Arthur EdwardsBroad Summer Research Program in Genomics

Cancer Program08/06/07

Genome-wide miRNA Expression Analysis in Lymphoma

miRNAs

Lymphoma

Why Lymphoma?

Source: American Cancer Society, 2006.

Men38,670

Women32,610

Deaths

Cases

Men10,370

Women9,360

Lymphoma

Hodgkin’slymphoma

Non-Hodgkin’slymphoma

7,350 patients(est. 2007)

56,390 patients(est. 2007)

Adapted from J.L Peck, SI 2007

09/01/06 – Stays at MGH

07/23/07 – Plays at Fenway

About 50% not so happy ending

Naive B-cells

AntigenMemory B-cells

Plasma cellsCentroblasts

Centrocytes

Diffuse Large B-Cell Lymphoma (DLBCL)

•DLBCL is a result of abnormal B-cell development.

•Mediastinal Large B-Cell Lymphoma (MLBCL) – Subtype of DLBCL with worse prognosis than DLBCL.

•Significant clinical and genetic heterogeneity.

Challenges to the Lymphoma Field

1. Lack of understanding of its molecular mechanisms

2. Lack of diagnostic / prognostic tools

3. Lack of effective therapeutic drugs

miRNAs

The start of something new: lin-4 and let-7

found in C.Elegans

Cell DeathCell proliferation

Differentiation

Physiological Responses

Expression Profiles Contain

Diagnostic Information

miRNAs as regulators of gene expression and biology

Some miRNAs play functional

roles in tumorgenesis particularly in

lymphoma“miR-17 cluster

cooperates with c-myc in lymphomagenesis”

Lu et. al. (2005) – Nature He et. al. (2005) – Nature Lee et. al. (1993) – Cell Reinhart et. al. (2000) - Nature

Controls n = Cell Line (HeLa) 9Cell Line (MCF-7) 9Cell Line (MOLT-4) 6Blank Controls 22Lymphoma Samples 242

288

Approach: genome-wide miRNA expression analysis

Diagnosis n = Lymphoma Cell Line 34Paired DLBCL 18Primary MLBCL 39Primary DLBCL 139Normal B-Cell 12

242

Overview of miRNA Profiling

Fig 1a. Plot of cell line controls and their relative expression values.

Quality Control of Technical Procedure

Fig 1b. Cell line controls cluster.

Molt4

MCF-7

HeLa

Plate 1

Plate 2

Plate 3

Code Category

Fig 2. Clustering of Normal B-Cell Samples

miRNA Expression Profiles Differentiate B-Cell Development

Naïve

Centroblast

Centrocyte

Memory

Code Category121

miRNA Expression Differentiates Primary Lymphoma Samples

Primary DLBCL

Primary MLBCL

Normal B-Cell

Naïve

Centroblast

Memory

Centrocyte

miR-17 cluster

Fig 3. Primary Lymphoma Samples Clustered

Code Category

miR-150

Non-Random Association of Patient Outcome

Fig 4a. DLBCL vs. MLBCL

MLBCL

DLBCL

Failure

Cure

No Data

Code Category1 2

Cluster 1

Cluster 2

Failure 20 20 40

Cure 8 27 35

28 47 75

p=0.018 Fisher’s Exact Test

Fig 4b. Correlation between Cure and Failure

Fig 5. Lymphoma Cell Lines Clustered

Lymphoma Cell Line Comparison

Hodgkin’s Lymphoma

DLBCL

Mantle Cell Lymphoma

MLBCL

miR-155

Conclusions

Classifying Primary Lymphoma Samples.

CB / CC – like lymphoma.

Naïve / memory - like lymphoma

Another class

miRNAs and prognosis.

miRNAs may give clues on molecular signatures in prognosis of lymphoma patients.

Lymphoma Cell Lines

Hodgkin’s Lymphoma have a different miRNA expression pattern

B-Cell Development

Two distinct patterns of miRNA expression.

CB / CC vs. Naïve / Memory

• Unraveling the functional aspect of miRNAs in B-Cell development and in lymphomagenesis.

• More comprehensive data analysis with additional clinical information.

• Integrative data analysis (Affy data, miRNA data, SNP data and sequence data)

Future Studies

Acknowledgements• Broad Members

– Jun Lu– Hao Zhang– Stefano Monti– Alper Uzun– Yuliya Kodysh– Arthur Liberzon– Xiaohui Xie– Jill Mesirov– Todd Golub

• Broad Summer Research Program in Genomics– Shawna Young– Bruce Birren– Maura Silverstein– Scott Breiding

• DFCI / Harvard Medical– Kunihiko Takeyama– Margaret Shipp

MIR WAY