression differences in non-chr21 genes seen in the smaller experiment fell away, and the differences in cell-type representation between lines did not correlate with trisomy 21. Results suggest that the initial smaller experiment picked up differences between small organoid samples and individual isogenic lines, which "averaged out" in the larger panel of isogenic lines. Our results indicate that even when organoid and batch variability are better controlled for, variation between isogenic cell lines (even subclones) may obscure, or be conflated with, subtle neurodevelopmental phenotypes that may be present in ∼2nd trimester DS brain development. Interestingly, despite this variability between organoid batches and lines, and the "fetal stage" of these organoids, an increase in secreted Aβ40 peptide levels-an Alzheimer-related cellular phenotype-was more strongly associated with trisomy 21 status than were neurodevelopmental shifts in cell-type composition.
Collapse
Affiliation(s)
- Jan T. Czerminski
- Medical Scientist Training Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Oliver D. King
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States,Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States,*Correspondence: Jeanne B. Lawrence,
| |
Collapse
|
2
|
Campbell AE, Arjomand J, King OD, Tawil R, Jagannathan S. A Targeted Approach for Evaluating DUX4-Regulated Proteins as Potential Serum Biomarkers for Facioscapulohumeral Muscular Dystrophy Using Immunoassay Proteomics. J Neuromuscul Dis 2023; 10:1031-1040. [PMID: 37899061 PMCID: PMC10657687 DOI: 10.3233/jnd-221636] [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] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is a progressive myopathy caused by misexpression of the double homeobox 4 (DUX4) embryonic transcription factor in skeletal muscle. Identifying quantitative and minimally invasive FSHD biomarkers to report on DUX4 activity will significantly accelerate therapeutic development. OBJECTIVE The goal of this study was to analyze secreted proteins known to be induced by DUX4 using the commercially available Olink Proteomics platform in order to identify potential blood-based molecular FSHD biomarkers. METHODS We used high-throughput, multiplex immunoassays from Olink Proteomics to measure the levels of several known DUX4-induced genes in a cellular myoblast model of FSHD, in FSHD patient-derived myotube cell cultures, and in serum from individuals with FSHD. Levels of other proteins on the Olink Proteomics panels containing these DUX4 targets were also examined in secondary exploratory analysis. RESULTS Placental alkaline phosphatase (ALPP) levels correlated with DUX4 expression in both cell-based FSHD systems but did not distinguish FSHD patient serum from unaffected controls. CONCLUSIONS ALPP, as measured with the Olink Proteomics platform, is not a promising FSHD serum biomarker candidate but could be utilized to evaluate DUX4 activity in discovery research efforts.
Collapse
Affiliation(s)
- Amy E. Campbell
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Oliver D. King
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
3
|
Krishnan G, Raitcheva D, Bartlett D, Prudencio M, McKenna-Yasek DM, Douthwright C, Oskarsson BE, Ladha S, King OD, Barmada SJ, Miller TM, Bowser R, Watts JK, Petrucelli L, Brown RH, Kankel MW, Gao FB. Poly(GR) and poly(GA) in cerebrospinal fluid as potential biomarkers for C9ORF72-ALS/FTD. Nat Commun 2022; 13:2799. [PMID: 35589711 PMCID: PMC9119980 DOI: 10.1038/s41467-022-30387-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 11/14/2021] [Accepted: 04/29/2022] [Indexed: 11/09/2022] Open
Abstract
GGGGCC repeat expansion in C9ORF72, which can be translated in both sense and antisense directions into five dipeptide repeat (DPR) proteins, including poly(GP), poly(GR), and poly(GA), is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we developed sensitive assays that can detect poly(GA) and poly(GR) in the cerebrospinal fluid (CSF) of patients with C9ORF72 mutations. CSF poly(GA) and poly(GR) levels did not correlate with age at disease onset, disease duration, or rate of decline of ALS Functional Rating Scale, and the average levels of these DPR proteins were similar in symptomatic and pre-symptomatic patients with C9ORF72 mutations. However, in a patient with C9ORF72-ALS who was treated with antisense oligonucleotide (ASO) targeting the aberrant C9ORF72 transcript, CSF poly(GA) and poly(GR) levels decreased approximately 50% within 6 weeks, indicating they may serve as sensitive fluid-based biomarkers in studies directed against the production of GGGGCC repeat RNAs or DPR proteins.
Collapse
Affiliation(s)
- Gopinath Krishnan
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | - Daniel Bartlett
- Biomarkers, Clinical Sciences Biogen, Cambridge, MA, 02142, USA
| | | | - Diane M McKenna-Yasek
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Catherine Douthwright
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | | | - Shafeeq Ladha
- Departments of Neurology and Translational Neuroscience, St. Joseph's Hospital and Medical Center and Barrow Neurological Institute, 350W Thomas Road, Phoenix, AZ, 85013, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, 4005 BSRB, 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Timothy M Miller
- Department of Neurology, Washington University, Saint Louis, MI, 63110, USA
| | - Robert Bowser
- Departments of Neurology and Translational Neuroscience, St. Joseph's Hospital and Medical Center and Barrow Neurological Institute, 350W Thomas Road, Phoenix, AZ, 85013, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | | | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Mark W Kankel
- Neuromuscular & Movement Disorders, Biogen, Cambridge, MA, 02142, USA.
- Apple Tree Partners (ATP) Research Labs, Branford, CT, 06405, USA.
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
| |
Collapse
|
4
|
Guo D, Daman K, Chen JJC, Shi MJ, Yan J, Matijasevic Z, Rickard AM, Bennett MH, Kiselyov A, Zhou H, Bang AG, Wagner KR, Maehr R, King OD, Hayward LJ, Emerson CP. iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling. eLife 2022; 11:e70341. [PMID: 35076017 PMCID: PMC8789283 DOI: 10.7554/elife.70341] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/13/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle myoblasts (iMyoblasts) were generated from human induced pluripotent stem cells (iPSCs) using an efficient and reliable transgene-free induction and stem cell selection protocol. Immunofluorescence, flow cytometry, qPCR, digital RNA expression profiling, and scRNA-Seq studies identify iMyoblasts as a PAX3+/MYOD1+ skeletal myogenic lineage with a fetal-like transcriptome signature, distinct from adult muscle biopsy myoblasts (bMyoblasts) and iPSC-induced muscle progenitors. iMyoblasts can be stably propagated for >12 passages or 30 population doublings while retaining their dual commitment for myotube differentiation and regeneration of reserve cells. iMyoblasts also efficiently xenoengrafted into irradiated and injured mouse muscle where they undergo differentiation and fetal-adult MYH isoform switching, demonstrating their regulatory plasticity for adult muscle maturation in response to signals in the host muscle. Xenograft muscle retains PAX3+ muscle progenitors and can regenerate human muscle in response to secondary injury. As models of disease, iMyoblasts from individuals with Facioscapulohumeral Muscular Dystrophy revealed a previously unknown epigenetic regulatory mechanism controlling developmental expression of the pathological DUX4 gene. iMyoblasts from Limb-Girdle Muscular Dystrophy R7 and R9 and Walker Warburg Syndrome patients modeled their molecular disease pathologies and were responsive to small molecule and gene editing therapeutics. These findings establish the utility of iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease pathogenesis and for the development of muscle stem cell therapeutics.
Collapse
Affiliation(s)
- Dongsheng Guo
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Katelyn Daman
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Jennifer JC Chen
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Meng-Jiao Shi
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Jing Yan
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Zdenka Matijasevic
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Transgenic Animal Modeling Core, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | | | | | | | - Haowen Zhou
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Anne G Bang
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery InstituteLa JollaUnited States
| | - Kathryn R Wagner
- Center for Genetic Muscle Disorders, Kennedy Krieger InstituteBaltimoreUnited States
| | - René Maehr
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Oliver D King
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Lawrence J Hayward
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Charles P Emerson
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Li Weibo Institute for Rare Disease Research, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| |
Collapse
|
5
|
Lek A, Zhang Y, Woodman KG, Huang S, DeSimone AM, Cohen J, Ho V, Conner J, Mead L, Kodani A, Pakula A, Sanjana N, King OD, Jones PL, Wagner KR, Lek M, Kunkel LM. Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy. Sci Transl Med 2021; 12:12/536/eaay0271. [PMID: 32213627 DOI: 10.1126/scitranslmed.aay0271] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 12/23/2019] [Accepted: 03/03/2020] [Indexed: 12/13/2022]
Abstract
The emergence of CRISPR-Cas9 gene-editing technologies and genome-wide CRISPR-Cas9 libraries enables efficient unbiased genetic screening that can accelerate the process of therapeutic discovery for genetic disorders. Here, we demonstrate the utility of a genome-wide CRISPR-Cas9 loss-of-function library to identify therapeutic targets for facioscapulohumeral muscular dystrophy (FSHD), a genetically complex type of muscular dystrophy for which there is currently no treatment. In FSHD, both genetic and epigenetic changes lead to misexpression of DUX4, the FSHD causal gene that encodes the highly cytotoxic DUX4 protein. We performed a genome-wide CRISPR-Cas9 screen to identify genes whose loss-of-function conferred survival when DUX4 was expressed in muscle cells. Genes emerging from our screen illuminated a pathogenic link to the cellular hypoxia response, which was revealed to be the main driver of DUX4-induced cell death. Application of hypoxia signaling inhibitors resulted in increased DUX4 protein turnover and subsequent reduction of the cellular hypoxia response and cell death. In addition, these compounds proved successful in reducing FSHD disease biomarkers in patient myogenic lines, as well as improving structural and functional properties in two zebrafish models of FSHD. Our genome-wide perturbation of pathways affecting DUX4 expression has provided insight into key drivers of DUX4-induced pathogenesis and has identified existing compounds with potential therapeutic benefit for FSHD. Our experimental approach presents an accelerated paradigm toward mechanistic understanding and therapeutic discovery of a complex genetic disease, which may be translatable to other diseases with well-established phenotypic selection assays.
Collapse
Affiliation(s)
- Angela Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA. .,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuanfan Zhang
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Keryn G Woodman
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shushu Huang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA.,First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China.,Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Alec M DeSimone
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA.,Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Justin Cohen
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Vincent Ho
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - James Conner
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lillian Mead
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Andrew Kodani
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Pakula
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Neville Sanjana
- New York Genome Center, New York, NY 10013, USA.,Department of Biology, New York University, New York, NY 10003, USA
| | - Oliver D King
- Wellstone Muscular Dystrophy Program, Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Kathryn R Wagner
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA.,Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Louis M Kunkel
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA. .,Department of Pediatrics and Genetics, Harvard Medical School, Boston, MA 02115, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
6
|
Schulte F, King OD, Paster BJ, Moscicki AB, Yao TJ, Van Dyke RB, Shiboski C, Ryder M, Seage G, Hardt M. Salivary metabolite levels in perinatally HIV-infected youth with periodontal disease. Metabolomics 2020; 16:98. [PMID: 32915320 PMCID: PMC7784422 DOI: 10.1007/s11306-020-01719-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/28/2020] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Salivary metabolite profiles are altered in adults with HIV compared to their uninfected counterparts. Less is known about youth with HIV and how oral disorders that commonly accompany HIV infection impact salivary metabolite levels. OBJECTIVE As part of the Adolescent Master Protocol multi-site cohort study of the Pediatric HIV/AIDS Cohort Study (PHACS) network we compared the salivary metabolome of youth with perinatally-acquired HIV (PHIV) and youth HIV-exposed, but uninfected (PHEU) and determined whether metabolites differ in PHIV versus PHEU. METHODS We used three complementary targeted and discovery-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflows to characterize salivary metabolite levels in 20 PHIV and 20 PHEU youth with and without moderate periodontitis. We examined main effects associated with PHIV and periodontal disease, and the interaction between them. RESULTS We did not identify differences in salivary metabolite profiles that remained significant under stringent control for both multiple between-group comparisons and multiple metabolites. Levels of cadaverine, a known periodontitis-associated metabolite, were more abundant in individuals with periodontal disease with the difference being more pronounced in PHEU than PHIV. In the discovery-based dataset, we identified a total of 564 endogenous peptides in the metabolite extracts, showing that proteolytic processing and amino acid metabolism are important to consider in the context of HIV infection. CONCLUSION The salivary metabolite profiles of PHIV and PHEU youth were overall very similar. Individuals with periodontitis particularly among the PHEU youth had higher levels of cadaverine, suggesting that HIV infection, or its treatment, may influence the metabolism of oral bacteria.
