RESEARCH UPDATE: GENE EXPRESSION IN SSC Monique Hinchcliff MD, MS Scleroderma Foundation Patient Education Day October 19, 2013 Northwestern University
Oct 19, 2014
RESEARCH UPDATE: GENE EXPRESSION IN SSC
Monique Hinchcliff MD, MS
Scleroderma Foundation Patient Education Day
October 19, 2013
Northwestern University
Overview
• Physical exam findings for patients with SSc
• Classification of patients with SSc
• Genomics
– What it is
– How to measure
• Gene expression analysis
• Results of recent genomics work in SSc
– How genomic approaches can be used to select the right therapy for the right patient
SSc Dogma
Disease subset Limited cutaneous
(lcSSc)
Diffuse cutaneous
(dcSSc)
Typical serum
autoantibody
produced
Anticentromere Anti-
topoisomerase
(Scl-70)
Pattern of lung
involvement
Pulmonary artery
hypertension
(PAH)
Interstitial lung
disease (ILD)
Major
pathophysiology
Vasculopathy
(Blood vessel
problems)
Fibrosis
(too much scar
tissue)
SSc treatments • Immune modulatory agents
– Methotrexate
– D-Penicillamine
– Cyclophosphamide
– Mycophenolate mofetil (inhibits an enzyme that controls lymphocyte proliferation)
– Stem cell transplant (allogeneic and autologous)
– Corticosteroids
• Biologics
– TNF- inhibitors
– Rituximab (Anti-B-lymphocyte antibody)
– Tocilizumab (IL-6 inhibitor)
– Abatacept (blocks CD28 binding to the antigen-presenting cell)
• CAT-192 (soluble TGF- inhibitor)
• Tyrosine kinase inhibitors – Imatinib mesylate (Gleevec)
– Nilotinib (Tasigna)
– Dasatinib (Sprycel)
• Others, many in the pipeline
Some responders, partial responders and non-responders.
Patients are different
Colon lung skin
healthy
SSc
Raynaud
phenomenon
Pulmonary
artery
hypertension
SSc Clinical trials
• Most have not demonstrated overall benefit
– Subsets of patients seem to respond
• Trials are limited
– SSc is a rare disease
– Diagnosis is often delayed
– Need to complete the trial in a timely manner
• Need better methods to enroll patients with similar SSc disease
Genomics (DNA, RNA) research
• Method to molecularly subset patients
– Blood (serum, plasma)
– Blood cells
– Skin biopsies
WHAT HAVE GENE EXPRESSION STUDIES TAUGHT US ABOUT SYSTEMIC SCLEROSIS?
First a brief gene expression introduction
Skin biopsies
• Performed before SSc treatment
• 4mm punch of skin removed
– Epidermis
– Dermis
• RNA isolated from the biopsy
DNA:
Your genes
RNA:
The code
to make
proteins
DNA= the menu
RNA= your order: Gene expression
Proteins= the meal
Gene expression studies use RNA
Gene expression test
NEJM 2006 354; 23
Viewing Microarray Data
200 10000 50.00 5.64
4800 4800 1.00 0.00
9000 300 0.03 -4.91
Cy5
Cy3
Patient Control
Log2(red/green)
Adapted Michael Whitfield, PhD Slide
Patient samples
>30,0
00 G
enes
Heat map
WHAT HAVE GENE EXPRESSION STUDIES TAUGHT US ABOUT SYSTEMIC SCLEROSIS?
Now we understand gene expression analyses (microarray)
Four to five groups of systemic sclerosis patients
17 diffuse SSc, 7 limited SSc, 3 morphea (another skin disease), 6 healthy controls
61 biopsies, 75 total microarrays
* p < 0.001
Milano A et al, PLoS ONE (2008)
*P<0.001
Fibroproliferative genes:
Cell cycle check point
DNA repair
Regulation of mitosis
Inflammatory genes:
Immune response
Response to pathogen
Lymphocyte proliferation
Normal-like genes:
Fatty acid biosynthesis
Lipid biosynthesis
Electron transport activity
Mycophenolate mofetil/MMF (Cellcept, Myfortic)
• Immunosuppressive agent
– Reduces production of inflammatory cells1
• FDA-approved for prevention of renal, liver and heart transplant rejection2
• Used in treatment of autoimmune disease (SSc3-7, lupus, myasthenia gravis, kidney disorders etc.)
• One of the treatment arms of Scleroderma Lung Study II
1 Ransom JT. Therapeutic Drug Monitoring. 1995 2 Villarroel MC et al. Drugs Today. 2009 3 Le EN et al. Ann Rheum Dis. 2011 4 Vanthuyne M et al. Clin Exp Rheumatol. 2007 5 Derk CT et al. Rheumatology. 2009 6 Herrick AL et al. Journal of Rheumatology. 2009 7 Nihtyanova SI et al. Rheumatology. 2007
10 diffuse SSc, 2 limited SSc, 13 stable SSc, and 10 healthy controls Baseline and longitudinal arm and back skin biopsies
4 MMF improvers and 3 MMF non-improvers
Journal of Investigative Dermatology 2013
Fibroproliferative
Inflammatory
Normal-like
MMF improvers
• Expression of 321 genes in skin at baseline is different between improvers and non-improvers
• This baseline signature may be useful in selecting appropriate patients for MMF therapy
• Ongoing work: Conduct a multi-center study to validate the MMF baseline signature and other signatures in skin
Hinchcliff et al Journal of Investigative Dermatology 2013
Future implications
• Patients who are likely to respond to MMF can be identified
• Patients who are not likely to respond to MMF can be identified and randomized to a different therapy
Summary
2010s: 4-5 SSc patient groups
• Fibroproliferative
– Diffuse 1
– Diffuse 2
• Limited
• Inflammatory
• Normal-like
Goal: Patient selection for clinical trials
• Molecular approaches – Genomic
– Proteomic
– Metabolomic
1980s: 2 SSc patient groups
• Limited
• Diffuse
Patient selection for clinical trials
• Disease duration
• Disease subtype
Thank you • Mentors:
– Rowland W. Chang, MD MPH
– John Varga, MD
– Michael Whitfield, PhD
• Clinical coordinators:
– Mary Carns, MS
– Sofia Podlusky, BA
• Bioinformatics:
– Chiang-Ching Huang, PhD
– Viktor Martyanov, PhD
– Jaclyn Taroni, BS
• Statistics
– Jungwha Lee, PhD
– Orit Almagor, MS
• Cardiology
– Sanjiv J Shah, MD
– Lauren Beussink-Nelson
• Chest radiology
– Arlene Sirajuddin, MD