Personalized Medicine Or Precision Medicine

4/27/2017

Personalized Medicine or Precision Medicine

Phillip Sharp Koch Institute for Integrative Cancer Research, Department of Biology, MIT

Personalized Verses Precision Medicine- NRC Report

Precision Medicine‐ tailoring medical treatment to characteristics of each patient‐ not creation of drugs unique to a patient

–challenge: create a drug for a patient?

National Research Council (US) Committee on A Framework for Developing a New Taxonomy of Disease. Toward Precision Medicine: Building a Knowledge Network for Biomedical Research and a New Taxonomy of Disease. Washington, DC: National Academies Press, 2011. 142p.

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Recent advances in Spinal Muscular Atrophy (SMA)

Kathy Kmonicek/CSHL Harbor Transcript. Cold Spring Harbor Laboratory. 2016; 36(2).

Released May 2016 Summary of the genetics of SMA

Telomeric Centromeric

SMN1 • One SMN1 (telomeric) and several C Deletion of SMN1 SMN2 T SMN2 (centromeric)1 • 95–98% of patients with SMA have a homozygous disruption of SMN1 SMN1 pre‐mRNA SMN2 pre‐mRNA • SMN2 encodes a truncated mRNA 6 7 8 6 7 8 isoform1 SMN2 mRNA o A critical nucleotide transition SMN1 mRNA in SMN2 mRNA results in a 6 8 6 7 8 nonfunctional protein • About 10% of SMN2 pre-mRNA Nonoligomerizing unstable truncated SMN protein is translated into full-length Normal full‐length SMN protein 3 SMN protein ~90% • The severity of the SMA phenotype is correlated with the number of SMN2 gene copies 1 Rapidly degraded

1. d’Ydewalle C & Sumner CJ. Neurotherapeutics. 2015;12:303-316; 2. Prior TW & Russman BS. GeneReviews®. http://www.ncbi.nlm.nih.gov/books/NBK1352/. Accessed Mar 2016; 3. Lunn MR & Wang CH. Lancet. 2008;371:2120-2133 Redrawn from Neurotherapeutics. 2015;12:303-316;

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Released May 2016 ASOs can modify splicing of SMN2

Without ASO • Screening of ASOs showed

that targeting ISS‐N1 in Intron hnRNP A1/2 intron 7 can increase 6 7 8 inclusion of exon 7 5’ 3’ • These ASOs compete with Exons 6 8 hnRNP A1/2 for binding to With ASO the ISS‐N1 site ASO

• ASOs with certain chemical Intron

modifications promoted 6 7 8 5’ 3’ inclusion of exon 7 in the ISS‐N1

final transcript 6 7 8

Redrawn from: Rigo F, et al. Antisense-based therapy for the treatment of spinal muscular atrophy. Journal of Cell Biology 1 October 2012;199 (1):21-25

UpdatedFull-length December 2016 SMN2 mRNA in thoracic spinal cord in nusinersen- treated infants with SMA compared with untreated infants with SMA

Healthy Nusinersen‐ infants Untreated SMA treated SMA RT‐PCR ABC WXYZ 123 analysis 6 7 8 Full-length SMN2 mRNA SMN 2 mRNA

6 8 Truncated SMNΔ7 mRNA 8080 69

60 mRNA 60 52 SMN2 50 % full-length SMN2 by group 40

SMN2 40 • Healthy infants / untreated SMA 26 25 26 = 15–26 20 2020 19 17 15 • Nusinersen-treated SMA = 50–69 % full-length  2.6-fold increase 00 % full-length A B C W X Y Z 1 2 3

Redrawn from Finkel RS, et al. Treatment of infantile-onset spinal muscular atrophy with nusinersen. Lancet. 2016 December 6;388(10063):3017-3026.

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Development of (the anti-sense oligonucleotide) Spinraza for treatment of SMA

1. Adrian Krainer (CSHL) collaborated with Frank Bennett of Ionis (2008)

2. Ionis Pharmaceutical developed the antisense oligonucleotide, founded by Stanley Crooke in 1989

3. Biogen licensed technology (2012) clinical trials (FDA approved 2016)

Francis Crick and James Watson (Molecular Genetics, G.S. Stent, 1971)

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The original operon model of Jacob and Monod, as proposed for the regulation of the lac genes of E. coli in 1961

I P O Z Y A DNA

mRNA

Inducer Protein

Inactive Active Galactosidase Permease Transacetylase repressor repressor

Stent, G.S. Molecular Genetics. 1st ed.1971.