Collapse
Affiliation(s)
- Fabian Schulte
- Forsyth Center for Salivary Diagnostics, Department of Applied Oral Sciences, The Forsyth Institute, 245 First Street, Cambridge, MA, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce J Paster
- Forsyth Center for Salivary Diagnostics, Department of Applied Oral Sciences, The Forsyth Institute, 245 First Street, Cambridge, MA, USA
| | - Anna-Barbara Moscicki
- Department of Pediatrics, Division of Adolescent and Young Adult Medicine, University of California, Los Angeles, CA, USA
| | - Tzy-Jyun Yao
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Caroline Shiboski
- Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA
| | - Mark Ryder
- Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA
| | - George Seage
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Markus Hardt
- Forsyth Center for Salivary Diagnostics, Department of Applied Oral Sciences, The Forsyth Institute, 245 First Street, Cambridge, MA, USA.
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA.
| | | |
Collapse
|
7
|
Batista AR, King OD, Reardon CP, Davis C, Shankaracharya, Philip V, Gray-Edwards H, Aronin N, Lutz C, Landers J, Sena-Esteves M. Ly6a Differential Expression in Blood-Brain Barrier Is Responsible for Strain Specific Central Nervous System Transduction Profile of AAV-PHP.B. Hum Gene Ther 2019; 31:90-102. [PMID: 31696742 DOI: 10.1089/hum.2019.186] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adeno-associated virus (AAV) gene therapy for neurological diseases was revolutionized by the discovery that AAV9 crosses the blood-brain barrier (BBB) after systemic administration. Transformative results have been documented in various inherited diseases, but overall neuronal transduction efficiency is relatively low. The recent development of AAV-PHP.B with ∼60-fold higher efficiency than AAV9 in transducing the adult mouse brain was the major first step toward acquiring the ability to deliver genes to the majority of cells in the central nervous system (CNS). However, little is known about the mechanism utilized by AAV to cross the BBB, and how it may diverge across species. In this study, we show that AAV-PHP.B is ineffective for systemic CNS gene transfer in the inbred strains BALB/cJ, BALB/cByJ, A/J, NOD/ShiLtJ, NZO/HILtJ, C3H/HeJ, and CBA/J mice, but it is highly potent in C57BL/6J, FVB/NJ, DBA/2J, 129S1/SvImJ, and AKR/J mice and also the outbred strain CD-1. We used the power of classical genetics to uncover the molecular mechanisms AAV-PHP.B engages to transduce CNS at high efficiency, and by quantitative trait locus mapping we identify a 6 Mb region in chromosome 15 with an logarithm of the odds (LOD) score ∼20, including single nucleotide polymorphisms in the coding region of 9 different genes. Comparison of the publicly available data on the genome sequence of 16 different mouse strains, combined with RNA-seq data analysis of brain microcapillary endothelia, led us to conclude that the expression level of Ly6a is likely the determining factor for differential efficacy of AAV-PHP.B in transducing the CNS across different mouse strains.
Collapse
Affiliation(s)
- Ana Rita Batista
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts.,Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Christopher P Reardon
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts.,Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Crystal Davis
- Rare and Orphan Disease Center, The Jackson Laboratory, Bar Harbor, Maine
| | - Shankaracharya
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Vivek Philip
- Rare and Orphan Disease Center, The Jackson Laboratory, Bar Harbor, Maine
| | - Heather Gray-Edwards
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Radiology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Neil Aronin
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Cathleen Lutz
- Rare and Orphan Disease Center, The Jackson Laboratory, Bar Harbor, Maine
| | - John Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Miguel Sena-Esteves
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts.,Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
| |
Collapse
|
8
|
Iyer S, Suresh S, Guo D, Daman K, Chen JCJ, Liu P, Zieger M, Luk K, Roscoe BP, Mueller C, King OD, Emerson CP, Wolfe SA. Precise therapeutic gene correction by a simple nuclease-induced double-stranded break. Nature 2019; 568:561-565. [PMID: 30944467 PMCID: PMC6483862 DOI: 10.1038/s41586-019-1076-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [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: 05/28/2018] [Accepted: 02/22/2019] [Indexed: 12/26/2022]
Abstract
Current programmable nuclease-based (e.g. CRISPR-Cas9) methods for precise correction of a disease-causing genetic mutation harness the Homology Directed Repair (HDR) pathway. However, this repair process requires co-delivery of an exogenous DNA donor to recode the sequence and can be inefficient in many cell types. Here, we show that disease-causing frameshift mutations resulting from microduplications can be efficiently reverted to the wild-type sequence simply by generating a double-strand break (DSB) near the center of the duplication. We demonstrate this in patient-derived cell lines for two diseases: Limb-Girdle Muscular Dystrophy 2G (LGMD2G)1 and Hermansky-Pudlak Syndrome Type 1 (HPS1)2. Clonal analysis of Streptococcus pyogenes Cas9 (SpyCas9) nuclease-treated LGMD2G iPSCs revealed that ~80% contained at least one wild-type allele and that this correction restored TCAP expression in LGMD2G iPSC-derived myotubes. Efficient genotypic correction was also observed upon SpyCas9 treatment of an HPS1 patient-derived B-lymphoblastoid cell line (B-LCL). Inhibition of PARP-1 (poly (ADP-ribose) polymerase) suppresses the nuclease-mediated collapse of the microduplication to the wild-type sequence, confirming that precise correction is mediated by the MMEJ (microhomology-mediated end joining) pathway. Analysis of editing by SpyCas9 and Lachnospiraceae bacterium ND2006 Cas12a (LbaCas12a) at non-pathogenic microduplications within the genome that range in length from 4 bp to 36 bp indicates that the correction strategy is broadly applicable to a wide range of microduplication lengths and can be initiated by a variety of nucleases. The simplicity, reliability and efficacy of this MMEJ-based therapeutic strategy should permit the development of nuclease-based gene correction therapies for a variety of diseases that are associated with microduplications.
Collapse
Affiliation(s)
- Sukanya Iyer
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sneha Suresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dongsheng Guo
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA
| | - Katelyn Daman
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennifer C J Chen
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA.,Office of the Vice-Principal (Research), Queen's University, Kingston, Ontario, Canada
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Marina Zieger
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Benjamin P Roscoe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.,COGEN Therapeutics, Cambridge, MA, USA
| | - Christian Mueller
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA.,Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA
| | - Charles P Emerson
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA. .,Wellstone Muscular Dystrophy Program, University of Massachusetts Medical School, Worcester, MA, USA. .,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA. .,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
| |
Collapse
|
9
|
Guo L, Kim HJ, Wang H, Monaghan J, Freyermuth F, Sung JC, O'Donovan K, Fare CM, Diaz Z, Singh N, Zhang ZC, Coughlin M, Sweeny EA, DeSantis ME, Jackrel ME, Rodell CB, Burdick JA, King OD, Gitler AD, Lagier-Tourenne C, Pandey UB, Chook YM, Taylor JP, Shorter J. Nuclear-Import Receptors Reverse Aberrant Phase Transitions of RNA-Binding Proteins with Prion-like Domains. Cell 2019; 173:677-692.e20. [PMID: 29677512 DOI: 10.1016/j.cell.2018.03.002] [Citation(s) in RCA: 309] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 11/22/2017] [Accepted: 02/28/2018] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) with prion-like domains (PrLDs) phase transition to functional liquids, which can mature into aberrant hydrogels composed of pathological fibrils that underpin fatal neurodegenerative disorders. Several nuclear RBPs with PrLDs, including TDP-43, FUS, hnRNPA1, and hnRNPA2, mislocalize to cytoplasmic inclusions in neurodegenerative disorders, and mutations in their PrLDs can accelerate fibrillization and cause disease. Here, we establish that nuclear-import receptors (NIRs) specifically chaperone and potently disaggregate wild-type and disease-linked RBPs bearing a NLS. Karyopherin-β2 (also called Transportin-1) engages PY-NLSs to inhibit and reverse FUS, TAF15, EWSR1, hnRNPA1, and hnRNPA2 fibrillization, whereas Importin-α plus Karyopherin-β1 prevent and reverse TDP-43 fibrillization. Remarkably, Karyopherin-β2 dissolves phase-separated liquids and aberrant fibrillar hydrogels formed by FUS and hnRNPA1. In vivo, Karyopherin-β2 prevents RBPs with PY-NLSs accumulating in stress granules, restores nuclear RBP localization and function, and rescues degeneration caused by disease-linked FUS and hnRNPA2. Thus, NIRs therapeutically restore RBP homeostasis and mitigate neurodegeneration.
