The Genomic Landscape of SMARCA4 Alterations and Associations with Outcomes in 2 Patients with Lung Cancer 3 4 Adam J

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Author Manuscript Published OnlineFirst on July 24, 2020; DOI: 10.1158/1078-0432.CCR-20-1825 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

1 The Genomic Landscape of SMARCA4 Alterations and Associations with Outcomes in 2 Patients with Lung Cancer 3 4 Adam J. Schoenfeld1, Chai Bandlamudi2*, Jessica A. Lavery3*, Joseph Montecalvo4*, Azadeh 5 Namakydoust1*, Hira Rizvi1,5, Jacklynn Egger5, Carla P. Concepcion6, Sonal Paul7, Maria E. 6 Arcila4, Yahya Daneshbod4, Jason Chang4, Jennifer L. Sauter4, Amanda Beras4, Marc Ladanyi4, 7 Tyler Jacks6,8, Charles M. Rudin1,5, Barry S. Taylor2, Mark T.A. Donoghue2, Glenn Heller3, 8 Matthew D. Hellmann1, Natasha Rekhtman4#, Gregory J. Riely1#

9 1Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, 10 Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY, USA 11 2Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA 12 3Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New 13 York, NY, USA 4Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 14 NY, USA 5Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer 15 Center, New York, NY, USA 6David H. Koch Institute for Integrative Cancer Research, 16 Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA 17 7Department of Medicine, New York-Presbyterian Brooklyn Methodist Hospital - Weill Cornell 18 Medicine, New York, NY, USA 8Howard Hughes Medical Institute, Massachusetts Institute of 19 Technology, Cambridge, MA 02139, USA. *Contributed equally # Co-senior authors

20 Correspondence to:

21 Dr. Gregory J. Riely 22 Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, 23 Memorial Sloan Kettering Cancer Center 24 1275 York Avenue, New York, NY, 10065, USA 25 +1 646-888-4199 26 [email protected]

27 Dr. Natasha Rekhtman 28 Thoracic Oncology Service, Department of Pathology, 29 Memorial Sloan Kettering Cancer Center 30 1275 York Avenue, New York, NY, 10065, USA 31 +1 212-639-6780 32 [email protected]

33 Running title: SMARCA4 Alterations in Lung Cancer 34 35 Acknowledgement of research support: 36 Supported by Memorial Sloan Kettering Cancer Center Support Grant/Core Grant (P30 CA008748) and 37 the Druckenmiller Center for Lung Cancer Research at MSK. ACS Postdoctoral Fellowship 130361-PF- 38 17-009-01-CDD. Koch Institute Quinquennial Postdoctoral Fellowship. MDH is a Damon Runyon Clinical 39 Investigator supported (in part) by the Damon Runyon Cancer Research Foundation (CI-98-18) and is a 40 member of the Parker Institute for Cancer Immunotherapy. This work was supported, in part, by a grant 41 from John and Georgia DallePezze to Memorial Sloan Kettering Cancer Center. 42 43 Disclosures: AN was a consultant for Bayer MEA is a consultant for AstraZeneca and received support 44 from Astrazeneca, Invivoscribe, and Raindance Technologies. JLS reports stock ownership in the 45 following companies: Pfizer, Thermo Fischer Scientific, Inc., Merck & Co Inc and Chemed Corp. ML has 46 received advisory board compensation from Boehringer Ingelheim, AstraZeneca, Bristol-Myers Squibb, 47 Takeda, and Bayer, and research support from LOXO Oncology and Helsinn Healthcare. TJ is a member 48 of the Board of Directors of Amgen and Thermo Fisher Scientific. He is also a co-Founder of Dragonfly

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49 Therapeutics and T2 Biosystems. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, 50 SQZ Biotech, and Skyhawk Therapeutics. None of these affiliations represent a conflict of interest with 51 respect to the design or execution of this study or interpretation of data presented in this manuscript. T.J. 52 laboratory currently also receives funding from the Johnson & Johnson Lung Cancer Initiative and The 53 Lustgarten Foundation for Pancreatic Cancer Research, but this funding did not support the research 54 described in this manuscript. CMR has consulted regarding oncology drug development with AbbVie, 55 Amgen, Ascentage, AstraZeneca, Bicycle, Celgene, Daiichi Sankyo, Genentech/Roche, Ipsen, Jansen, 56 Jazz, Lilly/Loxo, Pfizer, PharmaMar, Syros, and Vavotek; he serves on the SAB for Bridge Medicines and 57 Harpoon Therapeutics. MDH receives research support from Bristol-Myers Squibb; has been a 58 compensated consultant for Merck, Bristol-Myers Squibb, AstraZeneca, Genentech/Roche, Nektar, 59 Syndax, Mirati, Shattuck Labs, Immunai, Blueprint Medicines, Achilles, and Arcus; received travel 60 support/honoraria from AstraZeneca, Eli Lilly, and Bristol-Myers Squibb; has options from Shattuck Labs, 61 Immunai, and Arcus; has a patent filed by his institution related to the use of tumor mutation burden to 62 predict response to immunotherapy (PCT/US2015/062208), which has received licensing fees from 63 PGDx. GJR Memorial Sloan Kettering Cancer Center receives funding for research led by Dr. Riely from: 64 Mirati, Merck, Takeda, Roche, Pfizer, and Novartis.

67 Statement of translational relevance:

68 In this study, we characterize the clinical, molecular and histologic relationships of SMARCA4

69 genomic and protein alterations in lung cancer. SMARCA4 is the most commonly mutated

70 member of the SWI/SNF complex, with mutations occurring in 8% of patients with NSCLC.

