A SILICA VIEW OF PANOBINOSTAT’S EFFECT ON LEUKEMIA Ying Liu & Xuan Zhu

Final Project: Computational Methods in Health Informatics (HINF 5008)

July, 2014

LEUKEMIA

•  Cancer of the blood cells •  Bone marrow makes abnormal white blood cells •  Leukemia cells divide continuously •  Most common cancer in children; more often in old adults

Four main types of leukemia •  Acute myelocytic leukemia – AML •  Acute lymphocytic leukemia – ALL •  Chronic myelocytic leukemia – CML •  Chronic lymphocytic leukemia – CLL

PANOBINOSTAT (LBH589)

•  Developed by Novartis for the treatment of various cancers

•  A non-selective histone deacetylase inhibitor (HDAC inhibitor)

•  Clinical trials: •  Myelofibrosis (exploratory) •  AML (I/II) •  MDS (I/II) •  multiple myeloma (III) •  AIDS (I/II)

DeWoskin VA & Million RP,2013

RESEARCH AIMS

To evaluate the effect of panobinostat on ALL and AML by gene expression profile analysis

DATASETS

•  Downloaded from Gene Expression Omnibus (GEO) database

•  Microarray data from Affymetrix Human Gene 1.0 ST Array platform (32,321 probes)

Accession number

Citation Number of records

Brief description

GSE26790 Vilas-Zornoza A, et al. Leukemia 2012.

12 Gene expression profiles before and after

panobinostat treatment in ALL cells

GSE48558 Cramer-Morales K, et al. Blood 2013.

170 Gene expression profiles in AML and ALL patient

and cell-line samples

METHODS

  Microarray pre-processing: 32,321 probes

affy: Robust Multi-array Average (RMA)

  Filter: 13,259 probes

Remove probes (1) IQR < 1/5 global IQR; (2) ANOVA

  Select differential expression probes

limma: moderated t-statistic (Patient – Normal; Treat – No Treat) adj.P.Val < 0.05 & |logFC| > 1

OPPOSITE GENE EXPRESSION CHANGE IN PATIENT AND DRUG TREATMENT

  Selected probes Patient (GSE48558): 5061/13259 probes

  Heatmap logFC: fold expression change (log2)

Panobinostat (GSE26790)

Patient AML (18) B-ALL (27) T-ALL (13)

Normal Monocyte (6) B cell (11) T cell (17)

Signature 2612 2300 2440

Treat B-ALL (3) T-ALL (3)

No Treat B-ALL (3) T-ALL (3)

AML B-ALL T-ALL

Patient

B-ALL T-ALL

Panobinostat

log

FC

2

-2

METHODS

  Microarray pre-processing: 32,321 probes

affy: Robust Multi-array Average (RMA)

  Filter: 13,259 probes

Remove probes (1) IQR < 1/5 global IQR; (2) ANOVA

  Select differential expression probes

limma: moderated t-statistic (Patient – Normal; Treat – No Treat) adj.P.Val < 0.05 & |logFC| > 1

  Drug effect estimated by sum of logFC

Probe Patient Drug Drug Effect

A 5 -4 1

B -3 2 -1

B-ALL T-ALL

Panobinostat

B-ALL T-ALL

AML

BALLp TALLp

AMLp.B 0

631

431

59

372

94

66

21

AML B-ALL T-ALL

Patient

Probes with reverse expression in panobinostat treatment

Tumor (Leukemia) Inducer

ZAK (8046461) ETV6/TEL (7953981) RUNX1 (8070194) PLK1 (7994109) MYB (8122202) ZNF367 (8162601) CDK4 (7964522)

A B T B T

Patient Drug

CBX7 (8076185) NR4A2 (8055952)

Tumor Suppressor

A B T B T

Patient Drug

PANOBINOSTAT EFFECT ON LEUKEMIA SIGNATURE GENE EXPRESSION

log

FC

2

-2

105

05

10

Fold

Exp

ress

ion

Cha

nge

(log2

)

PANOBINOSTAT CORRECT ABNORMAL GENE EXPRESSION IN DIFFERENT TYPES OF LEUKEMIA

AML

Patient

B-ALL

Patient

T-ALL

Patient

Median 1.10 0.58 -1.01 0.03 1.16 1.06 SD 1.80 1.73 1.98 2.01 1.74 1.78

105

05

10

Fold

Exp

ress

ion

Cha

nge

(log2

)

105

05

10

Patient + Pan

Patient + Pan

Patient + Pan

Patient Patient Patient

p-value=0.095 p-value=0.024 p-value=1.22e-14

ANTI-LEUKEMIC EFFECT OF PANOBINOSTAT IN A MOUSE MODEL OF HUMAN ALL

Vilas-Zornoza A, Pro´sper F, Leukemia (2012)

B-ALL

T-ALL

CONCLUSION AND FUTURE DIRECTION

 Panobinostat partially reversed gene expression change in leukemia

  Identification of genes potentially regulated by panobinostat

 Applications: •  Study molecular mechanisms of panobinostat •  Predict diseases that may be treated by

panobinostat

 Develop a systematic quantitative approach