Biol 203 Molecular Basis of Genetic Diseases Spring 2015

Judith Tsipis Wed. 9:15-11:30

Biology 203 covers the molecular basis of Duchenne Muscular Dystrophy/Becker Muscular Dystrophy, Cystic Fibrosis, Spinal Muscular Atrophy, Lynch Syndrome and the PTEN-opathies. We will also cover two of the triplet-repeat expansion diseases: Fragile-X Syndrome and Friedrich’s Ataxia. For each topic we will take an historical perspective and follow the science up to the present day. So….we’ll focus on:

clinical characteristics of the disorder
inheritance pattern
localization of the gene in question - to a chromosome / to a specific region
cloning the cDNA and the gene for each disorder
characterizing the protein product of each gene / studying its function (when known)
identifying mutations in the gene / correlating genotype with phenotype when possible
current approaches to treatment and molecular therapeutics
molecular tests used for diagnosis, PND, and/or carrier testing
genetic counseling issues and cases

Goals of Bio 203:

Continue to gain confidence in reading scientific papers and understanding/explaining methodologies employed

Become skilled at giving presentations. It doesn't matter where you start out as long as you end up improving and maybe even learning to enjoy giving talks!
Learn in detail about several common genetic disorders in terms of their clinical features, inheritance pattern, genetic and molecular basis, diagnostic and screening technologies, therapeutic possibilities, challenges for GC, impact on families, etc.
Practice using Powerpoint. Guidelines for the use of Powerpoint are given on Latte.
Practice research/writing skills
Practice active listening skills and giving constructive feedback to peers - no Sudoku or crossword puzzles or cell phones or texting allowed in class!

Structure of Bio 203:

Each week you will be assigned a set of articles on the topic of the day. All articles will be available as PDF’s on Latte. You are all expected to read the Background Review Article(s) for the topic of the day and be ready with questions for further discussion. I would also recommend reading the Intro and Conclusions of the primary articles (high-lighted in grey) that will be presented. Each week we will have three presentations - one on each set of articles. Each student will give a total of 3 presentations in the course of the semester. All presentations will be peer-evaluated and self-evaluated using Qualtrics. This year I ask that you bring your laptops or tablets with you so we can complete the peer evaluations at the very end of class….hopefully we will get responses from all and your recall will still be good! The week following each presentation, students should meet with the instructor to go over the presentation and discuss ways to strengthen it.

Assignments are given on the attached schedule and will be posted on Latte.

In terms of the actual presentations:

Each should be about 25-30 minutes
Dress is business casual…
Check in with me if you have ANY questions about the papers or talk. I am here to help!
Review the PPT on Latte – it is designed to help you with your presentation
Suggested order for each paper presented is:
Authors/title/citation
Introductory and background information (both clinical and genetic or structural depending on your paper) on the disorder as of the publication date of the paper
Statement of the purpose of the paper followed by brief statement of the main conclusions in just enough detail so that audience knows what the aims of the paper were and what the researchers found.
Description of the paper in some detail including methods (though not at the level of 0.5 ml NaCl was added!) and relevant figures/tables. When appropriate, color code figures or type in text so that the most relevant information is adjacent to the figure. It is best not to present the paper in the order in which it was written - that is, don't do Materials and Methods as a separate section, rather integrate the M and M into the presentation in the context of the experiments and what the authors found
Conclusions and remaining questions

At the end of the semester you will write a term paper on a disease for which a genetic basis has been established and the causal gene has been molecularly investigated. Once you have chosen a topic, check with me to see if it is acceptable and to make sure that each of you chooses a different topic - and one that you have not explored in depth in an earlier class.

The paper is due July 15 and should include:

a clinical description of the disease
a description of its pattern of inheritance or genetic basis
a summary of what is known about the molecular basis of the disease, including how it was mapped and cloned
a detailed description of tests used to diagnose the disease and any tests used for prenatal diagnosis and/or carrier testing as appropriate
a summary of therapeutic strategies if any
an annotated list of resources for families affected by the disease including brochures as well as web-sites
a bibliography (references should include the title of each article /website as well as the citation and should follow the format set out by the APA).

During the first week of the Fall ’15 semester, you will give a presentation on your topic to the first and second year students and faculty. On the day of your presentation, provide each member of the group with a 2-3-page hand-out (including 4-5 important ref. and information on support groups) on your “disease.” We’ll aim for a “no presentation notes” presentation to completely wow the class of ’17!