71 Genomic, protein expression, and clinical outcome data identify two distinct classes of

72 SMARCA4 alterations. SMARCA4 alterations often co-occur with STK11, KEAP1, and KRAS

73 alterations, but they are a prognostic factor, independent of these alterations. Although patients

74 whose tumors have Class 1 SMARCA4 alterations (associated with protein expression loss)

75 have a very poor prognosis, they may have higher response rates to PD-(L)1 blockade despite

76 low PD-L1 expression.

91 ABSTRACT

92 Purpose: SMARCA4 mutations are among the most common recurrent alterations in

93 NSCLC, but the relationship to other genomic abnormalities and clinical impact has not

94 been established.

95 Experimental Design: To characterize SMARCA4 alterations in NSCLC, we analyzed

96 the genomic, protein expression, and clinical outcome data of patients with SMARCA4

97 alterations treated at Memorial Sloan Kettering.

98 Results: In 4813 tumors from patients with NSCLC, we identified 8% (n= 407) patients

99 with SMARCA4-mutant lung cancer. We describe two categories of SMARCA4

100 mutations: Class 1 mutations (truncating mutations, fusions and homozygous deletion)

101 and Class 2 mutations (missense mutations). Protein expression loss was associated

102 with Class 1 mutation (81% vs 0%, (P < 0.001)). Both classes of mutation co-occured

103 more frequently with KRAS, STK11, and KEAP1 mutations compared to SMARCA4

104 wildtype tumors (P < 0.001). In patients with metastatic NSCLC, SMARCA4 alterations

105 were associated with shorter overall survival, with Class 1 alterations associated with

106 shortest survival times (P < 0.001). Conversely, we found that treatment with immune

107 checkpoint inhibitors was associated with improved outcomes in patients with

108 SMARCA4-mutant tumors (P = 0.01), with Class 1 mutations having the best response

109 to ICIs (p = 0.027).

110 Conclusions: SMARCA4 alterations can be divided into two clinically relevant genomic

111 classes associated with differential protein expression as well as distinct prognostic and

112 treatment implications. Both classes co-occur with KEAP1, STK11, and KRAS

113 mutations, but individually represent independent predictors of poor prognosis. Despite

114 association with poor outcomes, SMARCA4-mutant lung cancers may be more sensitive

115 to immunotherapy.

116

117 Introduction

118 Genomic abnormalities in the subunits of the SWI/SNF chromatin remodeling complex

119 occur in approximately 20% of solid tumors and emerging data suggests that specific

120 alterations within this complex might affect outcomes in certain solid tumors (1-3). For

121 example, alterations in the SWI/SNF complex gene PBRM1 have been associated with

122 improved outcomes in patients with renal cell carcinoma treated with immune

123 checkpoint inhibitors (ICIs); refs. (3,4). In lung cancer, inactivation of the catalytic

124 subunit SMARCA4 (BRG1), is the most common alteration within the SWI/SNF complex

125 and has been associated with poor patient outcomes (1,5-10). SMARCA4 is one of two

126 mutually exclusive DNA-dependent ATPases, along with SMARCA2, involved in

127 transcriptional regulation of gene expression (11,12). Yet, the relationship between

128 SMARCA4 and other alterations within the complex genomic landscape of lung cancer

129 remains unclear.

130 Multiple studies have recently highlighted the importance of considering genes of

131 interest within the context of commonly co-occurring mutations (13-18). For example,

132 the identification of STK11, KEAP1, and TP53 mutant subgroups has changed the

133 paradigm of classifying KRAS-mutant lung cancers and non-small cell lung cancers

134 (NSCLCs) in general (13-15,18). These distinct subgroups correlate with differential

135 responses to immunotherapy and long-term outcomes (13,14,17,18). Further, in EGFR-

136 mutant lung cancer, mutations in TP53 and RB1 are associated with shorter response

137 to TKIs and transformation to small cell carcinoma (15,16). Previous studies have

138 shown that SMARCA4 alterations can co-occur in KRAS mutant tumors, yet they also

139 occur independently and less commonly with other driver oncogenes such as epidermal

140 growth factor receptor (EGFR); refs. (5,6). However, there are only limited data on

141 SMARCA4’s relationship to these other co-occurring mutations (8,10) and the

142 significance of SMARCA4 alterations among oncogene driven subsets of lung cancer is

143 unknown.

144 Increased understanding of the relationship of SMARCA4 in lung cancer may enable

145 new therapeutic opportunities in the future. Recently, SMARCA4 alterations have been

146 shown to be oncogenic drivers in a highly aggressive subset of ovarian cancer, small

147 cell carcinoma of the ovary, hypercalcemic type (SCCOHT) that shows increased

148 susceptibility to ICIs (19). Further, there have been case reports of durable responses to

149 ICIs in thoracic SMARCA4-deficient undifferentiated tumors and SMARCA4-deficient

150 lung carcinoma (20,21), but no studies have comprehensively evaluated treatment

151 outcomes in a large cohort of lung cancer patients. In this study, we characterize the

152 clinical, molecular, and histologic relationships of SMARCA4 genomic and protein

153 alterations in lung cancer.

154 Methods

155 We identified all patients with NSCLC of any stage with SMARCA4 alterations detected

156 by MSK-IMPACT NGS (22) until April of 2019 who were treated at Memorial Sloan

157 Kettering Cancer Center (MSK) for genomic analysis (Sup. Fig. 1).

158 SMARCA4 alterations were classified into two groups: SMARCA4 truncating mutations,

159 fusions and homozygous deletions were deemed “Class 1 alteration” and 2) SMARCA4

160 missense mutations or variants of unknown significance, or “Class 2 alteration” based

161 upon categorization in OncoKB (23). Tumors with concurrent Class 1 and Class 2

162 alterations were classified within the Class 1 category. A retrospective pathologic

163 analysis of expression of SMARCA4 in all cases of with SMARCA4 molecular

164 alterations was performed by immunohistochemistry using the previously described

165 methods (10).