Collapse
Affiliation(s)
- Lin Guo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38120, USA
| | - Hejia Wang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Monaghan
- Department of Pediatrics, Child Neurology and Neurobiology, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Fernande Freyermuth
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
| | - Julie C Sung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin O'Donovan
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38120, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zamia Diaz
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nikita Singh
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zi Chao Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Institute of Life Sciences, Southeast University, Nanjing, 210096 Jiangsu, China
| | - Maura Coughlin
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38120, USA
| | - Elizabeth A Sweeny
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Morgan E DeSantis
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meredith E Jackrel
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher B Rodell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason A Burdick
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Child Neurology and Neurobiology, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38120, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
10
|
Picariello T, Brown JM, Hou Y, Swank G, Cochran DA, King OD, Lechtreck K, Pazour GJ, Witman GB. A global analysis of IFT-A function reveals specialization for transport of membrane-associated proteins into cilia. J Cell Sci 2019; 132:jcs220749. [PMID: 30659111 PMCID: PMC6382014 DOI: 10.1242/jcs.220749] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 05/23/2018] [Accepted: 01/02/2019] [Indexed: 12/28/2022] Open
Abstract
Intraflagellar transport (IFT), which is essential for the formation and function of cilia in most organisms, is the trafficking of IFT trains (i.e. assemblies of IFT particles) that carry cargo within the cilium. Defects in IFT cause several human diseases. IFT trains contain the complexes IFT-A and IFT-B. To dissect the functions of these complexes, we studied a Chlamydomonas mutant that is null for the IFT-A protein IFT140. The mutation had no effect on IFT-B but destabilized IFT-A, preventing flagella assembly. Therefore, IFT-A assembly requires IFT140. Truncated IFT140, which lacks the N-terminal WD repeats of the protein, partially rescued IFT and supported formation of half-length flagella that contained normal levels of IFT-B but greatly reduced amounts of IFT-A. The axonemes of these flagella had normal ultrastructure and, as investigated by SDS-PAGE, normal composition. However, composition of the flagellar 'membrane+matrix' was abnormal. Analysis of the latter fraction by mass spectrometry revealed decreases in small GTPases, lipid-anchored proteins and cell signaling proteins. Thus, IFT-A is specialized for the import of membrane-associated proteins. Abnormal levels of the latter are likely to account for the multiple phenotypes of patients with defects in IFT140.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Tyler Picariello
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jason M Brown
- Department of Biology, Salem State University, Salem, MA 01970, USA
| | - Yuqing Hou
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Gregory Swank
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Deborah A Cochran
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Oliver D King
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - George B Witman
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| |
Collapse
|
11
|
Jones TI, King OD, Himeda CL, Homma S, Chen JCJ, Beermann ML, Yan C, Emerson CP, Miller JB, Wagner KR, Jones PL. Individual epigenetic status of the pathogenic D4Z4 macrosatellite correlates with disease in facioscapulohumeral muscular dystrophy. Clin Epigenetics 2015; 7:37. [PMID: 25904990 PMCID: PMC4405830 DOI: 10.1186/s13148-015-0072-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [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: 10/14/2014] [Accepted: 03/11/2015] [Indexed: 12/27/2022] Open
Abstract
Background Both forms of facioscapulohumeral muscular dystrophy (FSHD) are associated with aberrant epigenetic regulation of the chromosome 4q35 D4Z4 macrosatellite. Chromatin changes due to large deletions of heterochromatin (FSHD1) or mutations in chromatin regulatory proteins (FSHD2) lead to relaxation of epigenetic repression and increased expression of the deleterious double homeobox 4 (DUX4) gene encoded within the distal D4Z4 repeat. However, many individuals with the genetic requirements for FSHD remain asymptomatic throughout their lives. Here we investigated family cohorts of FSHD1 individuals who were either affected (manifesting) or without any discernible weakness (nonmanifesting/asymptomatic) and their unaffected family members to determine if individual epigenetic status and stability of repression at the contracted 4q35 D4Z4 array in myocytes correlates with FSHD disease. Results Family cohorts were analyzed for DNA methylation on the distal pathogenic 4q35 D4Z4 repeat on permissive A-type subtelomeres. We found DNA hypomethylation in FSHD1-affected subjects, hypermethylation in healthy controls, and distinctly intermediate levels of methylation in nonmanifesting subjects. We next tested if these differences in DNA methylation had functional relevance by assaying DUX4-fl expression and the stability of epigenetic repression of DUX4-fl in myogenic cells. Treatment with drugs that alter epigenetic status revealed that healthy cells were refractory to treatment, maintaining stable repression of DUX4, while FSHD1-affected cells were highly responsive to treatment and thus epigenetically poised to express DUX4. Myocytes from nonmanifesting subjects had significantly higher levels of DNA methylation and were more resistant to DUX4 activation in response to epigenetic drug treatment than cells from FSHD1-affected first-degree relatives containing the same contraction, indicating that the epigenetic status of the contracted D4Z4 array is reflective of disease. Conclusions The epigenetic status of the distal 4qA D4Z4 repeat correlates with FSHD disease; FSHD-affected subjects have hypomethylation, healthy unaffected subjects have hypermethylation, and nonmanifesting subjects have characteristically intermediate methylation. Thus, analysis of DNA methylation at the distal D4Z4 repeat could be used as a diagnostic indicator of developing clinical FSHD. In addition, the stability of epigenetic repression upstream of DUX4 expression is a key regulator of disease and a viable therapeutic target. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0072-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Takako I Jones
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Oliver D King
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Charis L Himeda
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Sachiko Homma
- Neuromuscular Biology & Disease Group, Departments of Neurology and Physiology & Biophysics, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118 USA
| | - Jennifer C J Chen
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Mary Lou Beermann
- Neuromuscular Biology & Disease Group, Departments of Neurology and Physiology & Biophysics, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118 USA
| | - Chi Yan
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; Key Lab of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan, 430070 People's Republic of China
| | - Charles P Emerson
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| | - Jeffrey B Miller
- Neuromuscular Biology & Disease Group, Departments of Neurology and Physiology & Biophysics, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118 USA
| | - Kathryn R Wagner
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA ; The Hugo W. Moser Research Institute, Kennedy Krieger Institute, and the Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205 USA
| | - Peter L Jones
- Department of Neurology and Department of Cell and Developmental Biology, The Wellstone Program, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development, Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, 31 Center Drive, Bethesda, MD USA
| |
Collapse
|
12
|
Jones TI, Yan C, Sapp PC, McKenna-Yasek D, Kang PB, Quinn C, Salameh JS, King OD, Jones PL. Identifying diagnostic DNA methylation profiles for facioscapulohumeral muscular dystrophy in blood and saliva using bisulfite sequencing. Clin Epigenetics 2014; 6:23. [PMID: 25400706 PMCID: PMC4232706 DOI: 10.1186/1868-7083-6-23] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [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: 07/10/2014] [Accepted: 10/17/2014] [Indexed: 12/20/2022] Open
Abstract
Background Facioscapulohumeral muscular dystrophy (FSHD) is linked to chromatin relaxation due to epigenetic changes at the 4q35 D4Z4 macrosatellite array. Molecular diagnostic criteria for FSHD are complex and involve analysis of high molecular weight (HMW) genomic DNA isolated from lymphocytes, followed by multiple restriction digestions, pulse-field gel electrophoresis (PFGE), and Southern blotting. A subject is genetically diagnosed as FSHD1 if one of the 4q alleles shows a contraction in the D4Z4 array to below 11 repeats, while maintaining at least 1 repeat, and the contraction is in cis with a disease-permissive A-type subtelomere. FSHD2 is contraction-independent and cannot be diagnosed or excluded by this common genetic diagnostic procedure. However, FSHD1 and FSHD2 are linked by epigenetic deregulation, assayed as DNA hypomethylation, of the D4Z4 array on FSHD-permissive alleles. We have developed a PCR-based assay that identifies the epigenetic signature for both types of FSHD, distinguishing FSHD1 from FSHD2, and can be performed on genomic DNA isolated from blood, saliva, or cultured cells. Results Samples were obtained from healthy controls or patients clinically diagnosed with FSHD, and include both FSHD1 and FSHD2. The genomic DNAs were subjected to bisulfite sequencing analysis for the distal 4q D4Z4 repeat with an A-type subtelomere and the DUX4 5’ promoter region. We compared genomic DNA isolated from saliva and blood from the same individuals and found similar epigenetic signatures. DNA hypomethylation was restricted to the contracted 4qA chromosome in FSHD1 patients while healthy control subjects were hypermethylated. Candidates for FSHD2 showed extreme DNA hypomethylation on the 4qA DUX4 gene body as well as all analyzed DUX4 5’ sequences. Importantly, our assay does not amplify the D4Z4 arrays with non-permissive B-type subtelomeres and accurately excludes the arrays with non-permissive A-type subtelomeres. Conclusions We have developed an assay to identify changes in DNA methylation on the pathogenic distal 4q D4Z4 repeat. We show that the DNA methylation profile of saliva reflects FSHD status. This assay can distinguish FSHD from healthy controls, differentiate FSHD1 from FSHD2, does not require HMW genomic DNA or PFGE, and can be performed on either cultured cells, tissue, blood, or saliva samples. Electronic supplementary material The online version of this article (doi:10.1186/1868-7083-6-23) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Takako I Jones
- The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Chi Yan
- The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; Key Lab of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 P.R. China
| | - Peter C Sapp
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Diane McKenna-Yasek
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Peter B Kang
- Department of Pediatrics, Division of Pediatric Neurology, University of Florida College of Medicine, 1600 SW Archer Road, Gainesville, FL 32607 USA
| | - Colin Quinn
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; Department of Neurology, Hospital of the University of Pennsylvania, 3400 Spruce St, 3 Gates, Philadelphia, PA 19104 USA
| | - Johnny S Salameh
- The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Oliver D King
- The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| | - Peter L Jones
- The Wellstone Program & The Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA ; The Eunice Kennedy Shriver National Institute of Child Health and Human Development Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655 USA
| |
Collapse
|
13
|
Lancaster AK, Nutter-Upham A, Lindquist S, King OD. PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. Bioinformatics 2014; 30:2501-2. [PMID: 24825614 DOI: 10.1093/bioinformatics/btu310] [Citation(s) in RCA: 312] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED Prions are self-templating protein aggregates that stably perpetuate distinct biological states and are of keen interest to researchers in both evolutionary and biomedical science. The best understood prions are from yeast and have a prion-forming domain with strongly biased amino acid composition, most notably enriched for Q or N. PLAAC is a web application that scans protein sequences for domains with P: rion- L: ike A: mino A: cid C: omposition. Users can upload sequence files, or paste sequences directly into a textbox. PLAAC ranks the input sequences by several summary scores and allows scores along sequences to be visualized. Text output files can be downloaded for further analyses, and visualizations saved in PDF and PNG formats. AVAILABILITY AND IMPLEMENTATION http://plaac.wi.mit.edu/. The Ruby-based web framework and the command-line software (implemented in Java, with visualization routines in R) are available at http://github.com/whitehead/plaac under the MIT license. All software can be run under OS X, Windows and Unix.
Collapse
Affiliation(s)
- Alex K Lancaster
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Andrew Nutter-Upham
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Oliver D King
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| |
Collapse
|
14
|
McLellan CA, Whitesell L, King OD, Lancaster AK, Mazitschek R, Lindquist S. Correction to Inhibiting GPI Anchor Biosynthesis in Fungi Stresses the Endoplasmic Reticulum and Enhances Immunogenicity. ACS Chem Biol 2014. [DOI: 10.1021/cb5000339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Zhang Y, King OD, Rahimov F, Jones TI, Ward CW, Kerr JP, Liu N, Emerson CP, Kunkel LM, Partridge TA, Wagner KR. Human skeletal muscle xenograft as a new preclinical model for muscle disorders. Hum Mol Genet 2014; 23:3180-8. [PMID: 24452336 DOI: 10.1093/hmg/ddu028] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Development of novel therapeutics requires good animal models of disease. Disorders for which good animal models do not exist have very few drugs in development or clinical trial. Even where there are accepted, albeit imperfect models, the leap from promising preclinical drug results to positive clinical trials commonly fails, including in disorders of skeletal muscle. The main alternative model for early drug development, tissue culture, lacks both the architecture and, usually, the metabolic fidelity of the normal tissue in vivo. Herein, we demonstrate the feasibility and validity of human to mouse xenografts as a preclinical model of myopathy. Human skeletal muscle biopsies transplanted into the anterior tibial compartment of the hindlimbs of NOD-Rag1(null) IL2rγ(null) immunodeficient host mice regenerate new vascularized and innervated myofibers from human myogenic precursor cells. The grafts exhibit contractile and calcium release behavior, characteristic of functional muscle tissue. The validity of the human graft as a model of facioscapulohumeral muscular dystrophy is demonstrated in disease biomarker studies, showing that gene expression profiles of xenografts mirror those of the fresh donor biopsies. These findings illustrate the value of a new experimental model of muscle disease, the human muscle xenograft in mice, as a feasible and valid preclinical tool to better investigate the pathogenesis of human genetic myopathies and to more accurately predict their response to novel therapeutics.
