Transcript FRDA Team Meeting Boston 31 May 2008

ASENT 2009
Biomarkers for Monitoring Treatment
with HDAC Inhibitors
James Rusche, PhD
RepliGen Corporation
RepliGen
HDAC Inhibitors as a Drug Target
HATs (histone acetyltransferases) are responsible for acetylation
HDACs (histone deacetylases) are responsible for deacetylation
 There are 11 identified HDAC enzymes which vary in tissue expression,
ontogeny, and target proteins for deacetylase activity.
 Pan inhibitor (SAHA) approved for treating cancer (Vorinostat).
 Many cell culture and animal studies have suggested HDAC inhibition is
efficacious in both neurodegenerative and neuropsychiatric diseases.
RepliGen
Trinucleotide Expansion Diseases
All have transcription dysregulation but Friedreich’s Ataxia is an intronic insert
with repeat length correlated to level of RNA and protein
Taken from: www.brain.riken.jp
RepliGen
HDAC Inhibitor Can Increase Frataxin Expression
Patient PBMC incubated with
HDACi for 48 hr
Relative Quantity
relative acetylation
ChIP at frataxin gene
indicates hypoacetylation
Pro
Up
GAA
Down
GAA
Pro
GM15851
Nat Gen (2006)v2,p551
Up
GAA
Down
GAA
GM15850
RGFP109 Dose Response (M)
RepliGen
Drug Effects on Gene Expression by Microarray
10 FRDA
10 Carrier
10 Control
Ficoll Leukocyte Isolation
DMSO
Control
HDACi
48h
Illumina BeadChip Human Arrays
Data Analysis
RepliGen
Gene Expression Changes Across Subject Types
• Drug induced expression changes generally common across subject type
• Large portion of genes with unique patient expression pattern are reversed by
HDACi treatment
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
FRDA
Carrier
FRDA106
Control106
Carrier106
RepliGen
QPCR Characterization of Drug Signature Genes
Pilot: Use 9 subjects with 23 genes to identify subset with consistent response to drug
15 FRDA
15 Carrier
15 Control
Ficoll Leukocyte Isolation
DMSO
Control
HDACi
48h
RT-QPCR- TAQMAN
Data Analysis
RepliGen
Fxn Induction Significantly Higher in FRDA Cells
Frataxin is a Disease Response Biomarker
A. FXN Transcript Level in Patients
B. FXN Induction in Response to 10 M RGFA8
***(<.0001)
Relative Quantity
Relative Quantity
***(<.0019)
NS
NS
RepliGen
Drug Effect Uniform Across All Subjects
FRDA
Log2 Fold Change
Carrier
Control
FXN
STX1A
CRIP2
FXYD1
Drug Effect Genes
PTRF
RepliGen
Log2 Fold Change
Comparison of Microarray and RT-QPCR
Drug Effect Genes
: avg microarray LFC for gene
RepliGen
Biomarker for Monitoring HDACi Activity

HDAC inhibitors can show gene expression
changes unique to a genotype or are common
across subject groups

RT-QPCR can be used to monitor “drug
signature” genes in diverse subject groups

Gene expression measures may prove useful to
characterize pharmacodynamic effects of HDAC
inhibitors in early trials of Neurodegenerative
conditions
RepliGen
Collaborations

Scripps Research
Institute
-

R. Brady
D. Herman
L. Soragni
J. Gottesfeld
-


UCLA
-
Erasme Hôpital
Brussels
Repligen
-
G. Coppola
D. Geschwind
-

-
CHoP
-
J. Farmer
D. Lynch



M. Rai
M. Pandolfo
H. Plasterer
A. Cooper
S. Sharma
M. Belmonte
S. Sethumadhavan
J. Rusche
FARA
GoFAR
MDA
RepliGen