Spring 2017

Proseminar: Molecular Basis of Genetic Diseases

Biology 203 covers the molecular basis ofDuchenne Muscular Dystrophy/Becker Muscular Dystrophy, Cystic Fibrosis, Spinal Muscular Atrophy, and Lynch Syndrome. We will also cover three of the triplet-repeat expansion diseases: Fragile-X Syndrome, Myotonic dystrophy I 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.
  • Improve your Powerpoint skills. 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 allexpected 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. Please 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 guidelines 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 andshould 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).

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.

Tues. 1/17ANDREAS and CDJudith

Tues. 1/24DMD #1Allie (1), Rhonda (2), Lindsay (3)

Tues. 1/31DMD #2Lorraine(1), Katrina (2), Yiru (3)

Tues. 2/7CF #1Katie (1), Anna-Lena (2), Ashley (3)

Tues. 2/14CF #2 Liz(1) Allie (2), Rhonda (3)

Tues.2/21WINTER BREAK-----

Tues.2/28FRAXA #1Lorraine (1), Lindsay (2), Katrina (3)

Tues. 3/7FRAXA #2Ashley(1), Yiru (2), Katie (3)

Tues. 3/14DM1Liz (1), Rhonda (2), Anna-Lena(3)

Tues. 3/21ACMG Meeting

Tues. 3/28FRDAAllie (1), Katrina (2), Lindsay(3)

Tues.4/4SMAYiru (1), Katie (2), Lorraine (3)

Tues. 4/11, 4/18SPRING BREAK

Tues. 4/25LYNCHLiz (1), Ashley (2), Anna-Lena (3)

Tues.5/2MAKE UP DATE

January 24, 2017

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.

Allie:

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.

Rhonda:

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.

Lindsay:

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 31, 2017

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

Lorraine:

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.)

Katrina:

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 (2015) Longitudinal effect of eteplirsen vs. historical control on ambulation in DMD. Accepted Article’, doi: 10.1002/ana.24555 in Annals Neurol)

(Goemans , N. et al (2016) Pharmacokinetics of Drisapersen in Duchenne Muscular Dystrophy: Results from an Open-Label Extension Study. PLoS One 11(9):e0161955. Doi 10.1371/journal. Pone 0161955

Duchenne Muscular Dystrophy The approval follows a protracted debate about the benefit of the medication. (2016)

Yiru:

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

(PTC Announces Results from Phase 3 ACT DMD Clinical Trial of Translarna™ (ataluren) in Patients with Duchenne Muscular Dystrophy

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

Chung, J. et al (2015) Twenty-Year Follow-Up of Newborn Screening for Patients with Muscular Dystrophy. Muscle and Nerve.

Natera White Paper on DMD Carrier Screening (2016)

Hayes, B. et al (2016). Duchenne Muscular Dystrophy: a Survey of Perspectives on Carrier Testing and Communication within Families. J. Gen. Counsel 25:443-453

February 7, 2017

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

Katie:

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.

Anna-Lena:

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.

Ashley:

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

(Elborn, et al (2016) Efficacy and safety of lumacaftor/ivacaftor combination

therapy in patients with cystic fibrosis homozygous for Phe508del CFTR by pulmonary function subgroup: a pooled analysis Lancet Respir Med 4: 617–26

February 14, 2017

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 PracticeGuidelines: Recommendations of the National Society of Genetic Counselors

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

Liz:

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)

Allie:

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

Rhonda:

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)

(Kharrazi M, et al (2015) California Cystic Fibrosis Newborn Screening Consortium. Newborn screening for cystic fibrosis in California. Pediatrics;136(6):1062–1072

Sosnay and Farrell (2015) Challenges in Cystic Fibrosis Newborn Screening and Recommendations for Primary Care Physicians.Pediatrics;136(6):1181–1184

The most comprehensive websites on CFTR mutations are:

CFTR 2 Website

Interesting reading….


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

February 28, 2017

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

Lorraine:

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.

Lindsay:

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.

Katrina:

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.

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 7, 2017

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

Just for the pro’s. Flora Tassone (2015) Advanced technologies for the molecular diagnosis of fragile X syndrome. Expert Review of Molecular Diagnostics 15: 1465-1473.

Ashley:

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)

Yiru:

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)

Katie:

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)

(Leehey, M. et al (2008) FMR1 repeat length predicts motor dysfunction in premutation carriers. Neurology 70: 1397-1402

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

Also for background: Hall, D. et al (2016) Neurological and endocrine ohenotypes of fragile X carrier women. Clin Genet 89: 60-67

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 3’ Intronic Repeats

March 14, 2017

Myotonic dystrophy I

Excellent review: Chau, A. et al (2015) Developmental Insights into the Pathology and Therapeutic Strategies for DM!: Back to the Basics. Developmental Dynamics 244:377-399

Liz:

1. (Brook, JD et al (1992) Molecular Basis of Myotonic Dystrophy: Expansion of a Trinucleotide (CTG) Repeat at the 3’ End of a Transcript Encoding a Protein Kinase Family Member. Cell 68:799-808)

Mankodi, A. et al (2000) Myotonic Dystrophy in Transgenic mice Expressing an Expanded CUG Repeat. Science 289: 1769-1772

and

Commentary by Tapscott, S. (2000) Deconstructing Myotonic Dystrophy Science 289: 1701-1702.

Rhonda:

2. Kanadia, R. et al (2003) A Muscleblind Knockout Model for Myotonic Dystrophy. Science 302: 1978-1981.

(Kanadia, RN et al (2006) Reversal of RNA missplicing and myotonia after muscleblind overexpression in a mouse poly (CUG) model for myotonic dystrophy. PNAS 103: 11748-11753 )

(Cooper, T. (2006) A Reversal of Misfortune for Myotonic Dystrophy? N Engl J Med 355: 1825-1827)

Anna-Lena:

3.Wheeler, T. et al (2009) Reversal of RNA Dominance by Displacement of Protein Sequestered on Triplet Repeat RNA. Science 325: 336-339

(Cooper, T. (2009) Neutralizing Toxic RNA. Science 325: 272-

Bisset, B. et al (2015) Therapeutic impact of systemic AAV-mediated RNA interference in a mouse model of myotonic dystrophy. Human Mol. Genet. 24: 4971-4983

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

March 28, 2017

Friedreich Ataxia

Background Reading:

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

Clinical summary info… FYI. Reetz, et al (2015) Biological and clinical characteristics of the European Friedreich’s Ataxia Consortium for Translational Studies (EFACTS) cohort: a cross-sectional analysis of baseline data. Lancet Neurol 2015; 174–82

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

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

Allie:

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)

Katrina:

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)

(Chutake, Y. et al (2016) Reversal of epigenetic promoter silencing in Friedreich ataxia by class I histone deacetylase inhibitor. Nucleic Acids Rese 44: 5095-510) Very detailed study so please just present the highlights of the paper.

Lindsay:

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