Please note: If you are a student with a documented disability on record at Brandeis University and wish to have a reasonable accommodation made for you in this class, please see me (Judith Tsipis) immediately.

Proseminar Schedule of Topics

A detailed list of the readings for each week – and the speaker assignments – follows. As you look at the list below, you’ll see 3 names assigned for each day/topic. The person who has a (1) after their name will present the first set of papers on the detailed syllabus, the person with a (2) will present the second set of papers on the detailed syllabus, and the person with a (3) after their name will present the third set of papers. When you look at the detailed syllabus for each day, you’ll find the names of the papers included in each set. For each set of papers, the main article to be presented is the one high-lighted in gray and it should be presented in its entirety. The others -which are listed in parentheses and are not highlighted - either include essential background material for the main paper or important results that follow the main paper. They need to be presented but not in the same level of detail as the main paper.

Wed. 1/14ANDREAS and CDJudith

Wed. 1/21DMD #1Abbe (1), Shawn (2), Danielle (3)

Wed. 1/28DMD #2Christine(1), Alicia (2), Kathy (3)

Wed. 2/4CF #1Megan (1), Lisa (2), Stacey (3)

Wed. 2/11CF #2 Daniela (1) Abbe (2), Shawn (3)

Wed. 2/18WINTER BREAK-----

Wed. 2/25FRAXA #1Christine (1), Danielle (2), Alicia (3)

Wed. 3/4FRAXA #2Stacey(1), Kathy (2), Megan (3)

Wed. 3/11FRDADaniela (1), Lisa (2), Shawn (3)

Wed. 3/18SMAAbbe (1), Alicia (2), Danielle(3)

Wed. 3/25ACMG Mtg------

Wed. 4/1LYNCHKathy (1), Stacey (2), Christine (3)

Wed. 4/8 SPRING BREAK

Wed 4/15PTENMegan (1), Daniela (2), Lisa (3)

Wed 4/22SNOW MAKE UP DATE

January 21, 2015

Duchenne/Becker Muscular Dystrophy #1

Background Reading:

Kunkel, L (2005) Cloning of the DMD Gene. Am. J. Hum. Genet. 76: 205-214.

O’Brien, KF and Kunkel, LM (2001). Dystrophin and muscular dystrophy: past, present and future. Molecular Genetics and Metabolism 74: 75-88.

Abbe:

1. ( Francke, U., et al. (1985) Minor Xp21 chromosome deletion in a male associated with expression of Duchenne muscular dystrophy, chronic granulomatous disease, retinitis pigmentosa, and McLeod syndrome. Am. J. Hum. Genet. 37: 250-267.)

Kunkel, L.M., et al. (1985) Specific cloning of DNA fragments absent from the DNA of a male patient with an X chromosome deletion. Proc. Natl. Acad. Sci. USA 82: 4778-4782.

Shawn:

2. Koenig, M., et al. (1987) Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals. Cell 50: 509-517.

Danielle:

3 Hoffman, E. P., et al. (1987) Dystrophin: The protein product of the Duchenne muscular dystrophy locus. Cell 51: 919-928.

(Hoffman, E. P., et al (1988) Characterization of dystrophin in muscle-biopsy specimens from patients with Duchenne's or Becker's muscular dystrophy. New Engl. J .Med. 318: 1363-1368)

January 28, 2015

Duchenne/Becker Muscular Dystrophy #2

Background Reading;

Laing, N. et al (2011) Molecular Diagnosis of Duchenne Muscular Dystrophy: Past Present and future in Relation to Implementing Therapies. Clin Biochem Rev 32: 129-134

Christine:

1. Koenig, M., et al (1989) The Molecular Basis for Duchenne versus Becker muscular dystrophy: Correlatiion of severity with type of deletion. Am. J. Hum. Genet. 45: 498-506.

(Specht, L.A., et al (1992) Prediction of dystrophin phenotype by DNA analysis in Duchenne/Becker muscular dystrophy. Pediatric Neurology 8: 432-436.)

Alicia:

2. , (Aartsma-Rus A.. et al (2004) Antisense-Induced Multiexon Skipping for Duchenne Muscular Dystrophy Makes More Sense. Am. J. Hum. Genet 74: 83-92)

(Mendell, J. et al (2013) Eteplirsen for the Treatment of Duchenne Muscular Dystrophy. Annals Neurol)

(Garde, D. (20140) FDA pulls back the curtain on Sarepta's latest DMD delay. Fiercebiotech.