166 Somatic alterations were identified using the MSK-IMPACT assay as previously

167 described (22). Individual genes were queried for distribution and enrichment among the

168 patients with and without SMARCA4 alterations. Frequencies of gene alterations by

169 SMARCA4 alteration were considered significant with a p-value < 0.05 and, to reduce

170 false discovery in multiple testing, FDR q-value < 0.10. Tumor mutation burden (TMB)

171 was normalized across each version of the MSK-IMPACT panel (341, 410, or 468

172 genes) and defined as the total number of mutations divided by the coding region

173 captured reported as mutations/megabase in each panel (0.897 megabases (Mb) for

174 341-, 1.017 Mb for 410-, and 1.139 Mb for 468-gene panel). PD-L1 expression was

175 scored as the percentage of tumor cells with membranous staining using predominantly

176 E1L3N antibody, as previously described (24).

177 Medical, pharmacy, and pathology records for all patients with metastatic NSCLC and

178 SMARCA4 alterations were reviewed to collect demographic, pathologic, and treatment

179 data. A random sample of patients with metastatic NSCLC who had MSK-IMPACT

180 without SMARCA4 alterations and were tested during the same time period was used

181 as a comparator group. The response to anti-PD-(L)1 therapy was determined

182 (database lock of April 1, 2019) using Response Evaluation Criteria in Solid Tumors

183 (RECIST) version 1.1. by thoracic radiologists. This study was approved by the

184 Institutional Review Board/Privacy Board at MSK and was in accordance with the

185 Belmont report for retrospective review of records and waiver of consent.

186 Statistical Methods

187 Patient and tumor characteristics were compared across SMARCA4 mutation classes

188 (Class 1, Class 2, wild type) using Chi-square tests and Kruskal-Wallis tests. Overall

189 survival (OS) defined from the date of metastatic diagnosis to death and accounted for

190 the left truncation time from metastatic diagnosis to IMPACT biopsy. Patients without

191 events were censored at their last known visit date. Survival curves and estimates of the

192 median survival time were generated using Kaplan-Meier methods and compared

193 across the three mutation classes using log-rank tests. A Cox proportional hazards

194 model was adjusted for age, sex, smoking status (never smoker, former light smoker,

195 former heavy smoker and current smoker), histology (adenocarcinoma, squamous,

196 other), as well as co-occurring STK11 and KEAP1 mutations, and TMB. Hazard ratios

197 (HR) and 95% confidence intervals (CI) are reported. Sub-analyses of OS were

198 performed among patients with KRAS mutations. Patients without follow-up after their

199 IMPACT pathology date were excluded from analyses (n = 5).

200 The response to immunotherapy as characterized by progression-free survival (PFS),

201 OS, and overall response rate (ORR) was examined among the subset of patients that

202 received immunotherapy. PFS was defined as the time from start of PD-(L)1 inhibitor to

203 clinical or radiographic progression, death, or the end of follow-up, and OS was defined

204 as the time from the start of PD-(L)1 inhibitor to death or the end of follow-up. PFS and

205 OS were analyzed using Kaplan Meier methods and Cox proportional hazards model

206 accounting for left truncation, again adjusted for age, sex, smoking status, histology,

207 TMB, and co-occurring STK11 and KEAP1 mutations. Best overall response was

208 defined as complete or partial response. Multivariable logistic regression was applied to

209 compare the likelihood of ORRR across SMARCA4 mutation classes adjusted for age,

210 TMB, PD-L1, STK11, and KEAP1.

211 To assess whether immunotherapy is associated with improved survival among patients

212 with Class 1 or 2 SMARCA4 mutations, we first calculated the propensity score,

213 probability of receipt of ICIs based on available variables (mutation class, age, sex,

214 race, smoking status, histology, TMB, co-occurring STK11 and KEAP1 mutations). We

215 then adjusted for the propensity score when comparing OS for patients that received

216 ICIs versus patients that did not via a Cox proportional hazards model accounting for

217 left truncation. A p-value <0.05 was considered statistically significant for all analyses.

218 Statistical analyses were performed with GraphPad Prism software version 7 (La Jolla,

219 CA, www.graphpad.com) and R version 3.6.1 software (www.r-project.org).(25)

220 Results

221 Spectrum of SMARCA4 genomic alterations

222 In patients with NSCLC tested by comprehensive next-generation sequencing (NGS),

223 8% (n = 407 of 4813) had a SMARCA4 alteration, with an array of SMARCA4

224 alterations identified (Fig. 1). SMARCA4 alterations were categorized into two groups

225 based upon the type of genomic abnormality: 1) “Class 1 alterations” included truncating

226 mutations deemed oncogenic, gene fusions, and homozygous deletions and 2) “Class 2

227 alterations” included all missense mutations and other variants of unknown significance

228 based upon categorization in OncoKB (23). Tumors with concurrent Class 1 and Class

229 2 SMARCA4 alterations were categorized as Class 1 tumors. In total, 212 patients (4%

230 of total, 52% of SMARCA4 variants) had tumors with Class 1 SMARCA4 alterations and

231 195 (4% of total, 48% of SMARCA4 variants) had tumors with Class 2 SMARCA4

232 alterations (Fig. 1).

