Name: a method for screening and validation of resistant mutations against kinase inhibitors
Uploaded: 2014-12-07T15:00:00
Description: Watch this Scientific Journal Video about A Method for Screening and Validation of Resistant Mutations Against Kinase Inhibitors at JoVE.com

This study was supported by grants to M.A. from NCI (1RO1CA155091), NHLBI (1R21HL114074) and the Leukemia Research Foundation. M.A. is a recipient of V-Scholar award from the V- Foundation. Authors are thankful to Dr. Sara Rohrabaugh for editing.

NOTE: All procedures in this protocol were conducted according to the National Institute of Health guidelines for the ethical treatment and care of animals, and according to an approved IACUC animal use protocol.
1. Cell Line Maintenance
<ol>
	<li>Culture BAF3 cells in RPMI-1640 medium supplemented with 10% fetal bovine serum and penicillin/streptomycin (100 units/ml and 100 &#181;g/ml) and spent culture medium of Wehi Cells. Grow HEK293T cells in DMEM supplemented with 10% fetal bovine seru...

<ol>
	<li>Huse, M., Kuriyan, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+conformational+plasticity+of+protein+kinases.">The conformational plasticity of protein kinases.</a> Cell. 109, 275-282 (2002).</li><li>Melnikova, I., Golden, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+protein+kinases.">Targeting protein kinases.</a> Nat Rev Drug Discov. 3, 993-994 (2004).</li><li>Cohen, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+kinases--the+major+drug+targets+of+the+twenty-first+century.">Protein kinases--the major drug targets of the twenty-first century.</a> Nat Rev Drug Discov. 1, 309-315 (2002).</li><li>Dancey, J., Sausville, E. 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J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activity+of+a+specific+inhibitor+of+the+BCR-ABL+tyrosine+kinase+in+the+blast+crisis+of+chronic+myeloid+leukemia+and+acute+lymphoblastic+leukemia+with+the+Philadelphia+chromosome.">Activity of a specific inhibitor of the BCR-ABL tyrosine kinase in the blast crisis of chronic myeloid leukemia and acute lymphoblastic leukemia with the Philadelphia chromosome.</a> N Engl J Med. 344, 1038-1042 (2001).</li><li>Druker, B. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+a+selective+inhibitor+of+the+Abl+tyrosine+kinase+on+the+growth+of+Bcr-Abl+positive+cells.">Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells.</a> Nat Med. 2, 561-566 (1996).</li><li>Gorre, M. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+resistance+to+STI-571+cancer+therapy+caused+by+BCR-ABL+gene+mutation+or+amplification.">Clinical resistance to STI-571 cancer therapy caused by BCR-ABL gene mutation or amplification.</a> Science. 293, 876-880 (2001).</li><li>Shah, N. 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Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+of+autoinhibition+and+STI-571/imatinib+resistance+revealed+by+mutagenesis+of+BCR-ABL.">Mechanisms of autoinhibition and STI-571/imatinib resistance revealed by mutagenesis of BCR-ABL.</a> Cell. 112, 831-843 (2003).</li><li>Azam, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activity+of+dual+SRC-ABL+inhibitors+highlights+the+role+of+BCR/ABL+kinase+dynamics+in+drug+resistance.">Activity of dual SRC-ABL inhibitors highlights the role of BCR/ABL kinase dynamics in drug resistance.</a> Proc Natl Acad Sci U S A. 103, 9244-9249 (2006).</li><li>Azam, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AP24163+inhibits+the+gatekeeper+mutant+of+BCR-ABL+and+suppresses+in+vitro+resistance.">AP24163 inhibits the gatekeeper mutant of BCR-ABL and suppresses in vitro resistance.</a> Chem Biol Drug Des. 75, 223-227 (2010).</li><li>Azam, M., Seeliger, M. 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R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Random+mutagenesis+reveals+residues+of+JAK2+critical+in+evading+inhibition+by+a+tyrosine+kinase+inhibitor.">Random mutagenesis reveals residues of JAK2 critical in evading inhibition by a tyrosine kinase inhibitor.</a> PLoS One. 7, 43437 (2012).</li><li>Weigert, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+resistance+to+JAK2+enzymatic+inhibitors+is+overcome+by+HSP90+inhibition.">Genetic resistance to JAK2 enzymatic inhibitors is overcome by HSP90 inhibition.</a> The Journal of experimental medicine. 209, 259-273 (2012).</li><li>Kesarwani, M., Huber, E., Azam, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overcoming+AC220+resistance+of+FLT3-ITD+by+SAR302503.">Overcoming AC220 resistance of FLT3-ITD by SAR302503.</a> Blood cancer journal. 3, 138 (2013).</li></ol>

The clinical success of Imatinib in treating CML demonstrated not only the potential of targeting the rouge kinases by small molecule inhibitors, but also uncovered limitations of targeted therapy: clinical relapse and emergence of drug resistance mutations in the target gene. Identification of resistance mutations helps in better clinical management and development of next-generation inhibitors. This protocol describes a methodology to identify drug-resistant mutations in the targeted gene. This method uses a randomly m...