Collapse
Affiliation(s)
- Yuanfan Zhang
- The Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA Graduate Program in Cellular and Molecular Medicine and
| | - Oliver D King
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Takako I Jones
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Jaclyn P Kerr
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and
| | - Naili Liu
- The Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Charles P Emerson
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Louis M Kunkel
- Program in Genomics, Division of Genetics, and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Terence A Partridge
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA
| | - Kathryn R Wagner
- The Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205, USA Graduate Program in Cellular and Molecular Medicine and Departments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
16
|
Paez-Cortez J, Krishnan R, Arno A, Aven L, Ram-Mohan S, Patel KR, Lu J, King OD, Ai X, Fine A. A new approach for the study of lung smooth muscle phenotypes and its application in a murine model of allergic airway inflammation. PLoS One 2013; 8:e74469. [PMID: 24040256 PMCID: PMC3767675 DOI: 10.1371/journal.pone.0074469] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/01/2013] [Indexed: 01/09/2023] Open
Abstract
Phenotypes of lung smooth muscle cells in health and disease are poorly characterized. This is due, in part, to a lack of methodologies that allow for the independent and direct isolation of bronchial smooth muscle cells (BSMCs) and vascular smooth muscle cells (VSMCs) from the lung. In this paper, we describe the development of a bi-fluorescent mouse that permits purification of these two cell populations by cell sorting. By subjecting this mouse to an acute allergen based-model of airway inflammation that exhibits many features of asthma, we utilized this tool to characterize the phenotype of so-called asthmatic BSMCs. First, we examined the biophysical properties of single BSMCs from allergen sensitized mice and found increases in basal tone and cell size that were sustained ex vivo. We then generated for the first time, a comprehensive characterization of the global gene expression changes in BSMCs isolated from the bi-fluorescent mice with allergic airway inflammation. Using statistical methods and pathway analysis, we identified a number of differentially expressed mRNAs in BSMCs from allergen sensitized mice that code for key candidate proteins underlying changes in matrix formation, contractility, and immune responses. Ultimately, this tool will provide direction and guidance for the logical development of new markers and approaches for studying human lung smooth muscle.
Collapse
MESH Headings
- Allergens/immunology
- Animals
- Asthma/genetics
- Asthma/immunology
- Asthma/pathology
- Bronchi/immunology
- Bronchi/metabolism
- Bronchi/pathology
- Bronchial Hyperreactivity/genetics
- Bronchial Hyperreactivity/immunology
- Bronchial Hyperreactivity/pathology
- Cell Size
- Disease Models, Animal
- Fluorescence
- Gene Expression
- Gene Expression Profiling
- Humans
- Immunization
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/pathology
- Mice
- Mice, Transgenic
- Muscle, Smooth, Vascular/immunology
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/immunology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Ovalbumin/immunology
- Phenotype
- Proteome/genetics
- Proteome/immunology
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Single-Cell Analysis
Collapse
Affiliation(s)
- Jesus Paez-Cortez
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ramaswamy Krishnan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Anneliese Arno
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Linh Aven
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Sumati Ram-Mohan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kruti R. Patel
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Jining Lu
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Oliver D. King
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Xingbin Ai
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Alan Fine
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
17
|
Chesi A, Staahl BT, Jovicic A, Couthouis J, Fasolino M, Raphael AR, Yamazaki T, Elias L, Polak M, Kelly C, Williams KL, Fifita JA, Maragakis NJ, Nicholson GA, King OD, Reed R, Crabtree GR, Blair IP, Glass JD, Gitler AD. Exome sequencing to identify de novo mutations in sporadic ALS trios. Nat Neurosci 2013; 16:851-5. [PMID: 23708140 PMCID: PMC3709464 DOI: 10.1038/nn.3412] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [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: 03/05/2013] [Accepted: 05/01/2013] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease whose causes are still poorly understood. To identify additional genetic risk factors, we assessed the role of de novo mutations in ALS by sequencing the exomes of 47 ALS patients and both of their unaffected parents (n = 141 exomes). We found that amino acid-altering de novo mutations were enriched in genes encoding chromatin regulators, including the neuronal chromatin remodeling complex (nBAF) component SS18L1 (also known as CREST). CREST mutations inhibited activity-dependent neurite outgrowth in primary neurons, and CREST associated with the ALS protein FUS. These findings expand our understanding of the ALS genetic landscape and provide a resource for future studies into the pathogenic mechanisms contributing to sporadic ALS.
Collapse
Affiliation(s)
- Alessandra Chesi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Brett T. Staahl
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ana Jovicic
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Maria Fasolino
- Neuroscience Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104
| | - Alya R. Raphael
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Tomohiro Yamazaki
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Laura Elias
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Meraida Polak
- Department of Neurology, Emory University, Atlanta, GA 30322
| | - Crystal Kelly
- Department of Neurology, Emory University, Atlanta, GA 30322
| | - Kelly L. Williams
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Jennifer A. Fifita
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicholas J. Maragakis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Garth A. Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Oliver D. King
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Gerald R. Crabtree
- Howard Hughes Medical Institute and Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ian P. Blair
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, 2139, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- Australian School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| |
Collapse
|
18
|
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal human neurodegenerative disease affecting primarily motor neurons. Two RNA-binding proteins, TDP-43 and FUS, aggregate in the degenerating motor neurons of ALS patients, and mutations in the genes encoding these proteins cause some forms of ALS. TDP-43 and FUS and several related RNA-binding proteins harbor aggregation-promoting prion-like domains that allow them to rapidly self-associate. This property is critical for the formation and dynamics of cellular ribonucleoprotein granules, the crucibles of RNA metabolism and homeostasis. Recent work connecting TDP-43 and FUS to stress granules has suggested how this cellular pathway, which involves protein aggregation as part of its normal function, might be coopted during disease pathogenesis.
Collapse
Affiliation(s)
- Yun R Li
- Medical Scientist Training Program and, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | |
Collapse
|
19
|
Stadler G, Rahimov F, King OD, Chen JCJ, Robin JD, Wagner KR, Shay JW, Emerson CP, Wright WE. Telomere position effect regulates DUX4 in human facioscapulohumeral muscular dystrophy. Nat Struct Mol Biol 2013; 20:671-8. [PMID: 23644600 PMCID: PMC3711615 DOI: 10.1038/nsmb.2571] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/19/2013] [Indexed: 11/09/2022]
Abstract
Telomeres may regulate human disease by at least two independent mechanisms. First, replicative senescence occurs once short telomeres generate DNA-damage signals that produce a barrier to tumor progression. Second, telomere position effects (TPE) could change gene expression at intermediate telomere lengths in cultured human cells. Here we report that telomere length may contribute to the pathogenesis of facioscapulohumeral muscular dystrophy (FSHD). FSHD is a late-onset disease genetically residing only 25-60 kilobases from the end of chromosome 4q. We used a floxable telomerase to generate isogenic clones with different telomere lengths from affected patients and their unaffected siblings. DUX4, the primary candidate for FSHD pathogenesis, is upregulated over ten-fold in FSHD myoblasts and myotubes with short telomeres, and its expression is inversely proportional to telomere length. FSHD may be the first known human disease in which TPE contributes to age-related phenotype.
Collapse
Affiliation(s)
- Guido Stadler
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Kim HJ, Kim NC, Wang YD, Scarborough EA, Moore J, Diaz Z, MacLea KS, Freibaum B, Li S, Molliex A, Kanagaraj AP, Carter R, Boylan KB, Wojtas AM, Rademakers R, Pinkus JL, Greenberg SA, Trojanowski JQ, Traynor BJ, Smith BN, Topp S, Gkazi AS, Miller J, Shaw CE, Kottlors M, Kirschner J, Pestronk A, Li YR, Ford AF, Gitler AD, Benatar M, King OD, Kimonis VE, Ross ED, Weihl CC, Shorter J, Taylor JP. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS. Nature 2013; 495:467-73. [PMID: 23455423 PMCID: PMC3756911 DOI: 10.1038/nature11922] [Citation(s) in RCA: 1067] [Impact Index Per Article: 97.0] [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: 01/05/2012] [Accepted: 01/17/2013] [Indexed: 01/18/2023]
Abstract
Algorithms designed to identify canonical yeast prions predict that around 250 human proteins, including several RNA-binding proteins associated with neurodegenerative disease, harbour a distinctive prion-like domain (PrLD) enriched in uncharged polar amino acids and glycine. PrLDs in RNA-binding proteins are essential for the assembly of ribonucleoprotein granules. However, the interplay between human PrLD function and disease is not understood. Here we define pathogenic mutations in PrLDs of heterogeneous nuclear ribonucleoproteins (hnRNPs) A2B1 and A1 in families with inherited degeneration affecting muscle, brain, motor neuron and bone, and in one case of familial amyotrophic lateral sclerosis. Wild-type hnRNPA2 (the most abundant isoform of hnRNPA2B1) and hnRNPA1 show an intrinsic tendency to assemble into self-seeding fibrils, which is exacerbated by the disease mutations. Indeed, the pathogenic mutations strengthen a 'steric zipper' motif in the PrLD, which accelerates the formation of self-seeding fibrils that cross-seed polymerization of wild-type hnRNP. Notably, the disease mutations promote excess incorporation of hnRNPA2 and hnRNPA1 into stress granules and drive the formation of cytoplasmic inclusions in animal models that recapitulate the human pathology. Thus, dysregulated polymerization caused by a potent mutant steric zipper motif in a PrLD can initiate degenerative disease. Related proteins with PrLDs should therefore be considered candidates for initiating and perhaps propagating proteinopathies of muscle, brain, motor neuron and bone.