EM of RNA/DNA hybrid of hexon mRNA/genome – 3 loops

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EST evidence has demonstrated several modes of variation for transcripts coming from a single locus

• Standard transcriptional activation • Alternative promoter usage • Exon inclusion/exclusion • 3' UTR utilization • All of the above

EST evidence has demonstrated several modes of variation for transcripts coming from a single locus

( ) • Oligonucleotide specific for exon included in splicing pattern (1) inhibits expression of function encoded by (1) isoform but not (2) isoform. • Gene sequence leads directly to design of oligonucleotide for treatment.

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Technology behind biotechnology

1) Recombinant DNA (1972) 2) DNA sequencing (1977) 3) Chemical DNA synthesis

Biogen Geneva 1978

Ralph Crane, Fortune Belinsky, Gene. DNA Can Build Companies, Too. Fortune. 1980 June 24;101(12):144.

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Cluster of high tech companies near MIT

Courtesy of MIT Entrepreneurship Initiative

Cambridge transformed from candy to biotechnology- Novartis International Research Center

Courtesy of MIT Tech Review

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Biotech transforms Kendall Square-1975

Courtesy of MIT Tech Review

Biotech transforms Kendall Square-2012

Courtesy of MIT Tech Review

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RNA Biology and new Therapeutics?

Celebrating the Nobel Prize for RNAi Drs. Andrew Fire and Craig Mello

nature collections. 2004 December.

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Human genetic-disease genes

1. ~3,000 Mendelian disease genes known

2. ~8% of live births—genetic disorder by early adulthood

3. Estimated—each child with genetic disorder costs ~$5,000,000

4. Diagnostic rate of genetic disorders: children ~11%, adults ~34%

Chong et al. The Genetic Basis of Mendelian Phenotypes. Am. J. Hum. Genet. 2015 August 6; 97(2): 1999-215.

Potential Conflicts of Interest

1. RNA interference (1998)—patents on biochemistry (1999–2001) MIT, Max Plank Germany, and U. of Massachusetts

2. Alnylam founded (2002)—research expenditures $1.5B

3. Co-founder, Board of Directors, Chair SAB

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RNA interference (siRNA)Therapeutic targets mRNAgene fromsilencing a gene

siRNA

DNA

mRNA

Therapeutic gene silencing

Protein Therapeutics

DNA

mRNA

Proteins Small Receptors Enzymes Molecules

Antibodies

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Nucleic acid delivery

• Importance and challenges • Viral vs. non- viral • Standard reagents are ineffective

Whitehead, K.A. et al. Knocking down barriers: advances in siRNA delivery. Nature Reviews Drug Disc. 2009 February;8:129-138.

Tissue and Cellular Uptake Targeting the liver: ASGPR and GalNAc

GalNAc-siRNA Conjugate • GalNAc ligand conjugated to chemically modified siRNA to mediate targeted delivery • Trivalent GalNAc carbohydrate cluster has nM affinity for ASGPR • Administered subcutaneously (SC)

GalNAc ligand

Varki, Ajit et.al. Essentials of Glycobiology. 2nd ed. La Jolla: Cold Spring Harbor Laboratory Press; 2009. 800 p.

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Optimizing chemistry improves stability, PK, potency and duration of effect

1000000 Liver Exposure Metabolic profiling in liver 100000

Standard Template Chemistry (STC) 10000

1000 (GalNAc)3 SCSTC S 5′ 100 ESC 10 AS 5′ (ng/g) Concentration Liver 0 50 100 150 200 Time (h) = 2′‐F = 2′‐O‐methyl Target KD 1.2 Enhanced Stabilization Chemistry (ESC) STC 1.0

S 5′ 20

40 AS 5′

60 ESC

= Enzymatic cleavage Knockdown% AT Serum

100 -10 0 10 20 30 40 Day

Dramatic increase in efficacy of siRNA delivery to hepatocytes in vivo

100

0.1 ED50 siRNA (mg/kg)

0.01 2006 2008 2010 2012 2014

Year Data from R. Meyers

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Hemophilia and Rare Bleeding Disorders

Genetic deficiency resulting in PATIENT POPULATION* inability to generate thrombin Hemophilia A and B and stop bleeding 1. Highest need is prophylaxis 200,000 for inhibitor patients and to avoid inhibitor worldwide formation in all patients with ~4,000 inhibitors 2. Global need due to frequent IV infusions, ability to manufacture, and cold chain *World Federation of Hemophilia. Report on the Annual Global Survey 2014. Montreal: World Federation of Hemophilia, 2015 October, 48 p.