Protein kinases are key regulatory enzymes of intracellular signal transduction pathways that seemingly modulate every cellular function. A proper control of kinase mediated signaling is crucial to homeostasis and development, which mostly relies on proper regulation of kinases, phosphatases and its degradation by UPS (ubiquitin proteasome system). Deregulated kinases are at the center stage of many cancers and implicated in host of human diseases 1. Human genome encodes more than 500 protein kinases that have been linked, directly or indirectly, to ~400 human diseases 2. These observations supported the concept for therapeutic targeting of kinases by small molecule inhibitors 3-5.
The demonstration of ABL kinase inhibitors, such as Imatinib, in the treatment of chronic myeloid leukemia (CML) provided the proof of concept for this approach6,7. This observation not only revolutionized the anti-kinase therapy but also enforced the idea to identify the genetic lesions in other neoplastic diseases for therapeutic targeting, which lead to discovery of oncogenic mutations in the JAK2 from polycythemia vera (PV) and patients with myeloproliferative neoplasms (MPN). This discovery generated great interest in treating MPNs by targeting JAK2 with small molecule kinase inhibitors. Now, almost a dozen of JAK2 inhibitors are in clinical trials and one of them has been approved recently for the treatment of myelofibrosis. While specific targeting of oncogenic kinases by small molecule inhibitors in cancers bring promising outcome, it also suffers from developing resistance to the treatment. In fact, so far, patients treated with kinase inhibitors, such as Imatinib, Gefitinib, Erlotinib and Dasatinib developed resistance mutations mostly by acquiring mutations in the kinase domain to which drug targets 8-10. Resistance as a result of gene mutation highlights the limitations of targeted monotherapy against the oncogenic kinases, and represents the next challenge in the development of ever more successful cancer chemotherapy. Mechanistic and functional consequences of drug resistance should provide a rationale for selection and design of complimentary compounds for drug development. Mutations identified via in vitro screens, have shown a high degree of correlation with those found in patients. Therefore, in vitro screening for mutations that confer drug-resistance for a given drug target pairs in clinical or preclinical development assists in identifying the resistance patterns that are likely to cause clinical relapse. The identification of these mutant forms is not only helpful in monitoring the patients for drug response and relapse but also essential for the design of more robust next generation inhibitors. For instance, development of next generation BCR/ABL inhibitors, Nilotinib and Ponatinib, were made possible because of greater mechanistic understandings gained from mutagenesis, structural, and functional studies.
Earlier, we have reported the results of our screen using random mutagenesis of BCR/ABL to reveal the spectrum of mutations conferring resistance to inhibitors such as Imatinib11,12, PD16632612, and AP2416313. The results not only identified the mutations conferring clinical resistance and disease relapse, but also provided the mechanistic understanding of drug resistance and principles governing the kinase function11,14. Here we provide additional methodological detail, using Ruxolitinib and JAK2 as a drug target pair, to enable a broader application of this screening strategy.