233 Relationship between class of SMARCA4 genomic alteration and protein

234 expression

235 We next explored the relationship between the genomic class of SMARCA4 alteration

236 and protein expression. Sufficient tissue for SMARCA4 immunohistochemical analysis

237 was available for 86 cases, including 62 tumors with Class 1 (truncating) alterations and

238 24 tumors with Class 2 (missense) alterations. SMARCA4 expression loss was

239 identified in 50 cases, all of which were tumors with Class 1 alterations (81% of Class 1

240 alterations). Overall, loss of SMARCA4 expression was significantly associated with

241 Class 1 alterations (P < 0.001; Fig. 1).

242 Molecular landscape associated with SMARCA4 alterations

243 To evaluate the genomic context of SMARCA4 alterations, we evaluated genomic

244 profiles of tumors harboring SMARCA4 alterations (n=407) and those without

245 SMARCA4 alterations (n=4406). Among commonly altered genes in lung cancer, the

246 most frequent co-occurring mutations with SMARCA4 alterations were TP53 (56%),

247 KEAP1 (41%), STK11 (39%) and KRAS (36%) (Fig. 2A and 2B).

248 We identified multiple genes that were associated with SMARCA4 alterations (Fig. 2C).

249 Mutations in STK11 and KEAP1 had the strongest association with SMARCA4 mutant

250 tumors compared to SMARCA4 wildtype tumors (P < 0.001, q < 0.001; P < 0.001, q <

251 0.001; Fig. 2B and 2C). Conversely EGFR alterations were strongly associated within

252 SMARCA4 wildtype tumors compared to SMARCA4 mutants (P < 0.001, q < 0.001).

253 SMARCA4 alterations occurred in the absence of KRAS, STK11, and KEAP1

254 alterations in 38% of cases (Fig. 2D). STK11 alterations occurred significantly more

255 frequently with Class 1 than Class 2 alterations (P < 0.001, q = 0.08, Sup. Table 1).

256 NKX2-1 and KEAP1 alterations also occurred more frequently with Class 1 alterations

257 (P = 0.002, q = 0.19; P = 0.01, q = 0.34 respectively) and EGFR alterations were

258 common with Class 2 alterations (P = 0.004, q = 0.19, Sup. Table 1).

259 Patient characteristics in advanced NSCLC by SMARCA4 alteration class

260 We then investigated how the findings from our molecular and expression analyses

261 related to clinical outcomes in patients with advanced NSCLC. Patient characteristics

262 among stage IV tumors with Class 1 (n=149) versus Class 2 (n=143) SMARCA4

263 alterations were generally similar (Table 1). The presence of a Class 1 or 2 SMARCA4

264 alteration was associated with history of smoking (P < 0.001) and non-adenocarcinoma

265 histology (P < 0.001) compared to patients with SMARCA4 wildtype NSCLC (n=996)

266 (Table 1). Among patients harboring either class of SMARCA4 mutation, 85% were

267 smokers and 84% had adenocarcinoma; the rest had predominantly NSCLC, not

268 otherwise classified.

269 Prognostic impact of Class 1 and Class 2 SMARCA4 alterations in advanced

270 NSCLC

271 Overall, we found that patients with metastatic NSCLC harboring either Class 1 or Class

272 2 SMARCA4 alterations had shorter overall survival compared to patients with

273 SMARCA4 wildtype NSCLC (p<0.001; Fig. 3A). Class 1 alterations were associated

274 with the poorest outcomes (Fig. 3A). The differences in outcomes held in the

275 multivariable survival analysis adjusted for age, sex, smoking status, histology, TMB,

276 and the presence of STK11 and/or KEAP1 mutations (Fig. 3A).

277 Given the heterogeneity of co-occurring mutations, we sought to further isolate the

278 specific impact of SMARCA4 alterations by examining within the context of a single

279 driver oncogene. We focused initially on 374 patients with tumors harboring KRAS

280 mutations. In these patients, the presence of Class 1 or Class 2 SMARCA4 alterations

281 was a poor prognostic factor and remained prognostic when accounting for age, sex,

282 smoking status, histology, TMB, and the presence of STK11 or KEAP1 mutations (Fig.

283 3B). Further, the addition of STK11 and/or KEAP1 was associated with decreased

284 survival, with patients with all three STK11, KEAP1, and SMARCA4 having the shortest

285 survival (P <0.001, Sup. Fig. 2).

286 Association with benefit of immunotherapy

287 Next, we analyzed the impact of ICIs on patient outcomes. Among patients with

288 SMARCA4 alterations, ICI use was associated with significantly improved survival from

289 the start of ICIs (HR 0.67, 95% CI 0.48, 0.92, P = 0.01) (Fig. 4A). When evaluating

290 known factors that predict outcomes to ICI, SMARCA4-mutant tumors had higher TMB

291 (P < 0.001, Fig. 4B) but were more likely to be PD-L1 low or negative (P = 0.03, Fig.

292 4C). Class 1 alterations had lower expression of PD-L1 and higher median TMB

293 compared to Class 2 alterations (Fig. 4B-C).

294 Finally, we sought to compare outcome among the two SMARCA4 mutant classes and

295 SMARCA4 wildtype NSCLC in patients who had received ICI. Overall response was

296 assessed in 445 out of 570 patients that received ICI. In unadjusted analyses, patients

297 who harbored Class 1 alterations had a higher ORR in comparison to Class 2

298 alterations or SMARCA4 wild-type tumors (P = 0.027, Fig. 4D). There was no difference

299 in progression-free survival (P = 0.74) or overall survival (P = 0.35) on ICIs by

300 SMARCA4 alteration status (Fig. 4E-F).

301 Discussion

302 Here, we identify two specific classes of SMARCA4 alterations associated with distinct

303 protein expression and differential negative clinical outcomes in patients with metastatic

304 NSCLC. While both classes of SMARCA4 alterations are associated with poor clinical

305 outcomes, Class 1 alterations, which are associated with protein loss, are the strongest

306 independent negative prognostic factor for patients, but respond best to ICIs. Despite

307 the negative prognostic impact compared to patients with SMARCA4 wildtype tumors,

308 patients with SMARCA4 alterations who received ICIs had better outcomes than those

309 who did not.

310 This study builds upon recent data that co-occurring STK11 and KEAP1 mutations in

311 lung cancer can significantly impact prognosis and responsiveness to therapy. STK11

312 and KEAP1 alterations are linked with poor prognosis and lack of response to

313 immunotherapy in KRAS-mutant tumors and more recently in all patients with NSCLC.