Kathy:

3. Welch, E.M. et al (2007) PTC124 targets genetic disorders caused by nonsense mutations. Nature 447: 87-93

(Bushby, K. et al (2014) Ataluren treatment of patients with nonsense mutation dystrophinopathy.

Muscle Nerve. 2014 Oct;50(4):477-87. doi: 10.1002/mus.24332.)

(PTC Therapeutics Receives Conditional Approval in the European Union for Translarna™ For the

Treatment of Nonsense Mutation Duchenne Muscular Dystrophy

***For discussion: Another approach to therapy….upregulation of utrophin as a therapy

Tinsley, J. et al (2011) Daily treatment with SMTC1100, a novel small molecule utrophin upregulator dramatically reduces the dystrophic symptoms in the mdx mouse. PLoS One May 6;6(5):e19189. doi: 10.1371/journal.pone.0019189.

***For discussion: Newborn Screening for DMD: Pro’s and Con’s? Males and Females?

Mendell, J. (2013) Report of MDA muscle disease symposium on newborn screening for Duchenne Muscular Dystrophy. Muscle and Nerve 48: 21-26.

February 4, 2015

Cystic Fibrosis #1

Background Reading:

Cutting, G. (2014) Cystic fibrosis genetics: from molecular understanding to clinical applications. Nat Rev Genet AOP, published online 18 November 2014; doi:10.1038/nrg3849. Extremely comprehensive but worth skimming and keeping as a reference

Megan:

1. (Tsui, L.-C., et al (1985) Cystic fibrosis defined by a genetically linked polymorphic DNA marker. Science 230: 1054-1057.)

Knowlton, R. G., et al (1985) A polymorphic DNA marker linked to cystic fibrosis is located on chromosome 7. Nature 318: 380382.

White, R., et al. (1985) A closely linked genetic marker for cystic fibrosis. Nature 318: 382-384.

Lisa:

2. ( Rommens, J.M. et al (1989) Identification of the Cystic Fibrosis Gene: Chromosome Walking and Jumping. Science 245, 1059-1065.)

Riordan, J.R., et al (1989) Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245: 1066-1073.

Stacey:

3. (Van Goor, F. et al (2011) Correction of the F508del-CFTR protein processing defect in vitro by the investigational drug VX-809. PNAS 108: 18843-18848. )

Clancy, JP et al (2012) Results of a phase IIa study of VX-809 , an investigational CFTR corrector compound, in subjects with cystic fibrosis homozygous for the F508del-CFTR mutation. Thorax 67: 12. - Lumacaftor for mis-folding mutations

Ramsey, B. et al (2011) A CFTR Potentiator in Patients with Cystic Fibrosis and the G551D Mutation. New Eng. J. Med. 365: 1663-1672  Ivacaftor for gating mutations

(Boyle, M. (2014) A CFTR corrector (lumacaftor) and a CFTR potentiator (ivacaftor) for treatment of patients with cystic fibrosis who have a phe508del CFTR mutation: a phase 2 randomised controlled trial. Lancet Resp. Med. 2: 527-538)

*** For general discussion

Kerem, E. (2014) Ataluren for the treatment of nonsense-mutation cystic fibrosis: a randomized, double-blind, placebo-controlled phase 3 trial. Lancet Respir Med 2, 539-47

February 11, 2015

Cystic Fibrosis #2

Background Reading:

The Cystic Fibrosis Genotype-Phenotype Consortium (1993) Correlation between genotype and phenotype in patients with cystic fibrosis. N. Engl. J. Med. 329, 1308-13

When a CF mutation’s in question

do consider its effect on digestion.

But CFTR genotype

will not predict phenotype

with regard to the pulmonary congestion!

By Elinor Lanfelder, MS, CGC, Oct. ‘98

Langfelder-Schwind, E. et al (2013) Molecular Testing for Cystic Fibrosis Carrier Status Practice Guidelines: Recommendations of the National Society of Genetic Counselors

J Genet Counsel DOI 10.1007/s10897-013-9636-9

Daniela:

1. Kiesewetter., et al (1993) A mutation in CFTR produces different phenotypes depending on chromosomal background. Nature Genetics 5: 274-278.

(Chillon, M. et al (1995) Mutations in the Cystic Fibrosis Gene in Patients with Congenital Absence of the Vas Deferens. N. Engl. J. Med 332: 1475-80.)

