RESEARCH UPDATE: GENE EXPRESSION IN SSC Monique Hinchcliff MD, MS Presented at the Scleroderma Patient Education Conference, Saturday, October 19, 2013 at Northwestern Memorial Hospital. Hosted by the Scleroderma Foundation, Greater Chicago Chapter and the Northwestern Scleroderma Program.

1. RESEARCH UPDATE: GENE EXPRESSION
IN SSC
Monique Hinchcliff MD, MS
Scleroderma Foundation Patient Education Day
October 19, 2013
Northwestern University

2. 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

3. SSc Dogma
Disease subset
Limited cutaneous
(lcSSc)
Diffuse cutaneous
(dcSSc)
Typical serum
autoantibody
produced
Anticentromere
Antitopoisomerase
(Scl-70)
Pattern of lung
involvement
Pulmonary artery
hypertension
(PAH)
Interstitial lung
disease (ILD)
Major
Vasculopathy
pathophysiology (Blood vessel
problems)
Fibrosis
(too much scar
tissue)

4. 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.

5. Patients are different
healthy
SSc
skin
Raynaud
phenomenon
lung
Colon
Pulmonary
artery
hypertension

6. 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

7. Genomics
(DNA, RNA) research
• Method to molecularly subset patients
– Blood (serum, plasma)
– Blood cells
– Skin biopsies

8. First a brief gene expression introduction
WHAT HAVE GENE EXPRESSION
STUDIES TAUGHT US ABOUT
SYSTEMIC SCLEROSIS?

9. Skin biopsies
• Performed before
SSc treatment
• 4mm punch of skin
removed
– Epidermis
– Dermis
• RNA isolated from
the biopsy

10. Gene expression studies use RNA
DNA:
Your genes
DNA= the menu

RNA:
The code
to make
proteins
RNA= your order: Gene expression

Proteins= the meal

11. Gene expression test
NEJM 2006 354; 23

12. Viewing Microarray Data
>30,000 Genes
Patient samples
Control Patient
200 10000 50.00 5.64
4800 4800 1.00 0.00
9000
300 0.03 -4.91
Cy5
Cy3
Log2(red/green)
Adapted Michael Whitfield, PhD Slide
Heat map

13. Now we understand gene expression analyses (microarray)
WHAT HAVE GENE EXPRESSION
STUDIES TAUGHT US ABOUT
SYSTEMIC SCLEROSIS?

14. 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
* 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
Milano A et al, PLoS ONE (2008)

15. 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
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
2 Villarroel

16. 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
Fibroproliferative
Inflammatory
Normal-like
Journal of Investigative Dermatology 2013

17. 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 multicenter study to validate the MMF
baseline signature and other
signatures in skin
Hinchcliff et al Journal of Investigative Dermatology 2013

18. 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

19. Summary
1980s: 2 SSc patient groups
• Limited
• Diffuse
Patient selection for clinical trials
• Disease duration
• Disease subtype
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

20. Thank you
•
•
•
•
•
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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