Psanobinostat (LBH589) is a drug candidate in the process of Phase I to III clinical trials for various cancers including acute myeloid leukemia (AML) (DeWoskin and Million, 2013). It also showed anti-cancer effect in acute lymphoblastic leukemia (ALL) (Vilas-Zornoza A et al., 2012). The goal of our project is to predict the therapeutic effect of panobinostat on leukemia through the comparison of gene expression profiles in disease and drug treated cells. Our results predict that many disease signature gene expressions can be reversed upon panobinostat treatment. Moreover, we identified many leukemia-related oncogenes and tumor suppressor genes as the potential targets regulated by panobinostat.

1. A SILICA VIEW OF
PANOBINOSTAT’S EFFECT ON
LEUKEMIA
Ying Liu & Xuan Zhu
Final Project: Computational Methods in
Health Informatics (HINF 5008)
July, 2014

2. 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

3. 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

4. RESEARCH AIMS
To evaluate the effect of panobinostat on ALL
and AML by gene expression profile analysis

5. 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

6. 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

7. 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
logFC
2
-2

8. 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

9. 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
logFC
2
-2

10. 1050510
FoldExpressionChange(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
1050510
FoldExpressionChange(log2)
1050510
Patient
+ Pan
Patient
+ Pan
Patient
+ Pan
Patient Patient Patient
p-value=0.095p-value=0.024p-value=1.22e-14

11. ANTI-LEUKEMIC EFFECT OF PANOBINOSTAT IN A
MOUSE MODEL OF HUMAN ALL
Vilas-Zornoza A, Pro´sper F, Leukemia (2012)
B-ALL
T-ALL

12. 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