(Rave-Harel, et al. (1997) The Molecular Basis of Partial Penetrance of Splicing Mutations in Cystic Fibrosis Am. J. Hum. Genet. 60: 87-94)

Abbe:

2. Cuppens, H. et al (1998) Polyvariant Mutant Cystic Fibrosis Transmembrane Conductance Regulator Genes. The polymorphic (TG)m locus explains the partial penetrance of the 5T polymorphism as a disease mutation. J. Clin. Invest. 101: 487-496.

Groman, J. et al (2004) Variation in a Repeat Sequence Determines Whether a Common Variant of the Cystic Fibrosis Transmembrane Conductance Regulator Gene Is Pathogenic or Benign. Am. J. Hum. Genet. 74: 176-179

Shawn:

3. ( Farrell, PM et al (2001) Early diagnosis of cystic fibrosis through neonatal screening prevents severe malnutrition and improves long-term growth. Pediatrics 107: 1-12)

Rock, MJ et al (2005) Newborn screening for cystic fibrosis in Wisconsin: Nine year experience with routine trypsinogen/DNAtesting. J Pediatr 147: S73-S77

( Tluczek A, et al, (2013) Long-term follow-up of cystic fibrosis newborn screening: Psychosocial functioning of adolescents and young adults, J Cyst

Fibros (2013),

The most comprehensive websites on CFTR mutations are:

CFTR 2 Website

Diseases of Unstable Repeat Expansion: A Case of Disease Caused by Loss of Protein Function.

February 25, 2015

Fragile X Syndrome #1:

Background Reading:

Nelson, D. et al (2013) The Unstable Repeats—Three Evolving Faces of Neurological Disease. Neuron 77: 825 -843

Finucane, B. et al (2012) Genetic Counseling and Testing for FMR1 Gene Mutations:

Practice Guidelines of the National Society of Genetic Counselors. J Genet Counsel) 21:752–760 DOI 10.1007/s10897-012-9524-8

Christine:

1. ( Lubs, H.A. (1969) A marker X chromosome. Am. J. Hum. Genet. 21:231-244)

(Warren et. al (1987) The fragile X site in somatic cell hybrids: An approach for molecular cloning of fragile sites. Science 237: 420)

Warren, et. al. (1990) Isolation of the human chromosomal band Xq28 within somatic cell hybrids by fragile X site breakage. Proc. Natl. Acad. Sci. USA 87: 3856-3860.

Danielle:

2. Verkerk, A.J.M.H. et al (1991) Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting variation in Fragile X syndrome. Cell 65: 905-914.

(Pieretti, M. et al (1991) Absence of expression of the FMR-1 gene in fragile X syndrome. Cell 66: 817-822)

Sutcliffe, J.S., et al (1992) DNA methylation represses FMR-1 transcription in Fragile X syndrome. Human Molec. Genet. 1: 397-400.

Alicia:

3. (Ashley, CT et al (1993) FMR1 Protein: Conserved RNP Family Domains and Selective RNA Binding. Science 262, 563-566.)

Darnell, JC et al (2001) Fragile X Mental Retardation Protein Targets G Quartet mRNA’s Important for Neuronal Function. Cell 107, 489-99.

Summarize only Smith, L and Cowan, C. (2103) Striking a balance in fragile X. Nature Med 19: 1370-1373

Diseases of Unstable Repeat Expansion:

A Case of Disease Caused by Loss of Protein Function (cont.)

And

A Case of Disease Caused by Altered RNA Function

March 4, 2015

Fragile X Syndrome #2

Background Reading:

Monaghan, K. et al (2013) ACMG Standards and Guidelines for fragile X testing: a revision to the disease-specific supplements to the Standards and Guidelines for Clinical Genetics Laboratories of the American College of Medical Genetics and Genomics

Genet Med:15(7):575–586

Hagerman, P. (2013) Fragile X associated tremor/ataxia syndrome (FXTAS): pathology and mechanisms . Acta Neuropathol 126: 1-19

Stacey:

1. Fu, Y.H. et al (1991) Variation of the CGG repeat at the Fragile X site results in genetic instability: resolution of the Sherman Paradox. Cell 67: 1047-1058.

(Eichler, E.E., et al (1994) Length of uninterrupted CGG repeats determines instability in the FMR1 gene. Nature Genetics 8: 88-94)

(Kronquist, K., Sherman, S., Spector, E. (2008) Clinical significance of tri-nucleotide repeats in Fragile X testing: A clarification of ACMG guidelines. Genetics in Medicine 10: 845-847)

Kathy:

2. Chen, L. et al (2010) An Information-Rich CGG Repeat Primed PCR that Detects the Full Range of Fragile X Expanded Alleles and Minimizes the Need for Southern Blot Analysis. J. Molecl Diagnostics 12: 589-600.