314 We find that SMARCA4 alterations are associated with STK11 and KEAP1 mutations

315 but are independent predictors of poor prognosis. SMARCA4 abnormalities in

316 combination with STK11 and/or KEAP1 mutations have an additive impact on

317 shortening survival. However, unlike STK11, SMARCA4 appears to be associated with

318 increased sensitivity to immunotherapy. Future studies of STK11 and KEAP1 should

319 incorporate exploration of SMARCA4 to further delineate the role of each co-occurring

320 mutation in influencing patient outcomes and SMARCA4 should be identified and tested

321 as a potential prognostic or predictive variable in prospective trials moving forward.

322 We observed that the spectrum of SMARCA4 alterations differentially impact protein

323 expression. Our findings are consistent with other recent analyses that assessed the

324 incidence of SMARCA4-mutant lung cancer and frequency of protein expression loss

325 with truncating mutations, supporting our classification schema (8,10). Interestingly,

326 while the effect of Class 1 (truncating) alterations was most profound, we also find that,

327 unexpectedly, patients with Class 2 (mis-sense, non-truncating) SMARCA4 alterations

328 had worse overall prognosis relative to patients with SMARCA4 wild-type tumors,

329 suggesting that function may be compromised in the setting of intact expression. Recent

330 preclinical work provides additional mechanistic support and reveals that missense

331 mutations of SMARCA4 modify the open chromatin landscape and induce pro-

332 oncogenic expression changes in MYC and its target genes, among others (26,27).

333 Our study is the first to evaluate how SMARCA4 alterations in NSCLC influence

334 sensitivity to ICIs. Recent analyses have shown that SMARCA4 and PBRM1 could be

335 associated with improved response to immunotherapy in subtypes of ovarian cancer

336 and renal cell cancer (4,19) and case reports have described durable responses to ICIs

337 in a patient with a thoracic SMARCA4-deficient undifferentiated tumor (also referred to

338 as a SMARCA4-deficient thoracic sarcoma) and a patient with NSCLC (20,21). Despite

339 high rates of PD-L1 negativity, patients with SMARCA4-mutant NSCLC appear to derive

340 significant benefit from PD-(L)1 blockade. Therefore, SMARCA4 mutation status should

341 be explored as a potentially novel biomarker of responsiveness to ICIs as a complement

342 to PD-L1 expression and TMB in NSCLC.

343 While there are no known currently effective targeted treatments for SMARCA4-mutant

344 NSCLCs, our study and others suggest SMARCA4 is a potential target in lung cancer

345 with distinct therapeutic vulnerabilities. For example, CDK4/6, AURKA, ATR, and EZH2

346 inhibition have recently shown antitumor activity in preclinical models of SMARCA4

347 deficient tumors (1,16,25,28-33). SMARCA2 could be a synthetic lethal vulnerability in

348 SMARCA4-mutant cancers. Prior reports have shown that SMARCA2 retains

349 expression in SMARCA4-mutant NSCLC and several SMARCA2 inhibitors are currently

350 in development to target this potential vulnerability (10,16). Future trials should explore

351 use of these agents alone or in combination with ICIs given the efficacy of anti-PD-(L)1

352 antibodies in our analysis.

353 This study is a single-institution retrospective analysis and therefore has some inherent

354 limitations. Unidentified factors associated with exposure and response to

355 immunotherapy and overall survival could bias our results. Nevertheless, we accounted

356 for all known potential variables that may influence outcomes. For example, we

357 developed and incorporated a risk score to account for a patient’s likelihood of receiving

358 anti-PD(L)1 therapy and used a Cox proportional hazards model for multivariate

359 analysis using the variables available. Analyses adjusting for PD-L1 expression are

360 limited by the modest number of patients with sufficient available tissue for retrospective

361 staining for PD-L1 and SMARCA4. Future studies that incorporate zygosity are also

362 needed to understand its impact on expression and clinical outcomes.

363 In sum, our report highlights that SMARCA4 alterations in lung cancer are uniquely

364 linked to response to immunotherapy and patient outcomes. We found that the

365 presence of SMARCA4 abnormalities is enriched in patients with KRAS, STK11, and

366 KEAP1 mutations, but independently contributes to shortened overall survival with these

367 co-occurring alterations. Despite these poor outcomes, patients with SMARCA4-mutant

368 lung cancers may also be more sensitive to immunotherapy, which may enable new

369 therapeutic options in the future.

370 References

371 1. Helming KC, Wang X, Roberts CWM. Vulnerabilities of mutant SWI/SNF 372 complexes in cancer. Cancer cell 2014;26(3):309-17 doi 373 10.1016/j.ccr.2014.07.018. 374 2. Kadoch C, Hargreaves DC, Hodges C, Elias L, Ho L, Ranish J, et al. Proteomic 375 and bioinformatic analysis of mammalian SWI/SNF complexes identifies 376 extensive roles in human malignancy. Nature genetics 2013;45(6):592-601 doi 377 10.1038/ng.2628. 378 3. Abou Alaiwi S, Nassar AH, Xie W, Bakouny Z, Berchuck JE, Braun DA, et al. 379 Mammalian SWI/SNF complex genomic alterations and immune checkpoint 380 blockade in solid tumors. Cancer Immunology Research 381 2020:canimm.0866.2019 doi 10.1158/2326-6066.Cir-19-0866. 382 4. Miao D, Margolis CA, Gao W, Voss MH, Li W, Martini DJ, et al. Genomic 383 correlates of response to immune checkpoint therapies in clear cell renal cell 384 carcinoma. Science (New York, NY) 2018;359(6377):801-6 doi 385 10.1126/science.aan5951. 386 5. Lovly CM, Gupta A, Lipson D, Otto G, Brennan T, Chung CT, et al. Inflammatory 387 myofibroblastic tumors harbor multiple potentially actionable kinase fusions. 388 Cancer Discov 2014;4(8):889-95 doi 10.1158/2159-8290.CD-14-0377.

