• Andrew Berglund Andrew Berglund

    Berglund Lab

Research   |   Publications   |   Berglund Lab Members 
 

Dr. Berglund’s scientific career has revolved around understanding the role of RNA in biology. The focus of his research is in neuromuscular diseases with the goal of translating basic science into therapeutic strategies using a combination of biochemical, cellular, genomic and computational approaches. For the last 16 years at the Universities of Oregon and Florida his research group has focused on RNA splicing with an emphasis on understanding the mechanisms of a common form of muscular dystrophy, myotonic dystrophy, as well as other microsatellite diseases such as amyotrophic lateral sclerosis (ALS), and spinocerebellar ataxias (SCAs).

 

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Research at the Berglund Lab
Ongoing Projects

The Berglund lab continues to focus on microsatellite diseases with the goal of translating basic science into clinical research using a combination of biochemical, cellular and genomic approaches.  As potential new therapies for neuromuscular and neurodegenerative diseases progress through preclinical and clinical evaluation, drug developers need new tools to design and conduct clinical trials. Research in the Berglund lab focuses on the identification of potential biomarkers and potential therapeutic molecules for microsatellite diseases such as myotonic dystrophy types 1 and 2 (DM1 and DM2), spinocerebellar ataxias (SCAs), and amyotrophic lateral sclerosis (ALS).

RNA Splicing and Disease

The Berglund lab uses a broad range of approaches to study the molecular mechanisms of neurological diseases that are caused by microsatellite repeat expansions.  For many of these diseases (DM, ALS and SCAs), RNA processing (pre-mRNA splicing) pathways are negatively impacted with specific changes in pre-mRNA splicing proposed to lead to symptoms observed in affected individuals. Many of the projects in the lab combine biochemical, molecular, and genomic approaches with cellular and other model systems to understand the mechanisms through which these diseases alter pre-mRNA splicing. In one project we have developed a framework to estimate MBNL concentration using splicing responses alone and validated it in a cell-based model and then applied it to myotonic dystrophy patient tissue. This allowed us to evaluate the ability of individual and combinations of splicing events from genomic data to predict functional MBNL concentration in human biopsies and the its potential use as a biomarker to distinguish mild, moderate, and severe cases of DM.

Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy. Wagner SD, Struck AJ, Gupta R, Farnsworth DR, Mahady AE, Eichinger K, Thornton CA, Wang ET, Berglund JA. PLoS Genet. 2016 Sep 28;12(9):e1006316. doi: 10.1371/journal.pgen.1006316. eCollection 2016 Sep. PMID: 27681373

Small Molecule Targeting of Toxic RNA

We are developing approaches to screen libraries of small molecules and mining the scientific literature to identify compounds that can be used to inhibit the production of toxic RNAs. Lead compounds that show promise inhibiting the production of the toxic RNAs will be studied further to understand the mechanisms through which they function.  This could provide fundamental information for the development of molecules with improved activity.  The goal of our research is to use the results from these fundamental studies to identify innovative strategies to reduce or correct the improper pre-mRNA splicing that occurs in the disease state. For example, we have recently shown that small molecules can be used to rescue the mis-splicing in cell and mouse models of myotonic dystrophy.  Our investigation into the mode of action of furamidine, a promising small molecule for rescue of mis-splicing in DM1 cells, showed that furamidine affects multiple pathways of DM1 pathogenesis and that it may work through multiple mechanisms to rescue DM1-associated mis-splicing events.

Combination Treatment of Erythromycin and Furamidine Provides Additive and Synergistic Rescue of Mis-splicing in Myotonic Dystrophy Type 1 Models Jenquin, J.R., Yang, H., Huigens, R.W., Nakamori, M., Berglund, A. ACS Pharmacol. Transl. Sci. · July 17, 2019

Furamidine Rescues Myotonic Dystrophy Type I Associated Mis-Splicing through Multiple Mechanisms. Jenquin JR, Coonrod LA, Silverglate QA, Pellitier NA, Hale MA, Xia G, Nakamori M, Berglund JA. ACS Chem Biol. 2018 Sep 21;13(9):2708-2718. doi: 10.1021/acschembio.8b00646. Epub 2018 Aug 27. PMID: 30118588

