research update: gene expression in ssc

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