Collapse
Affiliation(s)
- Hong Joo Kim
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Nam Chul Kim
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Yong-Dong Wang
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Emily A. Scarborough
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer Moore
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Zamia Diaz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyle S. MacLea
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO 80523, USA
| | - Brian Freibaum
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Songqing Li
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Amandine Molliex
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Anderson P. Kanagaraj
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Robert Carter
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| | - Kevin B. Boylan
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jack L. Pinkus
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steven A. Greenberg
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John Q. Trojanowski
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bryan J. Traynor
- Neuromuscular Diseases Research Group, Laboratory of Neurogenetics, Porter Neuroscience Building, NIA, NIH, Bethesda, MD 20892, USA
| | - Bradley N. Smith
- Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simon Topp
- King’s College London Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, London SE5 8AF, UK
| | - Athina-Soragia Gkazi
- King’s College London Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, London SE5 8AF, UK
| | - Jack Miller
- King’s College London Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, London SE5 8AF, UK
| | - Christopher E. Shaw
- King’s College London Centre for Neurodegeneration Research, Department of Clinical Neuroscience, Institute of Psychiatry, London SE5 8AF, UK
| | - Michael Kottlors
- Division of Neuropediatrics and Muscle Disorders, University Children's Hospital Freiburg, Freiburg, Germany
| | - Janbernd Kirschner
- Division of Neuropediatrics and Muscle Disorders, University Children's Hospital Freiburg, Freiburg, Germany
| | - Alan Pestronk
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Yun R. Li
- Medical Scientist Training Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alice Flynn Ford
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Benatar
- Neurology Department, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Oliver D. King
- Boston Biomedical Research Institute, Watertown, MA 02472, USA
| | - Virginia E. Kimonis
- Department of Pediatrics, Division of Genetics and Metabolism, University of California-Irvine, 2501 Hewitt Hall, Irvine, CA, 92696, USA
| | - Eric D. Ross
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO 80523, USA
| | - Conrad C. Weihl
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J. Paul Taylor
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38120, USA
| |
Collapse
|
21
|
Stadler G, King OD, Robin JD, Shay JW, Wright WE. Facioscapulohumeral muscular dystrophy: Are telomeres the end of the story? Rare Dis 2013; 1:e26142. [PMID: 25003004 PMCID: PMC3927483 DOI: 10.4161/rdis.26142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 07/08/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 01/01/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a progressive myopathy with a relatively late age of onset (usually in the late teens) compared with Duchenne and many other muscular dystrophies. The current FSHD disease model postulates that contraction of the D4Z4 array at chromosome 4q35 leads to a more open chromatin conformation in that region and allows transcription of the DUX4 gene. DUX4 mRNA is stable only when transcribed from certain haplotypes that contain a polyadenylation signal. DUX4 protein is hypothesized to cause FSHD by mediating cytotoxicity and impairing skeletal muscle differentiation. We recently showed in a cell culture model that DUX4 expression is regulated by telomere length, suggesting that telomere shortening during aging may be partially responsible for the delayed onset and progressive nature of FSHD. We here put our data in the context of other recent findings arguing that progressive telomere shortening may play a critical role in FSHD but is not the whole story and that the current disease model needs additional refinement.
Collapse
Affiliation(s)
- Guido Stadler
- Department of Cell Biology; University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Oliver D King
- Wellstone Program; Department of Cell & Developmental Biology; University of Massachusetts Medical School; Worcester, MA USA
| | - Jerome D Robin
- Department of Cell Biology; University of Texas Southwestern Medical Center; Dallas, TX USA
| | - Jerry W Shay
- Department of Cell Biology; University of Texas Southwestern Medical Center; Dallas, TX USA ; Center of Excellence in Genomic Medicine Research; King Abdulaziz University; Jeddah, Saudi Arabia
| | - Woodring E Wright
- Department of Cell Biology; University of Texas Southwestern Medical Center; Dallas, TX USA
| |
Collapse
|
22
|
Rahimov F, King OD, Leung DG, Bibat GM, Emerson CP, Kunkel LM, Wagner KR. Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers. Proc Natl Acad Sci U S A 2012; 109:16234-9. [PMID: 22988124 PMCID: PMC3479603 DOI: 10.1073/pnas.1209508109] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [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] [Indexed: 01/06/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a progressive neuromuscular disorder caused by contractions of repetitive elements within the macrosatellite D4Z4 on chromosome 4q35. The pathophysiology of FSHD is unknown and, as a result, there is currently no effective treatment available for this disease. To better understand the pathophysiology of FSHD and develop mRNA-based biomarkers of affected muscles, we compared global analysis of gene expression in two distinct muscles obtained from a large number of FSHD subjects and their unaffected first-degree relatives. Gene expression in two muscle types was analyzed using GeneChip Gene 1.0 ST arrays: biceps, which typically shows an early and severe disease involvement; and deltoid, which is relatively uninvolved. For both muscle types, the expression differences were mild: using relaxed cutoffs for differential expression (fold change ≥1.2; nominal P value <0.01), we identified 191 and 110 genes differentially expressed between affected and control samples of biceps and deltoid muscle tissues, respectively, with 29 genes in common. Controlling for a false-discovery rate of <0.25 reduced the number of differentially expressed genes in biceps to 188 and in deltoid to 7. Expression levels of 15 genes altered in this study were used as a "molecular signature" in a validation study of an additional 26 subjects and predicted them as FSHD or control with 90% accuracy based on biceps and 80% accuracy based on deltoids.
Collapse
Affiliation(s)
- Fedik Rahimov
- Program in Genomics, Division of Genetics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
| | - Oliver D. King
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
- Boston Biomedical Research Institute, Watertown, MA 02472
| | - Doris G. Leung
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205; Departments of
- Neurology and
| | - Genila M. Bibat
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205; Departments of
| | - Charles P. Emerson
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
- Boston Biomedical Research Institute, Watertown, MA 02472
| | - Louis M. Kunkel
- Program in Genomics, Division of Genetics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115
- The Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA 02115
| | - Kathryn R. Wagner
- Hugo W. Moser Research Institute at Kennedy Krieger Institute, Baltimore, MD 21205; Departments of
- Neurology and
- Neuroscience, The Johns Hopkins School of Medicine, Baltimore, MD 21205; and
| |
Collapse
|
23
|
McLellan CA, Whitesell L, King OD, Lancaster AK, Mazitschek R, Lindquist S. Inhibiting GPI anchor biosynthesis in fungi stresses the endoplasmic reticulum and enhances immunogenicity. ACS Chem Biol 2012; 7:1520-8. [PMID: 22724584 DOI: 10.1021/cb300235m] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In fungi, the anchoring of proteins to the plasma membrane via their covalent attachment to glycosylphosphatidylinositol (GPI) is essential and thus provides a valuable point of attack for the development of antifungal therapeutics. Unfortunately, studying the underlying biology of GPI-anchor synthesis is difficult, especially in medically relevant fungal pathogens because they are not genetically tractable. Compounding difficulties, many of the genes in this pathway are essential in Saccharomyces cerevisiae. Here, we report the discovery of a new small molecule christened gepinacin (for GPI acylation inhibitor) which selectively inhibits Gwt1, a critical acyltransferase required for the biosynthesis of fungal GPI anchors. After delineating the target specificity of gepinacin using genetic and biochemical techniques, we used it to probe key, therapeutically relevant consequences of disrupting GPI anchor metabolism in fungi. We found that, unlike all three major classes of antifungals in current use, the direct antimicrobial activity of this compound results predominantly from its ability to induce overwhelming stress to the endoplasmic reticulum. Gepinacin did not affect the viability of mammalian cells nor did it inhibit their orthologous acyltransferase. This enabled its use in co-culture experiments to examine Gwt1's effects on host-pathogen interactions. In isolates of Candida albicans, the most common fungal pathogen in humans, exposure to gepinacin at sublethal concentrations impaired filamentation and unmasked cell wall β-glucan to stimulate a pro-inflammatory cytokine response in macrophages. Gwt1 is a promising antifungal drug target, and gepanacin is a useful probe for studying how disrupting GPI-anchor synthesis impairs viability and alters host-pathogen interactions in genetically intractable fungi.
Collapse
Affiliation(s)
- Catherine A. McLellan
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge,
Massachusetts 02142, United States
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge,
Massachusetts 02142, United States
| | - Oliver D. King
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, Massachusetts
02472, United States
| | - Alex K. Lancaster
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge,
Massachusetts 02142, United States
| | - Ralph Mazitschek
- Center
for Systems Biology, Massachusetts General Hospital, Richard B. Simches
Research Center, 185 Cambridge Street, Suite 5.210, Boston, Massachusetts
02114, United States
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge,
Massachusetts 02142, United States
| |
Collapse
|
24
|
Gallardo CM, Gunapala KM, King OD, Steele AD. Daily scheduled high fat meals moderately entrain behavioral anticipatory activity, body temperature, and hypothalamic c-Fos activation. PLoS One 2012; 7:e41161. [PMID: 22815954 PMCID: PMC3397999 DOI: 10.1371/journal.pone.0041161] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/18/2012] [Indexed: 11/19/2022] Open
Abstract
When fed in restricted amounts, rodents show robust activity in the hours preceding expected meal delivery. This process, termed food anticipatory activity (FAA), is independent of the light-entrained clock, the suprachiasmatic nucleus, yet beyond this basic observation there is little agreement on the neuronal underpinnings of FAA. One complication in studying FAA using a calorie restriction model is that much of the brain is activated in response to this strong hunger signal. Thus, daily timed access to palatable meals in the presence of continuous access to standard chow has been employed as a model to study FAA in rats. In order to exploit the extensive genetic resources available in the murine system we extended this model to mice, which will anticipate rodent high fat diet but not chocolate or other sweet daily meals (Hsu, Patton, Mistlberger, and Steele; 2010, PLoS ONE e12903). In this study we test additional fatty meals, including peanut butter and cheese, both of which induced modest FAA. Measurement of core body temperature revealed a moderate preprandial increase in temperature in mice fed high fat diet but entrainment due to handling complicated interpretation of these results. Finally, we examined activation patterns of neurons by immunostaining for the immediate early gene c-Fos and observed a modest amount of entrainment of gene expression in the hypothalamus of mice fed a daily fatty palatable meal.
Collapse
Affiliation(s)
- Christian M. Gallardo
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Keith M. Gunapala
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Oliver D. King
- Boston Biomedical Research Institute, Watertown, Massachusetts, United States of America
| | - Andrew D. Steele
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
| |
Collapse
|
25
|
Jones TI, Chen JCJ, Rahimov F, Homma S, Arashiro P, Beermann ML, King OD, Miller JB, Kunkel LM, Emerson CP, Wagner KR, Jones PL. Facioscapulohumeral muscular dystrophy family studies of DUX4 expression: evidence for disease modifiers and a quantitative model of pathogenesis. Hum Mol Genet 2012; 21:4419-30. [PMID: 22798623 DOI: 10.1093/hmg/dds284] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), the most prevalent myopathy afflicting both children and adults, is predominantly associated with contractions in the 4q35-localized macrosatellite D4Z4 repeat array. Recent studies have proposed that FSHD pathology is caused by the misexpression of the DUX4 (double homeobox 4) gene resulting in production of a pathogenic protein, DUX4-FL, which has been detected in FSHD, but not in unaffected control myogenic cells and muscle tissue. Here, we report the analysis of DUX4 mRNA and protein expression in a much larger collection of myogenic cells and muscle biopsies derived from biceps and deltoid muscles of FSHD affected subjects and their unaffected first-degree relatives. We confirmed that stable DUX4-fl mRNA and protein were expressed in myogenic cells and muscle tissues derived from FSHD affected subjects, including several genetically diagnosed adult FSHD subjects yet to show clinical manifestations of the disease in the assayed muscles. In addition, we report DUX4-fl mRNA and protein expression in muscle biopsies and myogenic cells from genetically unaffected relatives of the FSHD subjects, although at a significantly lower frequency. These results establish that DUX4-fl expression per se is not sufficient for FSHD muscle pathology and indicate that quantitative modifiers of DUX4-fl expression and/or function and family genetic background are determinants of FSHD muscle disease progression.
