AWARD NUMBER: W81XWH TITLE: Defining New Treatment Approaches for KRAS-Mutant Lung Cancer. PRINCIPAL INVESTIGATOR: Eric Collisson

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1 AWARD NUMBER: W8XWH TITLE: Defining New Treatment Appraches fr KRAS-Mutant Lung Cancer PRINCIPAL INVESTIGATOR: Eric Cllissn CONTRACTING ORGANIZATION: University f Califrnia, San Francisc San Francisc, CA REPORT DATE: Octber 204 TYPE OF REPORT: Annual PREPARED FOR: U.S. Army Medical Research and Materiel Cmmand Frt Detrick, Maryland DISTRIBUTION STATEMENT: Apprved fr Public Release; Distributin Unlimited The views, pinins and/r findings cntained in this reprt are thse f the authr(s) and shuld nt be cnstrued as an fficial Department f the Army psitin, plicy r decisin unless s designated by ther dcumentatin.

2 REPORT DOCUMENTATION PAGE Frm Apprved OMB N Public reprting burden fr this cllectin f infrmatin is estimated t average hur per respnse, including the time fr reviewing instructins, searching existing data surces, gathering and maintaining the data needed, and cmpleting and reviewing this cllectin f infrmatin. Send cmments regarding this burden estimate r any ther aspect f this cllectin f infrmatin, including suggestins fr reducing this burden t Department f Defense, Washingtn Headquarters Services, Directrate fr Infrmatin Operatins and Reprts ( ), 25 Jeffersn Davis Highway, Suite 204, Arlingtn, VA Respndents shuld be aware that ntwithstanding any ther prvisin f law, n persn shall be subject t any penalty fr failing t cmply with a cllectin f infrmatin if it des nt display a currently valid OMB cntrl number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS.. REPORT DATE 2. REPORT TYPE 3. DATES COVERED Annual 9/30/203 9/29/204 Octber TITLE AND SUBTITLE Defining New Treatment Appraches fr KRAS-Mutant Lung Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W8XWH c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Eric Cllissn Eric.Cllissn@ucsf.edu 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) University f Califrnia San Francisc(UCSF) Department f Medicine-Hematlgy-Onclgy 2340 Sutter Street Suite # 29 San Francisc, CA 945 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 0. SPONSOR/MONITOR S ACRONYM(S) U.S. Army Medical Research and Materiel Cmmand Frt Detrick, Maryland SPONSOR/MONITOR S REPORT NUMBER(S) 2. DISTRIBUTION / AVAILABILITY STATEMENT Apprved fr Public Release; Distributin Unlimited 3. SUPPLEMENTARY NOTES N supplementary ntes 4. ABSTRACT: Lung cancer is a deadly malignancy. The mst cmmnly mutated ncgene we knw is KRAS. We d nt have a drug t inhibit KRAS, and medicinal chemistry appraches have exhausted leads. We need a new apprach t find new ways t inhibit this ncgene. Objective: T identify cellular cfactrs required fr KRAS G2D -driven NSCLC. Specific Aim. T identify gene prducts specifically essential fr KRAS-driven NSCLC, we will perfrm a shrna screen f thusands f muse genes, lking fr essentiality in multiple independent cell lines derived frm tw NSCLC GEMMs: ne RAFdependent and ne RAS-dependent. This Aim is underway and has verified that KRAS is indeed essential in the KRAS mutant muse cell lines. Specific Aim 2. T validate ur findings in human NSCLC we will test a panel f human NSCLC cell lines with knwn dependence n RAS fr their dependence n the elements (hits) identified in Aim. Study Design: In vitr shrna screen in Aim. Individual shrna validatin int human lines in Aim SUBJECT TERMS Nnsmall cell lung cancer, shrna screening 6. SECURITY CLASSIFICATION OF: Reprt a. REPORT b. ABSTRACT c. THIS PAGE 7. LIMITATION OF ABSTRACT 8. NUMBER OF PAGES 7 9a. NAME OF RESPONSIBLE PERSON USAMRMC 9b. TELEPHONE NUMBER (include area cde) Standard Frm 298 (Rev. 8-98) Prescribed by ANSI Std. Z39.8