389 6. Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, et al. 390 Mapping the hallmarks of lung adenocarcinoma with massively parallel 391 sequencing. Cell 2012;150(6):1107-20 doi 10.1016/j.cell.2012.08.029. 392 7. Reisman DN, Sciarrotta J, Wang W, Funkhouser WK, Weissman BE. Loss of 393 BRG1/BRM in human lung cancer cell lines and primary lung cancers: correlation 394 with poor prognosis. Cancer research 2003;63(3):560-6. 395 8. Dagogo-Jack I, Schrock AB, Kem M, Jessop N, Lee J, Ali SM, et al. 396 Clinicopathologic Characteristics of BRG1-Deficient NSCLC. J Thorac Oncol 397 2020 doi 10.1016/j.jtho.2020.01.002. 398 9. Bell EH, Chakraborty AR, Mo X, Liu Z, Shilo K, Kirste S, et al. SMARCA4/BRG1 399 Is a Novel Prognostic Biomarker Predictive of Cisplatin-Based Chemotherapy 400 Outcomes in Resected Non-Small Cell Lung Cancer. Clinical cancer research : 401 an official journal of the American Association for Cancer Research 402 2016;22(10):2396-404 doi 10.1158/1078-0432.Ccr-15-1468. 403 10. Rekhtman N, Montecalvo J, Chang JC, Alex D, Ptashkin RN, Ai N, et al. 404 SMARCA4-Deficient Thoracic Sarcomatoid Tumors Represent Primarily 405 Smoking-Related Undifferentiated Carcinomas Rather Than Primary Thoracic 406 Sarcomas. J Thorac Oncol 2020;15(2):231-47 doi 10.1016/j.jtho.2019.10.023. 407 11. Marquez-Vilendrer SB, Rai SK, Gramling SJ, Lu L, Reisman DN. Loss of the 408 SWI/SNF ATPase subunits BRM and BRG1 drives lung cancer development. 409 Oncoscience 2016;3(11-12):322-36 doi 10.18632/oncoscience.323. 410 12. Orvis T, Hepperla A, Walter V, Song S, Simon J, Parker J, et al. 411 BRG1/SMARCA4 inactivation promotes non-small cell lung cancer 412 aggressiveness by altering chromatin organization. Cancer research 413 2014;74(22):6486-98 doi 10.1158/0008-5472.Can-14-0061. 414 13. Arbour KC, Jordan EJ, Kim HR, Dienstag J, Yu H, Sanchez-Vega F, et al. Effects 415 of co-occurring genomic alterations on outcomes in patients with KRAS-mutant 416 non-small cell lung cancer. 2017:clincanres.1841.2017 doi 10.1158/1078- 417 0432.CCR-17-1841 %J Clinical Cancer Research. 418 14. Skoulidis F, Byers LA, Diao L, Papadimitrakopoulou VA, Tong P, Izzo J, et al. 419 Co-occurring Genomic Alterations Define Major Subsets of KRAS- 420 Mutant Lung Adenocarcinoma with Distinct Biology, Immune Profiles, and 421 Therapeutic Vulnerabilities. 2015;5(8):860-77 doi 10.1158/2159-8290.CD-14- 422 1236 %J Cancer Discovery. 423 15. Aggarwal C, Davis CW, Mick R, Thompson JC, Ahmed S, Jeffries S, et al. 424 Influence of TP53 Mutation on Survival in Patients With Advanced EGFR-Mutant 425 Non–Small-Cell Lung Cancer. 2018(2):1-29 doi 10.1200/po.18.00107. 426 16. Papillon JPN, Nakajima K, Adair CD, Hempel J, Jouk AO, Karki RG, et al. 427 Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 428 ATPase Activity for the Treatment of Brahma Related Gene 1 429 (BRG1)/SMARCA4-Mutant Cancers. Journal of medicinal chemistry 430 2018;61(22):10155-72 doi 10.1021/acs.jmedchem.8b01318. 431 17. Rizvi H, Sanchez-Vega F, La K, Chatila W, Jonsson P, Halpenny D, et al. 432 Molecular Determinants of Response to Anti-Programmed Cell Death (PD)-1 and 433 Anti-Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non-Small- 434 Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing. Journal