Collapse
|
26
|
Luby MD, Hsu CT, Shuster SA, Gallardo CM, Mistlberger RE, King OD, Steele AD. Food anticipatory activity behavior of mice across a wide range of circadian and non-circadian intervals. PLoS One 2012; 7:e37992. [PMID: 22662260 PMCID: PMC3360658 DOI: 10.1371/journal.pone.0037992] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/01/2012] [Indexed: 11/19/2022] Open
Abstract
When rodents are fed in a limited amount during the daytime, they rapidly redistribute some of their nocturnal activity to the time preceding the delivery of food. In rats, anticipation of a daily meal has been interpreted as a circadian rhythm controlled by a food-entrained oscillator (FEO) with circadian limits to entrainment. Lesion experiments place this FEO outside of the light-entrainable circadian pacemaker in the suprachiasmatic nucleus. Mice also anticipate a fixed daily meal, but circadian limits to entrainment and anticipation of more than 2 daily meals, have not been assessed. We used a video-based behavior recognition system to quantify food anticipatory activity in mice receiving 2, 3, or 6 daily meals at intervals of 12, 8, or 4-hours (h). Individual mice were able to anticipate as many as 4 of 6 daily meals, and anticipation persisted during meal omission tests. On the 6 meal schedule, pre-prandial activity and body temperature were poorly correlated, suggesting independent regulation. Mice showed a limited ability to anticipate an 18 h feeding schedule. Finally, mice showed concurrent circadian and sub-hourly anticipation when provided with 6 small meals, at 30 minute intervals, at a fixed time of day. These results indicate that mice can anticipate feeding opportunities at a fixed time of day across a wide range of intervals not previously associated with anticipatory behavior in studies of rats. The methods described here can be exploited to determine the extent to which timing of different intervals in mice relies on common or distinct neural and molecular mechanisms.
Collapse
Affiliation(s)
- Matthew D. Luby
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Cynthia T. Hsu
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Scott A. Shuster
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Christian M. Gallardo
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Ralph E. Mistlberger
- Department of Psychology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Oliver D. King
- Boston Biomedical Research Institute, Watertown, Massachusetts, United States of America
| | - Andrew D. Steele
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
| |
Collapse
|
27
|
Zarringhalam K, Ka M, Kook YH, Terranova JI, Suh Y, King OD, Um M. An open system for automatic home-cage behavioral analysis and its application to male and female mouse models of Huntington's disease. Behav Brain Res 2012; 229:216-25. [DOI: 10.1016/j.bbr.2012.01.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 01/01/2012] [Accepted: 01/05/2012] [Indexed: 12/13/2022]
|
28
|
Couthouis J, Hart MP, Erion R, King OD, Diaz Z, Nakaya T, Ibrahim F, Kim HJ, Mojsilovic-Petrovic J, Panossian S, Kim CE, Frackelton EC, Solski JA, Williams KL, Clay-Falcone D, Elman L, McCluskey L, Greene R, Hakonarson H, Kalb RG, Lee VMY, Trojanowski JQ, Nicholson GA, Blair IP, Bonini NM, Van Deerlin VM, Mourelatos Z, Shorter J, Gitler AD. Evaluating the role of the FUS/TLS-related gene EWSR1 in amyotrophic lateral sclerosis. Hum Mol Genet 2012; 21:2899-911. [PMID: 22454397 DOI: 10.1093/hmg/dds116] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease affecting motor neurons. Mutations in related RNA-binding proteins TDP-43, FUS/TLS and TAF15 have been connected to ALS. These three proteins share several features, including the presence of a bioinformatics-predicted prion domain, aggregation-prone nature in vitro and in vivo and toxic effects when expressed in multiple model systems. Given these commonalities, we hypothesized that a related protein, EWSR1 (Ewing sarcoma breakpoint region 1), might also exhibit similar properties and therefore could contribute to disease. Here, we report an analysis of EWSR1 in multiple functional assays, including mutational screening in ALS patients and controls. We identified three missense variants in EWSR1 in ALS patients, which were absent in a large number of healthy control individuals. We show that disease-specific variants affect EWSR1 localization in motor neurons. We also provide multiple independent lines of in vitro and in vivo evidence that EWSR1 has similar properties as TDP-43, FUS and TAF15, including aggregation-prone behavior in vitro and ability to confer neurodegeneration in Drosophila. Postmortem analysis of sporadic ALS cases also revealed cytoplasmic mislocalization of EWSR1. Together, our studies highlight a potential role for EWSR1 in ALS, provide a collection of functional assays to be used to assess roles of additional RNA-binding proteins in disease and support an emerging concept that a class of aggregation-prone RNA-binding proteins might contribute broadly to ALS and related neurodegenerative diseases.
Collapse
Affiliation(s)
- Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
King OD, Gitler AD, Shorter J. The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease. Brain Res 2012; 1462:61-80. [PMID: 22445064 DOI: 10.1016/j.brainres.2012.01.016] [Citation(s) in RCA: 486] [Impact Index Per Article: 40.5] [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: 12/14/2011] [Revised: 01/06/2012] [Accepted: 01/07/2012] [Indexed: 02/08/2023]
Abstract
Prions are self-templating protein conformers that are naturally transmitted between individuals and promote phenotypic change. In yeast, prion-encoded phenotypes can be beneficial, neutral or deleterious depending upon genetic background and environmental conditions. A distinctive and portable 'prion domain' enriched in asparagine, glutamine, tyrosine and glycine residues unifies the majority of yeast prion proteins. Deletion of this domain precludes prionogenesis and appending this domain to reporter proteins can confer prionogenicity. An algorithm designed to detect prion domains has successfully identified 19 domains that can confer prion behavior. Scouring the human genome with this algorithm enriches a select group of RNA-binding proteins harboring a canonical RNA recognition motif (RRM) and a putative prion domain. Indeed, of 210 human RRM-bearing proteins, 29 have a putative prion domain, and 12 of these are in the top 60 prion candidates in the entire genome. Startlingly, these RNA-binding prion candidates are inexorably emerging, one by one, in the pathology and genetics of devastating neurodegenerative disorders, including: amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U), Alzheimer's disease and Huntington's disease. For example, FUS and TDP-43, which rank 1st and 10th among RRM-bearing prion candidates, form cytoplasmic inclusions in the degenerating motor neurons of ALS patients and mutations in TDP-43 and FUS cause familial ALS. Recently, perturbed RNA-binding proteostasis of TAF15, which is the 2nd ranked RRM-bearing prion candidate, has been connected with ALS and FTLD-U. We strongly suspect that we have now merely reached the tip of the iceberg. We predict that additional RNA-binding prion candidates identified by our algorithm will soon surface as genetic modifiers or causes of diverse neurodegenerative conditions. Indeed, simple prion-like transfer mechanisms involving the prion domains of RNA-binding proteins could underlie the classical non-cell-autonomous emanation of neurodegenerative pathology from originating epicenters to neighboring portions of the nervous system. This article is part of a Special Issue entitled RNA-Binding Proteins.
Collapse
Affiliation(s)
- Oliver D King
- Boston Biomedical Research Institute, 64 Grove St., Watertown, MA 02472, USA.
| | | | | |
Collapse
|
30
|
Matsumiya LC, Sorge RE, Sotocinal SG, Tabaka JM, Wieskopf JS, Zaloum A, King OD, Mogil JS. Using the Mouse Grimace Scale to reevaluate the efficacy of postoperative analgesics in laboratory mice. J Am Assoc Lab Anim Sci 2012; 51:42-49. [PMID: 22330867 PMCID: PMC3276965] [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] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 07/06/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
Postoperative pain management in animals is complicated greatly by the inability to recognize pain. As a result, the choice of analgesics and their doses has been based on extrapolation from greatly differing pain models or the use of measures with unclear relevance to pain. We recently developed the Mouse Grimace Scale (MGS), a facial-expression-based pain coding system adapted directly from scales used in nonverbal human populations. The MGS has shown to be a reliable, highly accurate measure of spontaneous pain of moderate duration, and therefore is particularly useful in the quantification of postoperative pain. In the present study, we quantified the relative intensity and duration of postoperative pain after a sham ventral ovariectomy (laparotomy) in outbred mice. In addition, we compiled dose-response data for 4 commonly used analgesics: buprenorphine, carprofen, ketoprofen, and acetaminophen. We found that postoperative pain in mice, as defined by facial grimacing, lasts for 36 to 48 h, and appears to show relative exacerbation during the early dark (active) photophase. We find that buprenorphine was highly effective in inhibiting postoperative pain-induced facial grimacing in mice at doses equal to or lower than current recommendations, that carprofen and ketoprofen are effective only at doses markedly higher than those currently recommended, and that acetaminophen was ineffective at any dose used. We suggest the revision of practices for postoperative pain management in mice in light of these findings.
Collapse
Affiliation(s)
| | - Robert E Sorge
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Susana G Sotocinal
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - John M Tabaka
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Jeffrey S Wieskopf
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Austin Zaloum
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Oliver D King
- Boston Biomedical Research Institute, Watertown, Massachusetts
| | - Jeffrey S Mogil
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| |
Collapse
|
31
|
Halfmann R, Alberti S, Krishnan R, Lyle N, O'Donnell CW, King OD, Berger B, Pappu RV, Lindquist S. Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins. Mol Cell 2011; 43:72-84. [PMID: 21726811 DOI: 10.1016/j.molcel.2011.05.013] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 03/21/2011] [Accepted: 04/29/2011] [Indexed: 11/26/2022]
Abstract
Sequences rich in glutamine (Q) and asparagine (N) residues often fail to fold at the monomer level. This, coupled to their unusual hydrogen-bonding abilities, provides the driving force to switch between disordered monomers and amyloids. Such transitions govern processes as diverse as human protein-folding diseases, bacterial biofilm assembly, and the inheritance of yeast prions (protein-based genetic elements). A systematic survey of prion-forming domains suggested that Q and N residues have distinct effects on amyloid formation. Here, we use cell biological, biochemical, and computational techniques to compare Q/N-rich protein variants, replacing Ns with Qs and Qs with Ns. We find that the two residues have strong and opposing effects: N richness promotes assembly of benign self-templating amyloids; Q richness promotes formation of toxic nonamyloid conformers. Molecular simulations focusing on intrinsic folding differences between Qs and Ns suggest that their different behaviors are due to the enhanced turn-forming propensity of Ns over Qs.
Collapse
Affiliation(s)
- Randal Halfmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Sotocinal SG, Sorge RE, Zaloum A, Tuttle AH, Martin LJ, Wieskopf JS, Mapplebeck JCS, Wei P, Zhan S, Zhang S, McDougall JJ, King OD, Mogil JS. The Rat Grimace Scale: a partially automated method for quantifying pain in the laboratory rat via facial expressions. Mol Pain 2011; 7:55. [PMID: 21801409 PMCID: PMC3163602 DOI: 10.1186/1744-8069-7-55] [Citation(s) in RCA: 318] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/29/2011] [Indexed: 11/25/2022] Open
Abstract
We recently demonstrated the utility of quantifying spontaneous pain in mice via the blinded coding of facial expressions. As the majority of preclinical pain research is in fact performed in the laboratory rat, we attempted to modify the scale for use in this species. We present herein the Rat Grimace Scale, and show its reliability, accuracy, and ability to quantify the time course of spontaneous pain in the intraplantar complete Freund's adjuvant, intraarticular kaolin-carrageenan, and laparotomy (post-operative pain) assays. The scale's ability to demonstrate the dose-dependent analgesic efficacy of morphine is also shown. In addition, we have developed software, Rodent Face Finder®, which successfully automates the most labor-intensive step in the process. Given the known mechanistic dissociations between spontaneous and evoked pain, and the primacy of the former as a clinical problem, we believe that widespread adoption of spontaneous pain measures such as the Rat Grimace Scale might lead to more successful translation of basic science findings into clinical application.
