Genome Editing for Thalassemia
CAF Patient-Family Conference
21 June 2014
Daniel E. Bauer, MD PhD
Disclosures
• Consultant for Editas Medicine
Genetics: each cell carries a genome
ASHG.org
The genome is composed of DNA, 3 billion positions
education-portal.com
The genome includes lots of DNA …
education-portal.com
… with many genes …
… and even more non-coding DNA.
education-portal.com
Genome editing
Genome editing
Genome editing tools are sequence-specific nucleases
Genome editing tools have
two features:
1) Recognize specific DNA
sequences (i.e. specific
genes or non-coding
elements)
van der Oost. Science (2013) 339:768.
Genome editing tools are sequence-specific nucleases
Genome editing tools have
two features:
1) Recognize specific DNA
sequences (i.e. specific
genes or non-coding
elements)
van der Oost. Science (2013) 339:768.
Genome editing tools are sequence-specific nucleases
Genome editing tools have
two features:
1) Recognize specific DNA
sequences (i.e. specific
genes or non-coding
elements)
van der Oost. Science (2013) 339:768.
Genome editing tools are sequence-specific nucleases
Genome editing tools have
two features:
1)Recognize specific DNA
sequences (i.e. specific
genes or non-coding
elements)
2)Cut DNA (“nuclease”),
then a scar is left behind
van der Oost. Science (2013) 339:768.
Genome editing: cleavage repair can either disrupt original
sequence or replace it with a new copy
NEB.com
Genome editing: cleavage repair can either disrupt original
sequence or replace it with a new copy
“delete”
NEB.com
Genome editing: cleavage repair can either disrupt original
sequence or replace it with a new copy
“delete”
NEB.com
“copy and paste”
Two strategies for genetic therapy:
gene addition and genome editing
Fischer. Nature (2014) 510:226.
Two strategies for genetic therapy: addition and editing
• Gene addition:
• Feasible with existing technology; clinical trials ongoing.
• Early trial results appear exciting.
• Challenges:
1. Will enough of the added gene be made in the cells with the integration?
Will enough of the blood stem cells have the added gene?
2. Is the benefit durable? Will the added gene continue to function over days,
weeks, months, years, decades?
3. Is the added gene safe? Will its semi-random integration into the genome
change the function of other genes in the genome?
Fischer. Nature (2014) 510:226.
Two strategies for genetic therapy: addition and editing
• Gene editing:
• Promise of permanent repair of the underlying disease-causing mutation.
• Promise of specific beneficial change at the intended genomic site (e.g. bglobin gene) without impacting remainder of genome.
• Challenges:
1. Technology is in a relatively early stage and needs to be further
developed.
2. Can enough cells be edited to have therapeutic impact?
3. Will the editing be exquisitely specific, or will other regions of the genome
aside from the target be affected?
Fischer. Nature (2014) 510:226.
Thalassemia is caused by mutations of the a or b-globin genes
Many different mutations of the b-globin gene
cause b-thalassemia
The problem in b-thalassemia is too much a-globin
relative to b-globin
g-globin (fetal hemoglobin) can functionally substitute
for b-globin (adult hemoglobin)
BCL11A enhancer determines fetal hemoglobin level
Hardison and Blobel. Science (2013) 342:206.
BCL11A enhancer determines fetal hemoglobin level
Hardison and Blobel. Science (2013) 342:206.
BCL11A enhancer determines fetal hemoglobin level
Hardison and Blobel. Science (2013) 342:206.
The vision: mimicking common protective genetic variation for
therapeutic benefit
•
•
•
Collect blood stem cells from patient with b-thalassemia
Introduce sequence-specific nucleases to disrupt BCL11A enhancer
Reinfuse modified blood stem cells to patient
The vision: mimicking common protective genetic variation for
therapeutic benefit
•
•
•
Collect blood stem cells from patient with b-thalassemia
Introduce sequence-specific nucleases to disrupt BCL11A enhancer
Reinfuse modified blood stem cells to patient
•
•
•
•
•
Potential benefits:
Loss of BCL11A expression in red blood cells causing increased fetal hemoglobin
Spares BCL11A expression in other blood cells
Modification would be permanent
Survival advantage of cells (would outcompete unmodified cells)
Compared to gene addition, no semi-random insertion of material into the genome,
and no need for lifelong expression of foreign sequences
The vision: mimicking common protective genetic variation for
therapeutic benefit
•
•
•
Collect blood stem cells from patient with b-thalassemia
Introduce sequence-specific nucleases to disrupt BCL11A enhancer
Reinfuse modified blood stem cells to patient
•
•
•
•
•
Potential benefits:
Loss of BCL11A expression in red blood cells causing increased fetal hemoglobin
Spares BCL11A expression in other blood cells
Modification would be permanent
Survival advantage of cells (would outcompete unmodified cells)
Compared to gene addition, no semi-random insertion of material into the genome,
and no need for lifelong expression of foreign sequences
•
•
Potential risks:
Genome modification at sites other than the intended target
Preparation (“conditioning”) therapy for stem cell transplant (shared risk of both
gene addition and genome editing; potentially much less toxic than for
“allotransplant” (from related or unrelated donor)
Summary
• b-thalassemia results from mutations in b-globin, a
single gene within a large genome
• Gene addition adds a copy of b-globin by semirandom integration into the genome
– Currently being tested in early-phase clinical trials
– Challenges include: durable high-level expression; ensuring
other important genes are not disrupted due to integration
• Genome editing offers the promise of precise and
permanent genome modification to mimic protective
genetic variation (e.g. at BCL11A) or to repair b-globin
– Challenges include: effective delivery of genome editing tools
to cells to achieve efficient target disruption/repair; ensuring
modification is limited to intended target
Acknowledgments
Boston Children’s Hospital
Stuart Orkin
Jian Xu
Vijay Sankaran
Sophia Kamran
Matthew Canver
Carrie Lin
Abhishek Dass
Yuko Fujiwara
Zhen Shao
E. Crew Smith
Cong Peng
Hojun Li
Boston Children’s
Ellis Neufeld
David Williams
David Nathan
Jennifer Eile
Alan Cantor
Bill Pu
Dana-Farber Cancer Institute
GC Yuan
Luca Pinello
Broad Institute
Feng Zhang
Neville Sanjana
Ophir Shalem
Montreal Heart Institute
Guillaume Lettre
Samuel Lessard
Stanford University
Matthew Porteus
Richard Voit
University of Washington
John Stamatoyannopoulos
Peter Sabo
Jeff Vierstra
The vision: mimicking common protective genetic variation for
therapeutic benefit
•
Feasibility
ASH 2013 Abstracts #434 and 4213. Slide courtesy of Sangamo BioSciences.
The vision: mimicking common protective genetic variation for
therapeutic benefit
•
Feasibility
Tebas et al. NEJM (2014) 370:901.