Fitusiran for Hemophilia- siRNA inhibitors of Anti-thrombin (AT) Potential to Restore Hemostasis in Hemophilia

Genetically validated, liver‐expressed target gene Biomarker for POC Path to approval

Hemophilia A Plasma Biomarkers FVIIa FVII Established Endpoint AT Lowering, Annualized Bleeding Rate (ABR) FVIII FVIIIa FX Thrombin Generation 140 100

Hemophilia B 120 AT % Lowering 80 FIXFIX FIXa Peak Thrombin

100 (nM) Thrombin Peak FXa ATAT 60 80

FVa FV 60 40 AT Activity (%) AT Activity

Prothrombin Thrombin 40

20 20

Fibrinogen Fibrin 0 Photo courtesy of Guy Young, M.D. 0 Director, Hemostasis & Thrombosis Center at Children's -30 0Days 60 120 Hospital Los Angeles and Professor of Pediatrics, USC Keck School of Medicine Blood clot

Fitusiran Phase 1 results: Pasi et al., WFH, July 2016

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Other emerging liver targets

• Suppression of hemolysis in Paroxysmal Nocturnal Hemoglobinuria (PNH) patients

• Suppression of Hepatitis B replication

• Potential therapeutic for primary hyperoxaluria

• Potential treatment for hypercholesterolemia—PCSK9 target

Treatment effect is prolonged allowing dosing every 6 months

-40

-20

0 Treatment Placebo 20 100 mg

40 300 mg

60 (Change from Baseline)

Mean (SEM) % Knockdown PCSK9Mean (SEM) 80

100 012345 Months PCSK9 inhibitor injection

Fitzgerald, K. et al. A Highly Durable RNAi Therapeutic Inhibitor of PCSK9. The New England Journal of Medicine. 2017 January 5; 376:41‐51.

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1990-2003

Broad Institute (2003) large collaborative multidisciplinary science

Draft: (90%) Feb 2001 Finished: (99.3%) Apr 2003

Nature. 2001 February 15; 209.

Convergence timeline

Timeline: The three revolutions 2009: NAS mid-2000s: Academic releases A 1976: Biotech sector sectors start exploring New emerges with convergence Biology founding of report Genentech 1953: Discovery of DNA Structure

Convergence Molecular Biology Revolution Revolution Genomics Revolution

1950 19601970 1980 1990 2000 2010

2001: Human Genome Project, Celera publish working draft of human genome 1969: Salvador Luria, theorist of molecular biology, awarded Nobel Prize

Image and info credits (clockwise from top-left): DNAmazing.com, Gene.com, BioX.stanford.edu, qb3.org, mit.edu/ki, nap.edu, sciencemag.org, nature.com, nlm.nih.gov

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The Third Revolution

“Physicists gave engineers the electron and they created the IT revolution. Biologists gave engineers the gene and together they will create the future.”

- Susan Hockfield

Convergence

Convergence is a blueprint for innovation.

Advances in information technology, materials, imaging, nanotechnology, optics, and quantum physics, coupled with advances in computing, modeling, and simulation, have already transformed physical science. They are now beginning to transform life science as well.

Sharp Phillip A, Jacks Tyler, Hockfield, Susan. Convergence: The Future of Health. 2016 June; Cambridge, MA. Available from: http://www.convergencerevolution.net.

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Revolutions in engineering

1) Information technology 2) Storage and processing of large sets of data 3) Synthesis of composites of nanoscale 4) Micro-fabrication – tooling at nanoscale 5) Sensitive and quantitative measuring devices including imaging 6) Control technologies - dynamics

Information science for medical care‐ Kendall Square

Courtesy of MIT Tech Review

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White House Priorities- Brain Initiative Agencies should give priority to R&D investments…[including] research at the interfaces of biology, physical sciences, and engineering. Agencies should also give priority to the President's BRAIN (Basic Research through Advancing Innovative Neurotechnologies) Initiative. The BRAIN Initiative [Internet]. Washington, D.C. 2013 April 2. Available from: https://obamawhitehouse.archives.gov/BRAIN

The Koch Institute: A New Model for Cancer Research

Engineering

Biology Integration and Collaboration Discoveries and Solutions

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Angelika Dan Angela Sangeeta Michael Jianzhu Michael Frank Paula Michael Amon Anderson Belcher Bhatia Birnbaum Chen Cima Gertler Hammond Hemann

Omer David Yilmaz Housman

Michael Nancy Yaffe Hopkins

Dane Richard Wittrup Hynes

Forest Darrell White Irvine

Matthew Stefani Phillip Ram Scott Christopher Jackie Robert Angela Tyler Vander Heiden Spranger Sharp Sasisekharan Manalis Love Lees Langer Koehler Jacks

Institutions that combine a broad range of scientific and engineering disciplines in biosciences research

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From Convergence to Confluence

Tietê River. Wikipedia Commons. 2005 March 27. Available from: https://upload.wikimedia.org/wikipedia/commons/4/4d/Rio_Tietê_-_Cidade_de_Salto_1.jpg

Thank you for the opportunity to present this lecture. -Phil Sharp