Collapse
Affiliation(s)
- Susana G Sotocinal
- Department of Psychology and Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Rahimov F, King OD, Warsing LC, Powell RE, Emerson CP, Kunkel LM, Wagner KR. Gene expression profiling of skeletal muscles treated with a soluble activin type IIB receptor. Physiol Genomics 2011; 43:398-407. [PMID: 21266502 DOI: 10.1152/physiolgenomics.00223.2010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Inhibition of the myostatin signaling pathway is emerging as a promising therapeutic means to treat muscle wasting and degenerative disorders. Activin type IIB receptor (ActRIIB) is the putative myostatin receptor, and a soluble activin receptor (ActRIIB-Fc) has been demonstrated to potently inhibit a subset of transforming growth factor (TGF)-β family members including myostatin. To determine reliable and valid biomarkers for ActRIIB-Fc treatment, we assessed gene expression profiles for quadriceps muscles from mice treated with ActRIIB-Fc compared with mice genetically lacking myostatin and control mice. Expression of 134 genes was significantly altered in mice treated with ActRIIB-Fc over a 2-wk period relative to control mice (fold change > 1.5, P < 0.001), whereas the number of significantly altered genes in mice treated for 2 days was 38, demonstrating a time-dependent response to ActRIIB-Fc in overall muscle gene expression. The number of significantly altered genes in Mstn(-/-) mice relative to control mice was substantially higher (360), but for most of these genes the expression levels in the 2-wk treated mice were closer to the levels in the Mstn(-/-) mice than in control mice (P < 10⁻³⁰). Expression levels of 30 selected genes were further validated with quantitative real-time polymerase chain reaction (qPCR), and a correlation of ≥ 0.89 was observed between the fold changes from the microarray analysis and the qPCR analysis. These data suggest that treatment with ActRIIB-Fc results in overlapping but distinct gene expression signatures compared with myostatin genetic mutation. Differentially expressed genes identified in this study can be used as potential biomarkers for ActRIIB-Fc treatment, which is currently in clinical trials as a therapeutic agent for muscle wasting and degenerative disorders.
Collapse
Affiliation(s)
- Fedik Rahimov
- Program in Genomics, Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, USA
| | | | | | | | | | | | | |
Collapse
|
34
|
Cushman M, Johnson BS, King OD, Gitler AD, Shorter J. Prion-like disorders: blurring the divide between transmissibility and infectivity. J Cell Sci 2010; 123:1191-201. [PMID: 20356930 DOI: 10.1242/jcs.051672] [Citation(s) in RCA: 218] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Prions are proteins that access self-templating amyloid forms, which confer phenotypic changes that can spread from individual to individual within or between species. These infectious phenotypes can be beneficial, as with yeast prions, or deleterious, as with mammalian prions that transmit spongiform encephalopathies. However, the ability to form self-templating amyloid is not unique to prion proteins. Diverse polypeptides that tend to populate intrinsically unfolded states also form self-templating amyloid conformers that are associated with devastating neurodegenerative disorders. Moreover, two RNA-binding proteins, FUS and TDP-43, which form cytoplasmic aggregates in amyotrophic lateral sclerosis, harbor a 'prion domain' similar to those found in several yeast prion proteins. Can these proteins and the neurodegenerative diseases to which they are linked become 'infectious' too? Here, we highlight advances that define the transmissibility of amyloid forms connected with Alzheimer's disease, Parkinson's disease and Huntington's disease. Collectively, these findings suggest that amyloid conformers can spread from cell to cell within the brains of afflicted individuals, thereby spreading the specific neurodegenerative phenotypes distinctive to the protein being converted to amyloid. Importantly, this transmissibility mandates a re-evaluation of emerging neuronal graft and stem-cell therapies. In this Commentary, we suggest how these treatments might be optimized to overcome the transmissible conformers that confer neurodegeneration.
Collapse
Affiliation(s)
- Mimi Cushman
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 805b Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA
| | | | | | | | | |
Collapse
|
35
|
Jackson WS, Borkowski AW, Faas H, Steele AD, King OD, Watson N, Jasanoff A, Lindquist S. Spontaneous generation of prion infectivity in fatal familial insomnia knockin mice. Neuron 2009; 63:438-50. [PMID: 19709627 PMCID: PMC2775465 DOI: 10.1016/j.neuron.2009.07.026] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [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: 04/03/2009] [Revised: 07/20/2009] [Accepted: 07/30/2009] [Indexed: 11/18/2022]
Abstract
A crucial tenet of the prion hypothesis is that misfolding of the prion protein (PrP) induced by mutations associated with familial prion disease is, in an otherwise normal mammalian brain, sufficient to generate the infectious agent. Yet this has never been demonstrated. We engineered knockin mice to express a PrP mutation associated with a distinct human prion disease, fatal familial insomnia (FFI). An additional substitution created a strong transmission barrier against pre-existing prions. The mice spontaneously developed a disease distinct from that of other mouse prion models and highly reminiscent of FFI. Unique pathology was transmitted from FFI mice to mice expressing wild-type PrP sharing the same transmission barrier. FFI mice were highly resistant to infection by pre-existing prions, confirming infectivity did not arise from contaminating agents. Thus, a single amino acid change in PrP is sufficient to induce a distinct neurodegenerative disease and the spontaneous generation of prion infectivity.
Collapse
Affiliation(s)
- Walker S Jackson
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar AG, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E. Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat Genet 2009; 41:316-23. [PMID: 19234470 DOI: 10.1038/ng.337] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 01/27/2009] [Indexed: 02/07/2023]
Abstract
Cells respond to stimuli by changes in various processes, including signaling pathways and gene expression. Efforts to identify components of these responses increasingly depend on mRNA profiling and genetic library screens. By comparing the results of these two assays across various stimuli, we found that genetic screens tend to identify response regulators, whereas mRNA profiling frequently detects metabolic responses. We developed an integrative approach that bridges the gap between these data using known molecular interactions, thus highlighting major response pathways. We used this approach to reveal cellular pathways responding to the toxicity of alpha-synuclein, a protein implicated in several neurodegenerative disorders including Parkinson's disease. For this we screened an established yeast model to identify genes that when overexpressed alter alpha-synuclein toxicity. Bridging these data and data from mRNA profiling provided functional explanations for many of these genes and identified previously unknown relations between alpha-synuclein toxicity and basic cellular pathways.
Collapse
Affiliation(s)
- Esti Yeger-Lotem
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Tian W, Zhang LV, Taşan M, Gibbons FD, King OD, Park J, Wunderlich Z, Cherry JM, Roth FP. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 2008; 9 Suppl 1:S7. [PMID: 18613951 PMCID: PMC2447541 DOI: 10.1186/gb-2008-9-s1-s7] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [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] [Indexed: 12/31/2022] Open
Abstract
Background: Learning the function of genes is a major goal of computational genomics. Methods for inferring gene function have typically fallen into two categories: 'guilt-by-profiling', which exploits correlation between function and other gene characteristics; and 'guilt-by-association', which transfers function from one gene to another via biological relationships. Results: We have developed a strategy ('Funckenstein') that performs guilt-by-profiling and guilt-by-association and combines the results. Using a benchmark set of functional categories and input data for protein-coding genes in Saccharomyces cerevisiae, Funckenstein was compared with a previous combined strategy. Subsequently, we applied Funckenstein to 2,455 Gene Ontology terms. In the process, we developed 2,455 guilt-by-profiling classifiers based on 8,848 gene characteristics and 12 functional linkage graphs based on 23 biological relationships. Conclusion: Funckenstein outperforms a previous combined strategy using a common benchmark dataset. The combination of 'guilt-by-profiling' and 'guilt-by-association' gave significant improvement over the component classifiers, showing the greatest synergy for the most specific functions. Performance was evaluated by cross-validation and by literature examination of the top-scoring novel predictions. These quantitative predictions should help prioritize experimental study of yeast gene functions.
Collapse
Affiliation(s)
- Weidong Tian
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Longwood Avenue, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Abstract
When faced with a variable environment, organisms may switch between different strategies according to some probabilistic rule. In an infinite population, evolution is expected to favor the rule that maximizes geometric mean fitness. If some environments are encountered only rarely, selection may not be strong enough for optimal switching probabilities to evolve. Here we calculate the evolution of switching probabilities in a finite population by analyzing fixation probabilities of alleles specifying switching rules. We calculate the conditions required for the evolution of phenotypic switching as a form of bet-hedging as a function of the population size N, the rate theta at which a rare environment is encountered, and the selective advantage s associated with switching in the rare environment. We consider a simplified model in which environmental switching and phenotypic switching are one-way processes, and mutation is symmetric and rare with respect to the timescale of fixation events. In this case, the approximate requirements for bet-hedging to be favored by a ratio of at least R are that sN>log(R) and thetaN>square root R .
Collapse
Affiliation(s)
- Oliver D. King
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA,
| | - Joanna Masel
- Dpt. Ecology & Evolutionary Biology, University of Arizona, 1041 E Lowell St, Tucson AZ 85721, USA, Ph. 1 520 626 9888 Fax. 1 520 621 9190
| |
Collapse
|
39
|
Steele AD, Jackson WS, King OD, Lindquist S. The power of automated high-resolution behavior analysis revealed by its application to mouse models of Huntington's and prion diseases. Proc Natl Acad Sci U S A 2007; 104:1983-8. [PMID: 17261803 PMCID: PMC1794260 DOI: 10.1073/pnas.0610779104] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Automated analysis of mouse behavior will be vital for elucidating the genetic determinants of behavior, for comprehensive analysis of human disease models, and for assessing the efficacy of various therapeutic strategies and their unexpected side effects. We describe a video-based behavior-recognition technology to analyze home-cage behaviors and demonstrate its power by discovering previously unrecognized features of two already extensively characterized mouse models of neurodegenerative disease. The severe motor abnormalities in Huntington's disease mice manifested in our analysis by decreased hanging, jumping, stretching, and rearing. Surprisingly, behaviors such as resting and grooming were also affected. Unexpectedly, mice with infectious prion disease showed profound increases in activity at disease onset: rearing increased 2.5-fold, walking 10-fold and jumping 30-fold. Strikingly, distinct behaviors were altered specifically during day or night hours. We devised a systems approach for multiple-parameter phenotypic characterization and applied it to defining disease onset robustly and at early time points.
Collapse
Affiliation(s)
- Andrew D. Steele
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Walker S. Jackson
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Oliver D. King
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- *To whom correspondence should be addressed at:
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Massachusetts Institute of Technology, Cambridge, MA 02142. E-mail:
| |
Collapse
|
40
|
Masel J, King OD, Maughan H. The loss of adaptive plasticity during long periods of environmental stasis. Am Nat 2006; 169:38-46. [PMID: 17206583 PMCID: PMC1766558 DOI: 10.1086/510212] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [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: 12/22/2005] [Accepted: 08/14/2006] [Indexed: 11/03/2022]
Abstract
Adaptive plasticity allows populations to adjust rapidly to environmental change. If this is useful only rarely, plasticity may undergo mutational degradation and be lost from a population. We consider a population of constant size N undergoing loss of plasticity at functional mutation rate m and with selective advantage s associated with loss. Environmental change events occur at rate theta per generation, killing all individuals that lack plasticity. The expected time until loss of plasticity in a fluctuating environment is always at least tau, the expected time until loss of plasticity in a static environment. When mN > 1 and N theta >> 1, we find that plasticity will be maintained for an average of at least 10(8) generations in a single population, provided tau > 18/theta. In a metapopulation, plasticity is retained under the more lenient condition tau > 1.3/theta, irrespective of mN, for a modest number of demes. We calculate both exact and approximate solutions for tau and find that it is linearly dependent only on the logarithm of N, and so, surprisingly, both the population size and the number of demes in the metapopulation make little difference to the retention of plasticity. Instead, tau is dominated by the term 1/(m+s/2).