Engineering Proteins

We are developing novel synthetic muscleblind-like 1 (MBNL1) proteins, with altered and new activities, to provide insight into how this protein recognizes RNA and regulates splicing. We have recently published some of this work in Nucleic Acid Research describing an engineered MBNL1 RNA binding protein with improved specificity.  We showed that MBNL1’s zinc finger (ZF) domains have different activities with the first domain ZF1-2 driving splicing regulation while ZF3-4 acts as a general RNA binding domain. These studies suggest that synthetic MBNL proteins with altered splicing activity have the potential to be used as both tools for investigating splicing regulation and as potential protein therapeutics for DM and other repeat disease.

An engineered RNA binding protein with improved splicing regulation. Hale MA, Richardson JI, Day RC, McConnell OL, Arboleda J, Wang ET, Berglund JA. Nucleic Acids Res. 2018 Apr 6;46(6):3152-3168. doi: 10.1093/nar/gkx1304. PMID:  29309648

Genomics

RNA-seq is a powerful tool that is used to study the transcriptome. We use RNA-seq to compare the transcriptomes of DM models (cell and animal) as well as to determine how small molecules or how loss or gain of RNA binding proteins affect the transcriptome in these DM models. For example, in our recent study with furamidine we examined the global splicing and gene expression changes caused by furamidine in a DM1 mouse model. We were excited to observe that furamidine had significantly fewer off-target effects on the transcriptome compared to Actinomycin D, a small molecule that we had studied previously.

Furamidine Rescues Myotonic Dystrophy Type I Associated Mis-Splicing through Multiple Mechanisms. Jenquin JR, Coonrod LA, Silverglate QA, Pellitier NA, Hale MA, Xia G, Nakamori M, Berglund JA. ACS Chem Biol. 2018 Sep 21;13(9):2708-2718. doi: 10.1021/acschembio.8b00646. Epub 2018 Aug 27. PMID: 30118588

Models of Disease

For many years our group has used cell and animal models to identify small molecules to target the toxic CUG and CCUG repeats of DM in an effort to identify molecules that rescue the mis-splicing in DM. In addition to mouse models and disease specific human cell lines we have been collaborating with Dr. Karen Guillemin’s lab at the University of Oregon on developing and characterizing zebrafish models of myotoinic dystrophy.  The main focus of the zebrafish project is to the study the mechanisms underlying DM-related changes in gut motility and the microbiome since this has been a common issue among DM patients.

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model. deLorimier E, Coonrod LA, Copperman J, Taber A, Reister EE, Sharma K, Todd PK, Guenza MG, Berglund JA. Nucleic Acids Res. 2014 Nov 10;42(20):12768-78. doi: 10.1093/nar/gku941. Epub 2014 Oct 10. PMID: 25303993

RNA Structure

One of the mechanisms through which the CUG repeats and CCUG repeats (for myotonic dystrophy type 1 (DM1) and 2 (DM2) respectively) are toxic, is the sequestration of the muscleblind-like (MBNL) family of RNA binding proteins. The sequestration of MBNL proteins leads to many changes in splicing, which are implicated in causing the symptoms in DM.  It is therefore important to understand how MBNL proteins bind to their toxic and cellular RNA substrates to develop mechanisms to alleviate MBNL sequestration in DM1 and DM2.  MBNL proteins bind to a consensus YGCY RNA sequence and since CUG and CCUG expansion repeats are composed of YGCY motifs there are potentially hundreds to thousands of MBNL-binding sites in someone with a DM1 or DM2 expansion. Our lab has published work on replacing uridines with pseudouridine which induced structural stabilization, prevented MBNL1 binding, and rescued mis-splicing.  We continue to use crystallography and structure probing methods to better understand the structure of RNA in the context of DM and other repeat diseases.

Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility. deLorimier E, Hinman MN, Copperman J, Datta K, Guenza M, Berglund JA. J Biol Chem. 2017 Mar 10;292(10):4350-4357. doi: 10.1074/jbc.M116.770768. Epub 2017 Jan 27. PMID: 28130447

Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix. Coonrod LA, Lohman JR, Berglund JA. Biochemistry. 2012 Oct 23;51(42):8330-7. doi: 10.1021/bi300829w. Epub 2012 Oct 12. PMID: 23025897

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Berglund Lab Publications
Recent Publications

The potential of engineered eukaryotic RNA-binding proteins as molecular tools and therapeutics

Carl R. Shotwell, John D. Cleary,  J. Andrew Berglund
Wiley Interdisciplinary Reviews: RNA · November 03, 2019
 

A CTG repeat-selective chemical screen identifies microtubule inhibitors as selective modulators of toxic CUG RNA levels

Reddy K, Jenquin J, McConnell OL, Cleary JD, Richardson JI, Pinto BS, Haerle MC, Delgado E, Planco L, Nakamori M, Wang ET, Berglund JA.
PNAS · October 15, 2019
 

Mitigating RNA Toxicity in Myotonic Dystrophy using Small Molecules

Reddy K, Jenquin JR, Cleary JD, Berglund JA
Int. J Mol Sci · August 17, 2019
 

Combination Treatment of Erythromycin and Furamidine Provides Additive and Synergistic Rescue of Mis-splicing in Myotonic Dystrophy Type 1 Models

Jenquin, J.R., Yang, H., Huigens, R.W., Nakamori, M., Berglund, A.
ACS Pharmacol. Transl. Sci. · July 17, 2019
 

Repeat-associated RNA structure and aberrant splicing

Hale MA, Johnson NE, Berglund JA.
Biochim Biophys Acta Gene Regul Mech · July 16, 2019


Furamidine Rescues Myotonic Dystrophy Type I Associated Mis-Splicing through Multiple Mechanisms

Jenquin JR, Coonrod LA, Silverglate QA, Pellitier NA, Hale MA, Xia G, Nakamori M, Berglund JA
ACS Chemical Biology · September 21, 2018


An engineered RNA binding protein with improved splicing regulation

Hale MA, Richardson JI, Day RC, McConnell OL, Arboleda J, Wang ET, Berglund JA
Nucleic Acids Res · April 06, 2018


Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility

deLorimier E, Hinman MN, Copperman J, Datta K, Guenza M, Berglund JA
J Biol Chem · March 10, 2017


Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy

Wagner SD, Struck AJ, Gupta R, Farnsworth DR, Mahady AE, Eichinger K, Thornton CA, Wang ET, Berglund JA
PLoS Genet · September 16, 2016


Conservation of context-dependent splicing activity in distant Muscleblind homologs

Oddo JC, Saxena T, McConnell OL, Berglund JA, Wang ET
Nucleic Acids Research · September 30, 2016


Actinomycin D Specifically Reduces Expanded CUG Repeat RNA in Myotonic Dystrophy Models

Siboni RB, Nakamori M, Wagner SD, Struck AJ, Coonrod LA, Harriott SA, Cass DM, Tanner MK, Berglund JA.
Cell Reports · December 22, 2015


Biological Efficacy and Toxicity of Diamidines in Myotonic Dystrophy Type 1 Models

Siboni RB, Bodner MJ, Khalifa MM, Docter AG, Choi JY, Nakamori M, Haley MM, Berglund JA
J Med Chem · August 13, 2015


Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

deLorimier E, Coonrod LA, Copperman J, Taber A, Reister EE, Sharma K, Todd PK, Guenza MG, Berglund JA
Nucleic Acids Research · November 10, 2014


Computational approaches to mine publicly available databases

Voelker RB, Cresko WA, Berglund JA
Methods in Molecular Biology · January 27, 2014


Alternative pre-mRNA splicing

Wagner SD, Berglund JA.
Methods in Molecular Biology · January 27, 2014


Reducing levels of toxic RNA with small molecules

Coonrod LA, Nakamori M, Wang W, Carrell S, Hilton CL, Bodner MJ, Siboni RB, Docter AG, Haley MM, Thornton CA, Berglund JA.
ACS Chemical Biology · November 15, 2013


Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix

Coonrod LA, Lohman JR, Berglund JA
Biochemistry · October 23, 2012


Combinatorial Mutagenesis of MBNL1 Zinc Fingers Elucidates Distinct Classes of Regulatory Events

Purcell J, Oddo JC, Wang ET, Berglund JA.
Molecular Cell Biology · October 01, 2012

Berglund Lab News