3 Table f Cntents Page. Intrductin. 2. Keywrds. 3. Accmplishments Impact Changes/Prblems Prducts Participants & Other Cllabrating Organizatins 4 8. Special Reprting Requirements 4 9. Appendices 4 (number all pages except the appendices, but d include the appendices in page cunt n the sf 298 frm blck 8)

4 The text f the reprt must include all sectins addressed in the table f cntents t include: INTRODUCTION: As targeted therapies imprve the lives f many with certain types f lung cancer, KRASmutant nn-small cell lung cancer (NSCLC) stands ut as a deadly and prly treated exceptin. We have n effective therapies fr these patients. This prject innvates and reinvigrates the search fr direct ways t inhibit KRAS mutant NSCLC, a challenge we must meet t make prgress in this clinically challenging NSCLC subset. Mutant KRAS, like ALK r EGFR, is a bne fide NSCLC driver. Unlike ALK r EGFR hwever, KRAS is nt a kinase. The traditinal chemical screening apprach t drug develpment is prly suited fr nnkinases in general and fr the RAS inhibitr prblem in particular. Chemical screening underperfrms because inhibiting RAS wuld paradxically require a cmpund t reactivate the RAS GTPase r act thugh sme ther nvel mechanism. As such, drug cmpanies target prtein-directed screening techniques have and will cntinue t fail in this endeavr. Innvative screening platfrms and/r methds are desperately needed. Hypthesis: KRAS des nt signal alne. A genetically encded cfactr (e.g. structural prtein r nncding RNA r metablic regulatr) is required fr mutant KRAS t drive NSCLC. Since autchthnus KRAS G2D driven GEMMs develp NSCLC, their genme necessarily harbrs and expresses this (these) cfactr(s), which can in turn be discvered by shrna depletin. Objectives: T identify cellular cfactrs required fr KRAS G2D (but nt BRAF V600E )-driven NSCLC. KEYWORDS: Prvide a brief list f keywrds (limit t 20 wrds). Kras, Lung cancer, ncgene addictin. ACCOMPLISHMENTS: The PI is reminded that the recipient rganizatin is required t btain prir written apprval frm the awarding agency Grants Officer whenever there are significant changes in the prject r its directin. What were the majr gals f the prject? Specific Aim. T identify gene prducts specifically essential fr KRAS-driven NSCLC, we will perfrm a shrna screen f thusands f muse genes, lking fr essentiality in multiple independent cell lines derived frm tw NSCLC GEMMs: ne RAF-dependent[] and ne RAS-dependent[2] Specific Aim 2. T validate ur findings in human NSCLC we will test a panel f human NSCLC cell lines with knwn dependence n RAS[4] fr their dependence n the elements (hits) identified in Aim. What was accmplished under these gals? KRAS mutatin is ne f the mst cmmn ncgenic drivers in lung, pancreatic and cln cancers. Despite having knwn this fr mre than three decades, pharmaclgical inhibitin f mutant KRAS in cancers has remained an elusive gal. Our research initiative is driven by the need t discver elements essential fr KRAS-driven tumrigenesis. Such elements can then be tested fr synthetic lethality-based therapeutic appraches t KRAS-addicted cancers. In rder t identify genes specifically required fr KRAS-driven cancers, we cnducted a pled shrt hairpin RNA (shrna) screen in genetically mdified muse mdel (GEMM)-derived lung and pancreatic tumr cell lines. These cell lines carried a KRAS r BRAF mutatin. While mst f the KRAS mutant lines were KRAS addicted, BRAF mutants were nt. Our gal was t find genes that, when depleted, wuld inhibit the survival f KRAS-addicted tumr cells but nt KRAS independent cells. We used a muse-specific barcded shrna library f 27,500 shrnas targeting 4,625 genes. These genes were selected n the basis f their invlvement in cancer-assciated signaling pathways and/r drug targeting ability. We briefly describe belw hw the screen was perfrmed with fcus n ne f the target resulting frm the screen and experiments t test it in lung cancer. shrna screen design and analysis: We infected KRAS-addicted and KRAS-independent muse cancer cell lines with lentiviruses expressing the shrna library. Since a lentivirus integrates int the genme f cell, if an shrna decreases the viability f the cell, its abundance will decrease ver the length f the screen. We can bserve such drp ut shrnas by cmparing the relative abundance f shrnas at the end f the screen t a baseline cntrl representing the library. We infected the cell t get 40% transductin efficiency t ensure that majrity f cells were infected with shrna-carrying virus. The screen was designed t achieve 000 fld cverage f the library and was carried ut t allw 8 t 0 ppulatin