Collapse
Affiliation(s)
- Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
| | | | | |
Collapse
|
41
|
Zhang LV, King OD, Wong SL, Goldberg DS, Tong AHY, Lesage G, Andrews B, Bussey H, Boone C, Roth FP. Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 2005; 4:6. [PMID: 15982408 PMCID: PMC1175995 DOI: 10.1186/jbiol23] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 02/21/2005] [Accepted: 04/08/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence homology, and expression correlation. Recurring patterns of interconnection, or 'network motifs', have revealed biological insights for networks containing either one or two types of interaction. RESULTS To study more complex relationships involving multiple biological interaction types, we assembled an integrated Saccharomyces cerevisiae network in which nodes represent genes (or their protein products) and differently colored links represent the aforementioned five biological interaction types. We examined three- and four-node interconnection patterns containing multiple interaction types and found many enriched multi-color network motifs. Furthermore, we showed that most of the motifs form 'network themes' -- classes of higher-order recurring interconnection patterns that encompass multiple occurrences of network motifs. Network themes can be tied to specific biological phenomena and may represent more fundamental network design principles. Examples of network themes include a pair of protein complexes with many inter-complex genetic interactions -- the 'compensatory complexes' theme. Thematic maps -- networks rendered in terms of such themes -- can simplify an otherwise confusing tangle of biological relationships. We show this by mapping the S. cerevisiae network in terms of two specific network themes. CONCLUSION Significantly enriched motifs in an integrated S. cerevisiae interaction network are often signatures of network themes, higher-order network structures that correspond to biological phenomena. Representing networks in terms of network themes provides a useful simplification of complex biological relationships.
Collapse
Affiliation(s)
- Lan V Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Oliver D King
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Sharyl L Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Debra S Goldberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Amy HY Tong
- Banting and Best Department of Medical Research and Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Guillaume Lesage
- Department of Biology, McGill University, Montreal PQ H3A 1B1, Canada
| | - Brenda Andrews
- Banting and Best Department of Medical Research and Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Howard Bussey
- Department of Biology, McGill University, Montreal PQ H3A 1B1, Canada
| | - Charles Boone
- Banting and Best Department of Medical Research and Department of Medical Genetics and Microbiology, University of Toronto, Toronto ON M5G 1L6, Canada
| | - Frederick P Roth
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| |
Collapse
|
42
|
Wong SL, Zhang LV, Tong AHY, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H, Boone C, Roth FP. Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A 2004; 101:15682-7. [PMID: 15496468 PMCID: PMC524818 DOI: 10.1073/pnas.0406614101] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Indexed: 11/18/2022] Open
Abstract
Genetic interactions define overlapping functions and compensatory pathways. In particular, synthetic sick or lethal (SSL) genetic interactions are important for understanding how an organism tolerates random mutation, i.e., genetic robustness. Comprehensive identification of SSL relationships remains far from complete in any organism, because mapping these networks is highly labor intensive. The ability to predict SSL interactions, however, could efficiently guide further SSL discovery. Toward this end, we predicted pairs of SSL genes in Saccharomyces cerevisiae by using probabilistic decision trees to integrate multiple types of data, including localization, mRNA expression, physical interaction, protein function, and characteristics of network topology. Experimental evidence demonstrated the reliability of this strategy, which, when extended to human SSL interactions, may prove valuable in discovering drug targets for cancer therapy and in identifying genes responsible for multigenic diseases.
Collapse
Affiliation(s)
- Sharyl L Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Abstract
We point out biases in the algorithms used by Itzkovitz et a. [Phys. Rev. E 68, 026127 (2003)] to assess their approximate formulas for the average number of occurrences of certain subgraphs in random graphs with prescribed degree sequences.
Collapse
|
44
|
Abstract
MOTIVATION Predicting the outcome of specific experiments (such as the growth of a particular mutant strain in a particular medium) has the potential to allow researchers to devote resources to experiments with higher expected numbers of 'hits'. RESULTS We use decision trees to predict phenotypes associated with Saccharomyces cerevisiae genes on the basis of Gene Ontology (GO) functional annotations from the Saccharomyces Genome Database (SGD) and other phenotypic annotations from the Yeast Phenotype Catalog at the Munich Information Center for Protein Sequences (MIPS). We assess the methodology in three ways: (1) we use cross-validation on the phenotypic annotations listed in MIPS, and show ROC curves indicating the tradeoff between true-positive rate and false-positive rate; (2) we do a literature-search for 100 of the predicted gene-phenotype associations that are not listed in MIPS, and find evidence for 43 of them; (3) we use deletion strains to experimentally assess 61 predicted gene-phenotype associations not listed in MIPS; significantly more of these deletion strains show abnormal growth than would be expected by chance.
Collapse
Affiliation(s)
- Oliver D King
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, Massachusetts, 02115, USA
| | | | | | | | | | | |
Collapse
|
45
|
Abstract
SUMMARY FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate include the ability to handle ranked input lists, and a Monte Carlo simulation approach that is more appropriate to determine significance than other methods, such as Bonferroni or idák p-value correction. FuncAssociate currently supports 10 organisms (Vibrio cholerae, Shewanella oneidensis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Caenorhaebditis elegans, Drosophila melanogaster, Mus musculus, Rattus norvegicus and Homo sapiens). AVAILABILITY FuncAssociate is freely accessible at http://llama.med.harvard.edu/Software.html. Source code (in Perl and C) is freely available to academic users 'as is'.
Collapse
Affiliation(s)
- Gabriel F Berriz
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, Boston, MA 02115, USA
| | | | | | | | | |
Collapse
|
46
|
Abstract
Evidence for specific protein-protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are frequent among large-scale studies, and that error frequency depends on the large-scale method used. Despite knowledge of the error-prone nature of interaction evidence, edges (connections) in this network are typically viewed as either present or absent. However, use of a probabilistic network that considers quantity and quality of supporting evidence should improve inference derived from protein networks. Here we demonstrate inference of membership in a partially known protein complex by using a probabilistic network model and an algorithm previously used to evaluate reliability in communication networks.
Collapse
Affiliation(s)
- Saurabh Asthana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | |
Collapse
|
47
|
Zhang LV, Wong SL, King OD, Roth FP. Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 2004; 5:38. [PMID: 15090078 PMCID: PMC419405 DOI: 10.1186/1471-2105-5-38] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Accepted: 04/16/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying all protein-protein interactions in an organism is a major objective of proteomics. A related goal is to know which protein pairs are present in the same protein complex. High-throughput methods such as yeast two-hybrid (Y2H) and affinity purification coupled with mass spectrometry (APMS) have been used to detect interacting proteins on a genomic scale. However, both Y2H and APMS methods have substantial false-positive rates. Aside from high-throughput interaction screens, other gene- or protein-pair characteristics may also be informative of physical interaction. Therefore it is desirable to integrate multiple datasets and utilize their different predictive value for more accurate prediction of co-complexed relationship. RESULTS Using a supervised machine learning approach--probabilistic decision tree, we integrated high-throughput protein interaction datasets and other gene- and protein-pair characteristics to predict co-complexed pairs (CCP) of proteins. Our predictions proved more sensitive and specific than predictions based on Y2H or APMS methods alone or in combination. Among the top predictions not annotated as CCPs in our reference set (obtained from the MIPS complex catalogue), a significant fraction was found to physically interact according to a separate database (YPD, Yeast Proteome Database), and the remaining predictions may potentially represent unknown CCPs. CONCLUSIONS We demonstrated that the probabilistic decision tree approach can be successfully used to predict co-complexed protein (CCP) pairs from other characteristics. Our top-scoring CCP predictions provide testable hypotheses for experimental validation.
Collapse
Affiliation(s)
- Lan V Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sharyl L Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Oliver D King
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick P Roth
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
48
|
Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP. Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat Biotechnol 2004; 22:214-9. [PMID: 14730315 DOI: 10.1038/nbt930] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2003] [Accepted: 10/31/2003] [Indexed: 11/09/2022]
Abstract
Tandem mass spectrometry (MS/MS) has emerged as a cornerstone of proteomics owing in part to robust spectral interpretation algorithms. Widely used algorithms do not fully exploit the intensity patterns present in mass spectra. Here, we demonstrate that intensity pattern modeling improves peptide and protein identification from MS/MS spectra. We modeled fragment ion intensities using a machine-learning approach that estimates the likelihood of observed intensities given peptide and fragment attributes. From 1,000,000 spectra, we chose 27,000 with high-quality, nonredundant matches as training data. Using the same 27,000 spectra, intensity was similarly modeled with mismatched peptides. We used these two probabilistic models to compute the relative likelihood of an observed spectrum given that a candidate peptide is matched or mismatched. We used a 'decoy' proteome approach to estimate incorrect match frequency, and demonstrated that an intensity-based method reduces peptide identification error by 50-96% without any loss in sensitivity.
Collapse
|
49
|
King OD, Roth FP. A non-parametric model for transcription factor binding sites. Nucleic Acids Res 2003; 31:e116. [PMID: 14500844 PMCID: PMC206482 DOI: 10.1093/nar/gng117] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2003] [Revised: 06/18/2003] [Accepted: 08/11/2003] [Indexed: 11/12/2022] Open
Abstract
We introduce a non-parametric representation of transcription factor binding sites which can model arbitrary dependencies between positions. As two parameters are varied, this representation smoothly interpolates between the empirical distribution of binding sites and the standard position-specific scoring matrix (PSSM). In a test of generalization to unseen binding sites using 10-fold cross-validation on known binding sites for 95 TRANSFAC transcription factors, this representation outperforms PSSMs on between 65 and 89 of the 95 transcription factors, depending on the choice of the two adjustable parameters. We also discuss how the non- parametric representation may be incorporated into frameworks for finding binding sites given only a collection of unaligned promoter regions.
Collapse
Affiliation(s)
- Oliver D King
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, SGMB-322, Boston, MA 02115, USA
| | | |
Collapse
|
50
|
Abstract
The Gene Ontology (GO) Consortium has produced a controlled vocabulary for annotation of gene function that is used in many organism-specific gene annotation databases. This allows the prediction of gene function based on patterns of annotation. For example, if annotations for two attributes tend to occur together in a database, then a gene holding one attribute is likely to hold the other as well. We modeled the relationships among GO attributes with decision trees and Bayesian networks, using the annotations in the Saccharomyces Genome Database (SGD) and in FlyBase as training data. We tested the models using cross-validation, and we manually assessed 100 gene-attribute associations that were predicted by the models but that were not present in the SGD or FlyBase databases. Of the 100 manually assessed associations, 41 were judged to be true, and another 42 were judged to be plausible.
Collapse
Affiliation(s)
- Oliver D King
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | |
Collapse
|