<table border="0" cellpadding="0" cellspacing="0" width="1074">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:344px;">name of Materials/Equipment</td>
			<td style="width:161px;">Company</td>
			<td style="width:116px;">Catalog Number</td>
			<td style="width:453px;">Comments/ Description</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cell and Tissue culture&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">BaF3 Cells</td>
			<td>ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HEK293T cells</td>
			<td>ATCC</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-JAK2-V617F-puro.GW</td>
			<td>A gift from Ross Levine</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-JAK2-V617F/Y931C.GW</td>
			<td>Made in house</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-JAK2-V617F/L983F.GW</td>
			<td>Made in house</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-JAK2-V617F/P58A.GW</td>
			<td>Made in house</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-V617F-Cherry.GW</td>
			<td>Made in house</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-JAK2-V617F/Y931C-cherry.GW</td>
			<td>Made in house</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-JAK2-V617F/L983F-cherry.GW</td>
			<td>Made in house</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">pMSCV-Luciferase-puro.GW</td>
			<td>Made in house</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">RPMI</td>
			<td>Cellgro (corning)</td>
			<td>15-040-CV</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMEM</td>
			<td>Cellgro (corning)</td>
			<td>15-013-CV</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Penn/Strep</td>
			<td>Cellgro (corning)</td>
			<td>30-002-CI</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">FBS</td>
			<td>Atlanta biological</td>
			<td>S11150</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Trypsin EDTA 1X</td>
			<td>Cellgro (corning)</td>
			<td>25-052-CI</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1XPBS</td>
			<td>Cellgro (corning)</td>
			<td>21-040-CV</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">L-Glutamine</td>
			<td>Cellgro (corning)</td>
			<td>25-005-CL</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Puromycin</td>
			<td>Gibco (life technologies)</td>
			<td>A11138-03</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Protamine sulfate</td>
			<td>Sigma</td>
			<td>P3369</td>
			<td>5mg/ml stock in water</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Trapan Blue solution (0.4%)</td>
			<td>Sigma</td>
			<td>T8154</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMSO</td>
			<td>Cellgro (corning)</td>
			<td>25-950-CQC</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">INCB018424 (Ruxolitinib)</td>
			<td>ChemieTeK</td>
			<td>941678-49-5</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">WST-1</td>
			<td>Roche</td>
			<td>11644807001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.45uM acro disc filter</td>
			<td>PALL</td>
			<td>2016-10</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">70um nylon cell stariner</td>
			<td>Becton Dickinson</td>
			<td>352350</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bacterial Culture</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">XL-1 red E.Coli cells</td>
			<td>Agilent Tech</td>
			<td>200129</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SOC</td>
			<td>New England Biolabs</td>
			<td>B90920s</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ampicillin</td>
			<td>Sigma</td>
			<td>A0166</td>
			<td>100mg/ml stock solution&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Bacto agar</td>
			<td>Difco</td>
			<td>214050</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Terrific broth</td>
			<td>Becton Dickinson</td>
			<td>243820</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Agarose</td>
			<td>Genemate</td>
			<td>E-3119-500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Kits</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dneasy Blood&#38; tissue kit</td>
			<td>Qiagen</td>
			<td>69506</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Expand long template PCR system</td>
			<td>Roche</td>
			<td>1168134001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Wizard Sv gel and PCR clean up system</td>
			<td>Promega</td>
			<td>A9282</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Pure Yield plasmid mini prep system</td>
			<td>Promega</td>
			<td>A1222</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PCR Cloning System with Gateway Technology with pDONR 221 &#38; OmniMAX 2 Competent Cells</td>
			<td>Invitrogen</td>
			<td>12535029</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Gateway&#160; LR Clonase Enzyme mix&#160;</td>
			<td>Invitrogen</td>
			<td>11791019</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mouse reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vivo-Glo Luciferin in-vivo Grade</td>
			<td>Promega</td>
			<td>P1043</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1/2cc Lo-Dose u-100 insulin syringe 28 G1/2</td>
			<td>Becton Dickinson</td>
			<td>329461</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mortor pestle</td>
			<td>Coor tek&#160;</td>
			<td colspan="2">60316 and 60317</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Isoflorane (Isothesia TM)</td>
			<td>Butler Schien</td>
			<td>29405</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;"></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Instruments</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">NAPCO series 8000 WJ CO2 incubator</td>
			<td>Thermo scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Swing bucket rotor centrifuge 5810R</td>
			<td>Eppendorf</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TC-10 automated cell counter</td>
			<td>Bio-RAD</td>
			<td></td>
			<td>This is not necessary, one can use standard hemocytomemetr for cell counting</td>
		</tr>
	</tbody>
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a method for screening and validation of resistant mutations against kinase inhibitors

The discovery of BCR/ABL as a driver oncogene in chronic myeloid leukemia (CML) resulted in the development of Imatinib, which, in fact, demonstrated the potential of targeting the kinase in cancers by effectively treating the CML patients. This observation revolutionized drug development to target the oncogenic kinases implicated in various other malignancies, such as, EGFR, B-RAF, KIT and PDGFRs. However, one major drawback of anti-kinase therapies is the emergence of drug resistance mutations rendering the target to have reduced or lost affinity for the drug. Understanding the mechanisms employed by resistant variants not only helps in developing the next generation inhibitors but also gives impetus to clinical management using personalized medicine. We reported a retroviral vector based screening strategy to identify the spectrum of resistance conferring mutations in BCR/ABL, which has helped in developing the next generation BCR/ABL inhibitors. Using Ruxolitinib and JAK2 as a drug target pair, here we describe in vitro screening methods that utilizes the mouse BAF3 cells expressing the random mutation library of JAK2 kinase.

Emergence of genetic mutations poses great challenge for the targeted anti kinase therapy. Mutational studies, besides providing mechanistic and functional insights that are instrumental in selection and design of next-generation drug development, also allows better clinical management and may in future be more helpful for personalized treatment. In this experiment, we show screening for ruxolitinib resistance mutations in JAK2-V617F kinase (Figure 1). We constructed pMSCV-JAK2-V617F-cherry.gateway vecto...

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A Method for Screening and Validation of Resistant Mutations Against Kinase Inhibitors

Emergence of genetic resistance against kinase inhibitor therapy poses significant challenge for effective cancer therapy. Identification and characterization of resistant mutations against a newly developed drug helps in better clinical management and next generation drug design. Here, we describe our protocol for in vitro screening and validation of resistant mutations.

The discovery of BCR/ABL as a driver oncogene in chronic myeloid leukemia (CML) resulted in the development of Imatinib, which, in fact, demonstrated the ...

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