5 dublings pst transductin (end pint). Abundance f shrna in the baseline and end pint cell is determined by PCR based recvery f barcded shrna fllwed by deep sequencing. shrna depletin ver time was cmputed using the R package, Differential expressin analysis fr sequence cunt data (DESeq). Since we are interested in discvering synthetic lethal relatin with KRAS, we impsed a KRAS drput cutff n the screens. KRAS mutant cells that depleted 50% KRAS shrna (3 ut f 6 hairpins) and BRAF mutant cells that did nt lse any KRAS hairpins were nly selected fr the next rund f analyses. Ptential hits are shrna target genes that drp ut in KRAS mutant lines but nt in BRAF mutant lines. We prepared 2 separate lists f such genes fr lung and pancreatic lines and then lked fr hits cmmn t bth. This was dne t select targets cmmn t different KRAS-driven cancers irrespective f the tissue type. We fund 23 hits cmmn t bth tumr types. We further shrtlisted the hits by excluding essential Figure : KRAS-essential Hits frm muse shrna screen with the gene AVEN at the tp f the list. Fig 2: Validatin f AVEN in muse (A) and human cell lines (B) Crrelatin f AVEN and KRAS dependence in human cell lines is pltted (D) using data in panels B and C. genes such as prteasme and plymerase subunits. The shrt listed genes were then scred using Bayesian classifier f gene essentiality. This gave us 4 ptential hits including KRAS (Figure ). Amng these, AVEN, apptsis, caspase activatin inhibitr gene, shwed the strngest crrelatin t KRAS essentiality. We als cnfirmed that AVEN was expressed in muse and human lung as well as pancreatic tumr lines and we selected AVEN fr further validatin experiments. We validated AVEN essentiality in KRASaddicted muse and human lines (Fig 2A-C). Imprtantly, we bserved a psitive crrelatin between AVEN and KRAS dependence in human lung and pancreatic lines by AVEN sirna experiments (Fig 2D). In rder t further substantiate the relevance f AVEN in lung cancer, we generated an isgenic human lung cell line system t islate the interactin between KRAS and AVEN. Immrtalized human trachebrnchial epithelial cells (AALE) were transfrmed by expressing ncgenic KRAS G2D. Expressin f ncgenic KRAS G2D makes the AALE cells KRAS-dependent and cnfers n them the ability t frm clnies in anchrage independent assay. Kncking dwn AVEN in the KRAS transfrmed AALE cells significantly reduced their clny frmatin ability. In shrt, we have cnvincing evidence that AVEN is a KRAS-essential element in human KRAS-driven cancers. We plan t test this relatin in viv as the next step. We hypthesize that AVEN depletin makes KRAS-addicted cells mre vulnerable t appttic stress. We will test this hypthesis in ur future experiments. What pprtunities fr training and prfessinal develpment has the prject prvided? I require each f the trainees in my lab t cmplete a written individual develpment plans (IDP) annually. I meet with each f the trainees in my lab annually t discuss prgress during the past year, as well as the develpment pints utlined in their IDP. During the first 2 years f a graduate student s tenure in my lab, I advise the student weekly. Fr students wh have advanced t candidacy, and fr pstdcs, I advise every 2

