large-scale shrna screens to identify novel combination therapies for the treatment of cancer mark...
TRANSCRIPT
Large-scale shRNA screens to identify novel combination
therapies for the treatment of cancer
Mark A. Gregory, Ph.D
Research InstructorDeGregori Lab
BIOS 6660
BIOS 6660 Lecture: shRNA synthetic lethal screening
Overview:
1) Biological problem: Chronic Myeloid Leukemia (CML) -finding the right genes to target to improve CML therapy
2) Approach: large-scale shRNA synthetic lethal screening
3) How shRNA screen data can be translated into a therapy
4) New biological problem: Acute Myeloid Leukemia (AML) -finding the right genes to target to improve AML therapy
• Chronic myeloid leukemia (CML) is a myeloproliferative disorder of hematopoietic stem cell origin that is characterized by the t(9;22) translocation, which gives rise to a shortened chromosome 22, the “Philadelphia chromosome” (Ph).
• This results in a novel fusion protein, p210 Bcr-Abl, that has constitutive tyrosine kinase activity and is causative in the disease.
• CML is a triphasic disease, beginning with a relatively stable chronic phase that lasts on average 4-5 years, progressing into an accelerated phase (6-18 months), and terminating in fatal blast crisis (~6 months).
• Imatinib mesylate (Gleevec is a small-molecule Bcr-Abl kinase inhibitor that has revolutionized the treatment of CML.
Chronic Myeloid Leukemia (CML)
Bcr-Abl
ATP substrate
P P P Y
Effector
Effector
Mechanism of action of imatinib
substrate
YP
substrate
Y
Bcr-AblImatinib substrate
Y
proliferationsurvival
growth arrestapoptosis
Imatinib is an effective treatment for Bcr-Abl+ leukemia, but it is
not a cure Imatinib induces remarkable hematological and
cytogenetic responses in chronic phase CML patients However, imatinib fails to completely eradicate Bcr-
Abl+ leukemic cells (Bcr-Abl remains detectable in >95% of responding patients)
CML patients often develop resistance to imatinib through mutation or amplification of Bcr-Abl
Advanced phase CML (blast crisis) and Bcr-Abl+ acute lymphoblastic leukemia (ALL) are poorly responsive to imatinib therapy
A second generation of more potent Bcr-Abl inhibitors has been developed (nilotinib, dasatinib) but they do not solve these problems
Our approach: Design and perform unbiased large-scale loss-of-function screen (synthetic lethal) utilizing an shRNA library to identify gene targets that, when inhibited, potentiate the efficacy of imatinib in killing CML cells
Our problem: Bcr-Abl inhibition alone is insufficient to effectively eleminate leukemic cells in CML and in Bcr-Abl+ ALL
Our hypothesis: Targeting an additional gene product may potentiate the efficacy of Bcr-Abl inhibitors in eliminating Bcr-Abl+ cells and lead to complete eradication of the disease
How do we find such genes?
Synthetic Lethality Concept
A B
A B
A B
Alive
Alive
Dead
Gene A: Bcr-Abl Gene B: unknown (screen for using RNAi)
Harnessing the power of RNAi
SYNTHETIC LETHAL
SCREENING
Our RNAi Synthetic Lethal Screen on CML
Imatinib(Bcr-Abl inhibitor)
K562CML cells
puro
*
* Genome-wide Library contains 4-10 shRNA’s per gene, targeting all human genes = 200,000 different shRNAs. Delivered to cells using lentivirus.
3X (triplicate cultures)
3X (triplicate cultures)
http://www.sigmaaldrich.com
RNA Product(shRNA)
Polylinker for cloning
PuromycinResistanc
e for selection in mammalian cells
Ori and AmpRes for replication and expansion in E. coli
21bp siRNAsequences
Lentiviral Packaging Element
5’ and 3’ LTRs for viral transcription control
TRC = The RNA Consortium
Plasmid used to make shRNA containing virus
Lentiviral transduction delivers a single shRNA to every cell
S = SYNTHETIC LETHAL
shRNA inhibitsgene in pathway
VehicleSS
SSS
Inhibitor S
S S
(e.g Bcr-Abl)
shRNA1
shRNA2
shRNA3
shRNA4
shRNA5
shRNA6
Control Treatment
80 90
40 40
100 100
100 0
60 50
60 80
Deep Sequencing Data
shRNA counts
Deep sequencing is used to quantify shRNA’s
= strong synthetic lethal
What did we find in CML screen?
identified shRNA’s targeting 146 genes as under-represented >16-fold (confidence interval > 99.5%) in imatinib-treated vs. untreated cells ie. these shRNA’s cooperated with imatinib in CML cell killing. The genes these shRNA’s target =
SLIM’s : Synthetic Lethal with Imatinib Mesylate
PKC
Wnt5a
CaMKII
G prot
PLCPDE
Fzd
Calcn
DAG
Major SLIM pathway: Noncanonical Wnt/Ca2+ pathway
NFAT
IP3Ca2+
Calm
IL-4cytokines nucleus
NF-kB AP-1
Cyclosporin A (CsA)
Almost every gene in this pathway came up in screen with one or more shRNA as beingSynthetic Lethal with Imatinib Mesylate
The calcineurin inhibitor CsA cooperates with imatinib in killing K562 blast crisis CML cells in vitro
after72 hr treatment
(0, 1, 2.5, or 5 µM)
• CsA potently inhibits NFAT activity in CML cells
CsA
0.10 1.0 µM imatinib
Combined therapy with CsA and Bcr-Abl inhibitor dasatinib leads to prolonged survival in a mouse model of Bcr-Abl+ leukemia
Gregory et al., Cancer Cell (2010)
Dasatinib and Cyclosporine in Treating Patients With Chronic Myelogenous Leukemia Refractory or Intolerant to Imatinib Mesylate
Official Title ICMJ: Exploiting Synergy in Chronic Myelogenous Leukemia: A Phase Ib Evaluation of Dasatinib Plus Cyclosporine in Patients With Ph+ Leukemia (ESCAPE1b)
Brief Summary :This phase I trial studies the side effects and the best way to give dasatinib and cyclosporine in treating patients with chronic myelogenous leukemia (CML) refractory or intolerant to imatinib mesylate. Dasatinib may stop the growth of cancer cells by blocking some of the enzymes needed for cell growth. Cyclosporine may help dasatinib work better by making cancer cells more sensitive to the drug. Giving dasatinib together with cyclosporine may be an effective treatment for CML.