435 of clinical oncology : official journal of the American Society of Clinical Oncology 436 2018;36(7):633-41 doi 10.1200/jco.2017.75.3384. 437 18. Skoulidis F, Arbour KC, Hellmann MD, Patil PD, Marmarelis ME, Awad MM, et al. 438 Association of STK11/LKB1 genomic alterations with lack of benefit from the 439 addition of pembrolizumab to platinum doublet chemotherapy in non-squamous 440 non-small cell lung cancer. Journal of Clinical Oncology 2019;37(15_suppl):102- 441 doi 10.1200/JCO.2019.37.15_suppl.102. 442 19. Jelinic P, Ricca J, Van Oudenhove E, Olvera N, Merghoub T, Levine DA, et al. 443 Immune-Active Microenvironment in Small Cell Carcinoma of the Ovary, 444 Hypercalcemic Type: Rationale for Immune Checkpoint Blockade. Journal of the 445 National Cancer Institute 2018;110(7):787-90 doi 10.1093/jnci/djx277. 446 20. Naito T, Umemura S, Nakamura H, Zenke Y, Udagawa H, Kirita K, et al. 447 Successful treatment with nivolumab for SMARCA4-deficient non-small cell lung 448 carcinoma with a high tumor mutation burden: A case report. 2019;10(5):1285-8 449 doi 10.1111/1759-7714.13070. 450 21. Henon C, Blay J-Y, Massard C, Mir O, Bahleda R, Dumont S, et al. Long lasting 451 major response to pembrolizumab in a thoracic malignant rhabdoid-like 452 SMARCA4-deficient tumor. Annals of Oncology 2019;30(8):1401-3 doi 453 10.1093/annonc/mdz160 %J Annals of Oncology. 454 22. Cheng DT, Mitchell TN, Zehir A, Shah RH, Benayed R, Syed A, et al. Memorial 455 Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets 456 (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing 457 Clinical Assay for Solid Tumor Molecular Oncology. The Journal of molecular 458 diagnostics : JMD 2015;17(3):251-64 doi 10.1016/j.jmoldx.2014.12.006. 459 23. Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, et al. OncoKB: 460 A Precision Oncology Knowledge Base. JCO precision oncology 2017;2017 doi 461 10.1200/po.17.00011. 462 24. Schoenfeld AJ, Rizvi H, Bandlamudi C, Sauter JL, Travis WD, Rekhtman N, et al. 463 Clinical and molecular correlates of PD-L1 expression in patients with lung 464 adenocarcinomas^✰. Annals of Oncology 2020;31(5):599- 465 608 doi 10.1016/j.annonc.2020.01.065. 466 25. Xue Y, Meehan B, Macdonald E, Venneti S, Wang XQD, Witkowski L, et al. 467 CDK4/6 inhibitors target SMARCA4-determined cyclin D1 deficiency in 468 hypercalcemic small cell carcinoma of the ovary. Nature communications 469 2019;10(1):558 doi 10.1038/s41467-018-06958-9. 470 26. Hodges HC, Stanton BZ, Cermakova K, Chang CY, Miller EL, Kirkland JG, et al. 471 Dominant-negative SMARCA4 mutants alter the accessibility landscape of 472 tissue-unrestricted enhancers. Nat Struct Mol Biol 2018;25(1):61-72 doi 473 10.1038/s41594-017-0007-3. 474 27. Stanton BZ, Hodges C, Calarco JP, Braun SM, Ku WL, Kadoch C, et al. Smarca4 475 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nature 476 genetics 2017;49(2):282-8 doi 10.1038/ng.3735. 477 28. Zernickel E, Sak A, Riaz A, Klein D, Groneberg M, Stuschke M. Targeting of 478 BRM sensitizes BRG1 mutant lung cancer cell lines to radiotherapy. Molecular 479 cancer therapeutics 2018 doi 10.1158/1535-7163.Mct-18-0067.

480 29. Vangamudi B, Paul TA, Shah PK, Kost-Alimova M, Nottebaum L, Shi X, et al. 481 The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug 482 Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 483 Inhibitor Studies. Cancer research 2015;75(18):3865-78 doi 10.1158/0008- 484 5472.Can-14-3798. 485 30. Fillmore CM, Xu C, Desai PT, Berry JM, Rowbotham SP, Lin YJ, et al. EZH2 486 inhibition sensitizes BRG1 and EGFR mutant lung tumours to TopoII inhibitors. 487 Nature 2015;520(7546):239-42 doi 10.1038/nature14122. 488 31. Kurashima K, Kashiwagi H, Shimomura I, Suzuki A, Takeshita F, Mazevet M, et 489 al. SMARCA4 deficiency-associated heterochromatin induces intrinsic DNA 490 replication stress and susceptibility to ATR inhibition in lung adenocarcinoma. 491 NAR Cancer 2020;2(2) doi 10.1093/narcan/zcaa005. 492 32. Lissanu Deribe Y, Sun Y, Terranova C, Khan F, Martinez-Ledesma J, Gay J, et 493 al. Mutations in the SWI/SNF complex induce a targetable dependence on 494 oxidative phosphorylation in lung cancer. Nature medicine 2018;24(7):1047-57 495 doi 10.1038/s41591-018-0019-5. 496 33. Tagal V, Wei S, Zhang W, Brekken RA, Posner BA, Peyton M, et al. SMARCA4- 497 inactivating mutations increase sensitivity to Aurora kinase A inhibitor VX-680 in 498 non-small cell lung cancers. Nature communications 2017;8(1):14098 doi 499 10.1038/ncomms14098.

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517 Figure Legends

518 Figure 1. Spectrum of SMARCA4 alterations by class and association with SMARCA4

519 protein expression. (A) The distribution of Class 1 SMARCA4 alterations (n=212) and

520 protein expression (n =62). (B) The distribution of Class 2 SMARCA4 alterations (n=95)

521 and protein expression (n =24). Green QLQ, Gln, Leu, Gln motif; Red HSA,

522 helicase/SANT-associated domain; Blue BRK, Brahma and Kismet domain; Yellow

523 DEXDc, DEAD-like helicase superfamily domain; Purple SNF2_N, SNF2 family N-

524 terminal domain; Orange HELICc, helicase superfamily C-terminal domain; Pink Bromo,

525 bromodomain.

526 Figure 2. Genomic context of SMARCA4 alterations. (A) Most frequent co-occurring

527 alterations by SMARCA4 alteration. (B) Distribution of SMARCA4 alteration by

528 commonly altered gene subgroups in NSCLC. (C) Frequency of altered individual genes

529 within SMARCA4 mutant vs SMARCA4 wildtype subgroups. Genes labeled red were

530 associated with significantly differential PD-L1 expression (q value <0.10). (D)

531 Distribution of SMARCA4, STK11, KRAS, and KEAP1 alterations within NSCLC cohort.

532 Figure 3. Survival by SMARCA4 alteration class. (A) Overall survival among all

533 patients, with multivariate model (right). (B) Overall survival among patients with KRAS

534 mutations, with multivariate model (right).