6 tw weeks, and encurage prductive gal setting tward the pursuit f a chsen career. I als encurage students and pstdcs t attend 4 training seminars prvided by the UCSF Office f Career and Prfessinal Develpment. Hw were the results disseminated t cmmunities f interest? "Nthing t Reprt." What d yu plan t d during the next reprting perid t accmplish the gals? "Nthing t Reprt." 2. IMPACT: Describe distinctive cntributins, majr accmplishments, innvatins, successes, r any change in practice r behavir that has cme abut as a result f the prject relative t: This prject established a new mdel system fr testing KRAS dependency in cancer. These Findings are being expanded upn. This much larger prject is a cllabrative effrt between many screening scientists lking at varius mlecular appraches at KRAS inhibitin using the cell panel defined herein. What was the impact n ther disciplines? This wrk has set the cnceptual underpinnings fr the use f muse derived cancer cell lines fr screens in cancers. Future iteratins f these screens culd, fr example, be used with emerging systems such as CAS9-Crispr r small mlecule appraches. What was the impact n technlgy transfer? Nthing t Reprt." What was the impact n sciety beynd science and technlgy? Nthing t Reprt." 3. CHANGES/PROBLEMS: The Prject Directr/Principal Investigatr (PD/PI) is reminded that the recipient rganizatin is required t btain prir written apprval frm the awarding agency Grants Officer whenever there are significant changes in the prject r its directin. If nt previusly reprted in writing, prvide the fllwing additinal infrmatin r state, "Nthing t Reprt," if applicable: Changes in apprach and reasns fr change Nthing t Reprt." Actual r anticipated prblems r delays and actins r plans t reslve them Nthing t Reprt." Changes that had a significant impact n expenditures Nthing t Reprt. Significant changes in use r care f human subjects, vertebrate animals, bihazards, and/r select agents Nthing t Reprt.". Significant changes in use r care f human subjects Nthing t Reprt." Significant changes in use r care f vertebrate animals. Nthing t Reprt." Significant changes in use f bihazards and/r select agents 3

7 Nthing t Reprt." 4. PRODUCTS: List any prducts resulting frm the prject during the reprting perid. If there is nthing t reprt under a particular item, state "Nthing t Reprt." Publicatins, cnference papers, and presentatins Nthing t Reprt. Jurnal publicatins. We are currently validating the AVEN gene using in viv systems, as prpsed in Aim 2. Once these validatin experiments are cmpleted, we anticipate submitting this wrk fr publicatin within the 205 calendar year. Bks r ther nn-peridical, ne-time publicatins. Nthing t Reprt Other publicatins, cnference papers, and presentatins. Dr. Malik, the pstdctral fellw wrking n this prject, has submitted this wrk fr presentatin at the 205 Salk Institute muse mdels f human cancer cnference. Website(s) r ther Internet site(s) Nthing t Reprt Technlgies r techniques A new technlgy f srts emerged frm this grant. That is a cllectin f muse cell lines with knwn KRAS dependence. They will be shared with academic researchers n a cllabrative basis upn request. Inventins, patent applicatins, and/r licenses Nthing t Reprt Other Prducts Nthing t Reprt." PARTICIPANTS & OTHER COLLABORATING ORGANIZATIONS What individuals have wrked n the prject? N Change Has there been a change in the active ther supprt f the PD/PI(s) r senir/key persnnel since the last reprting perid? Nthing t Reprt What ther rganizatins were invlved as partners? Nthing t Reprt 5. SPECIAL REPORTING REQUIREMENTS COLLABORATIVE AWARDS: Nt applicable QUAD CHARTS: Nt applicable 6. APPENDICES: N/A 4