(Yrigollen, C. et al (2012) AGG interruptions within the maternal FMR1 gene reduce

the risk of offspring with fragile X syndrome. Genetics in medicine 14: 730-736)

(Nolin, S. et al (2014) Fragile X full mutation expansions are inhibited by one or

more AGG interruptions in premutation carriers. Genet in Med, advance online publication 11 September 2014. doi:10.1038/gim.2014.106)

Megan:

3. Tassone, F. et al (2000) Elevated levels of FMR1 mRNA in carrier males: a new mechanism of involvement in Fragile X syndrome. Am J Med Genet 66: 6-15)

(Todd PK, et al (2013) CGG repeat associated translation mediates neurodegeneration in fragile X tremor ataxia syndrome. Neuron 2013, 78(3):440–455.)

For class discussion: Newborn screening for FraX

Tassone, F. (2014) Newborn Screening for Fragile X. JAMA Neurol. 71(3): 355–359

Diseases of Unstable Repeat Expansion: A Case of Disease Caused by an Intronic GAA Triplet that Leads to Mitochondrial Dysfunction

March 11, 2015

Friedreich Ataxia

Background Reading:

Delatycki, M. et al (2012) Clinical Features of Friedreich Ataxia. Journal of Child Neurology 27(9) 1133-1137

Yandim, C. et al (2013) Gene regulation and epigenetics in Friedreich’s

Ataxia. J Neurochem 126 (Suppl. 1): 21-42

Gottesfeld, J. et al (2013) Increasing frataxin gene expression with histone

deacetylase inhibitors as a therapeutic approach for Friedreich’s ataxia. J.. Neurochem

126 (Suppl. 1): 147-154

Daniela:

1. Campuzano, V. et al (1996) Friedreich’s Ataxia: Autosomal Recessive Disease Caused by an Intronic GAA Triplet Repeat Expansion. Science 271: 1423-1427

Filla, A. et al (1996) The Relationship between Trinucleotide (GAA) Repeat Length and Clinical Features in Friedreich Ataxia. Am. J. Hum. Genet 59: 554-560

Montermini, L. eta l (1997) The Friedreich ataxia GAA triplet repeat: premutation and normal alleles. Hum Molec Genet 6: 1261-1266)

Lisa:

2. Campuzano, V. et al (1997) Frataxin is reduced in Friedreich ataxia patients and is associated with mitochondrial membranes. Human Molec Genet 6: 1771-1780

(Chutake, YK et al (2014) Epigenetic Promoter Silencing in Friedreich Ataxia is Dependent on Repeat Length. Ann Neurol;76:522–528)

(Soragni, E. et al (2014) Epigenetic Therapy for Friedreich Ataxia. Ann Neurol 76:489–508)

Shawn:

3. Rotig, A. et al (1997) Aconitase and mitochondrial iron-sulphur protein deficiency in Friedreich ataxia. Nature Genet 17: 215-217

(Richardson, D. et al (2009) The ins and outs of mitochondrial iron-loading: the metabolic defect in Friedreich’s ataxia. J Mol Med 88: 323-329)

(Arpa J et al (2014) Triple therapy with deferiprone, idebenone and riboflavin in Friedreich’s ataxia Acta Neurol Scand: 129: 32–40.

March 18, 2015

Spinal Muscular Atrophy Type I

Background Reading:

Brochures from SMA Foundation on Genetics of SMA and Understanding Spinal Muscular Atrophy

Markowitz, J.et al (2012) Spinal Muscular Atrophy: A Clinical and Research Update. Pediatric Neurology 46 (2012) 1e12

Singh, P. et al (2013) Current advances in drug development in spinal muscular atrophy. Curr Opin Pediatr 25: 682-688

Abbe:

1.(Melki, J. et al (1990) Gene for chronic proximal spinal muscular atrophies maps to chromosome 5q. Nature 344: 767-768)

(Gillam, T.C., Brzustowicz, L.M. et al (1990) Genetic homogeneity between acute and chronic forms of spinal muscular atrophy. Nature 345: 823-825)

Lefebvre, S. et al (1995) Identification and Characterization of a Spinal Muscular Atrophy-Determining Gene. Cell 80: 158-165

Alicia:

2.Lorson, C. et al (1999) A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. PNAS 96: 6307-6311

Mailman, et al (2002) Molecular analysis of spinal muscular atrophy and modification of the phenotype by SMN2. Genetics in Medicine 4: 20-26.