ClinicalTrials.gov Identifier:NCT01426334
These data eventually led to a Phase 1 clinical trial exploringDasatinib + CsA
Demonstrates how a functional genomics screen can identifya therapeutic strategy that rapidly translates to the clinic for potential patient benefit
New biological problem:Acute Myeloid Leukemia
Acute myeloid leukemia is a heterogeneous disease characterized by the uncontrolled proliferation of hematopoietic progenitor cells
An estimated 13,780 new cases of AML were diagnosed in U.S. in 2011 and there were >10,000 estimated deaths from AML
Response to chemotherapy is poor and most patients will die of their disease (only 40% of patients <60 yo and only 10% of older patients will remain in remission >5 years)
We are desparate for better therapies
Confronting a Broad Spectrum of Diseases With Diverse Outcomes
SEER database, scientific literature
Comparison of Diseases by Survival Rate, Age of Onset & Incidence
Median 5-year Survival Rate
MM NHL CLL
CML
MPD
HL
ALL
Ave
rage
Age
of
Ons
et
58,000
4,300
Incidence
AML
MDS
Targeting AML: FLT3
FLT3 (fms-like tyrosine kinase 3) is receptor tyrosine kinase expressed on hematopoietic progenitor cells
Activating mutations of FLT3 (ITD and TK domain) are present in 30-40% of AMLs and are associated with aggressive disease and poor prognosis
FLT3 is a potentially promising therapeutic target for treatment of AML
FLT3 signaling
Promotes growth, proliferation and survival
FLT3 inhibitors fail to achieve durable remissions in AML
In clinical trials, FLT3 inhibitors (e.g. CEP-701, AC220) show significant anti-leukemic activity in FLT3 mutated (FLT3MT) AML
However, most of the responses consisted of a clearance of peripheral leukemic blasts and major reductions in bone marrow blasts were not typically achieved
Responses were transient with patients blasts returning within a few weeks to a few months
Problem: FLT3 inhibition alone is insufficient to effectively eleminate leukemic cells in FLT3MT AML
Our hypothesis: Targeting additional genes may potentiate the efficacy of FLT3 inhibitors in eliminating FLT3 leukemic cells and lead to complete eradication of the disease
Our approach: Large-scale shRNA synthetic lethal screen
Our RNAi Synthetic Lethal Screen on AML
CEP-701(FLT3 inhibitor)
MolmAML cells
puro
*
* Genome-wide Library contains 4-10 shRNA’s per gene, targeting all human genes = 200,000 different shRNAs. Delivered to cells using lentivirus.
3X (triplicate cultures)
3X (triplicate cultures)
Give sequencing datasets to BIOS 6660 students for Bioinformatics Analysis.
Ask them to identify genes that are “SLAMs” – Synthetic Lethal in Acute Myeloid Leukemia.
Align sequences to shRNA Library
Accounting for:• Relative shRNA representation• Correlation between distinct
shRNAs targeting the same gene• Replication across experiments
(typically 3 Vehicle, 3 Treatment)
Pathways Analysis
(Ingenuity, DAVID, KEGG)
Aik Choon TanJihye Kim VALIDATION
What are we looking for in the final analysis?
1) A list of the top genes identified as SLAMs
2) A list of the top SLAM pathways
3) An idea for a potentially promising combination therapy, i.e. FLT3 inhibitor + drug X that will more effectively treat or cure AML.
Publications from our group employing synthetic lethal screening
Alvarez-Calderon F, Gregory MA, and DeGregori J. Using functional genomics to overcome
therapeutic resistance in hematological malignancies. Immunol Res. 2013 Mar;55(1-3):100-15.
Gregory MA, Phang TL, Neviani P, Alvarez-Calderon F, Eide CA, O'Hare T, Zaberezhnyy V, Williams RT, Druker BJ, Perrotti D, and Degregori J. Wnt/Ca2+/NFAT signaling maintains survival of Ph+ leukemia cells upon inhibition of Bcr-Abl. Cancer Cell. 2010 Jul 13;18(1):74-87.
Casás-Selves M, Kim J, Zhang Z, Helfrich BA, Gao D, Porter CC, Scarborough HA, Bunn PA Jr, Chan DC, Tan AC, and Degregori J. Tankyrase and the Canonical Wnt Pathway Protect Lung Cancer Cells from EGFR Inhibition. Cancer Res. 2012 Aug 15;72(16):4154-64.
Porter CC, Kim J, Fosmire S, Gearheart CM, van Linden A, Baturin D, Zaberezhnyy V, Patel PR, Gao D, Tan AC, and DeGregori J. Integrated genomic analyses identify WEE1 as a critical mediator of cell fate and a novel therapeutic target in acute myeloid leukemia. Leukemia. 2012 Jun;26(6):1266-76.
Sullivan KD, Padilla-Just N, Henry RE, Porter CC, Kim J, Tentler JJ, Eckhardt SG, Tan AC, DeGregori J, and Espinosa JM. ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53. Nat Chem Biol. 2012 Jul;8(7):646-54. doi: 10.1038/nchembio.965.