535 Figure 4. PD-L1 expression, tumor mutational burden, and immune checkpoint inhibitor

536 (ICI) outcomes. (A) Overall survival among patients with SMARCA4 alterations who did

537 and did not receive ICIs. (B) Tumor mutational burden (TMB) by SMARCA4 alteration

538 class. (C) PD-L1 expression frequency by SMARCA4 alteration class. (D) Overall

539 response rate by SMARCA4 alteration class. (E) Progression-free survival by

540 SMARCA4 alteration class. (F) Overall survival by SMARCA4 alteration class.

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556 Table 1: Clinical characteristics of patients with advanced NSCLC by SMARCA4

557 alteration class.

SMARCA4 SMARCA4 SMARCA4 Characteristic Class 1 Class 2 Wild type P-value (N = 149) (N = 143) (N = 996)

Median Age (Q1, Q3) 65 (58, 72) 65 (59, 72) 65 (58, 73) 0.7 Sex 0.052

Female 74 (50%) 78 (55%) 593 (60%)

Male 75 (50%) 65 (45%) 403 (40%)

Race 0.13

White 124 (83%) 125 (87%) 775 (78%)

Black 7 (5%) 7 (5%) 57 (6%)

Asian 10 (7%) 6 (4%) 101 (10%)

Other 8 (5%) 5 (4%) 63 (6%)

Smoking <0.001

Never smoker 17 (11%) 26 (18%) 315 (32%)

Former light (<15 py) 20 (13%) 19 (13%) 165 (17%)

Former heavy (>15 py) 80 (54%) 71 (50%) 373 (37%)

Current smoker 32 (21%) 27 (19%) 131 (13%)

Histology <0.001

Adenocarcinoma 121 (81%) 125 (87%) 914 (92%)

Other 28 (19%) 18 (13%) 82 (8%)

558 py: pack years

559

Figure 1 A. 5

0 # SMARCA4 Mutations HSA SNF2_N

0 400 800 1200 1647aa Class 1 SMARCA4 alterations 0 20 40 60 80 100 % of tumors Protein Lost Protein Retained

B. T910M 7

# SMARCA4 Mutations 0 HSA SNF2_N

0 400 800 1200 1647aa Class 2 SMARCA4 alterations 0 20 40 60 80 100 % of tumors Protein Lost Protein Retained

Figure 2 A. B. SMARCA4 100% 25 TP53 56% SMARC44 mt 20

KEAP1 41% 15

STK11 39% 10 % of patient s KRAS 36% 5

EGFR 14% 0 14 Genetic Alteration Inframe mutation Missense mutation Truncating mutation 140) exon TP53 MT n = 75) n = 147) n = 86) Fusions Amplification Deep deletion No alterations STK11n = 625MT) KRAS MT n = 2519) n = 53) ( ALK( fusion EGFR MT RET (fusion ET n = 36) KEAP1(n = 352MT) ( (n = 1394) ( BRAFV600( EROS1 fusion (n = 1 M (

C. 60% D. q value < 0.10 q value > 0.10 TP53

SMARCA4 155 910 KRAS

40% 37 23 70

KRAS 137 24 18 201 EGFR

20% CDKN2A 65 148 36 STK11 Frequency in SMARCA4 wildtype tumors CDKN2B 132 PIK3CA 46 MET KEAP1 CDK4 MYC

0% STK11 133 KEAP1

0% 20% 40% 60% Frequency in SMARCA4 mutant tumors Downloaded from clincancerres.aacrjournals.org on September 25, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on July 24, 2020; DOI: 10.1158/1078-0432.CCR-20-1825 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

Figure 3

A. N = 1288 Hazard Ratio 95% CI p value 1.00 +++++++++++ SMARCA4 mutation type <0.001 +++ Mutation Status: +++++++ + Wild type -- -- +++++++ Wild type (n = 996) ++++++++++ + Class 1 alteration (n = 149) ++++ ++++++++ Class 2 2.01 1.58, 2.55 +++++++ + Class 2 alteration (n = 143) + + ++++ 1.59 1.25, 2.04 + +++++++ Class 1 + ++ +++ +++++ Sex 0.2 +++++ + +++++++++++++++++++++ Female -- -- 0.75 + ++ +++++++ +++ + +++++++++ + ++++++++++++ Male 1.12 0.95, 1.31 + ++++++++ ++++++++ Age (10 years) 1.22 1.13, 1.32 <0.001 +++++++++ p <0.001 + ++ ++++ + + +++ Smoking status 0.005 + +++ ++++++++++ + ++++++++++++ Never smoker -- -- + ++++++++ + +++ +++++ 1.23, 2.03 0.50 ++ ++++++++++++ Former light (<15 pack-year) 1.58 ++++++ ++++++++++++++ ++++++ Former heavy (>15 pack year) 1.21 0.96, 1.51 ++ +++++++ ++ +++ Current smoker 1.27 0.96, 1.69 +++++ + + ++++++++ + + +++++++ Histology <0.001 + + ++++++++++++++ ++ ++++++++++++++ -- -- Overall survival probability Overall + Adenocarcinoma + + +++++++++++++++ ++ +++ +++++++ 0.25 +++++++++++ Non-adenocarcinoma 1.79 1.38, 2.33 + + ++ ++++++ ++++ ++++++++ Tumor mutation burden (TMB) <0.001 +++ ++ +++ +++++ +++++ 0.98 0.97, 0.99 + + +++++ ++ ++ STK11 <0.001 + + + ++ +++++++ Negative -- -- ++ + + Positive 1.52 1.23, 1.88 0.00 KEAP1 0.036 Negative -- -- 0 6 12 18 24 30 36 42 48 54 60 Positive 1.26 1.02, 1.55 Months

B. N = 374 Hazard Ratio 95% CI p value SMARCA4 mutation type <0.001 1.00 +++ + Wild type -- -- +++ Mutation Status: + + + Wild type (n = 264) Class 2 2.75 1.84, 4.11 ++ ++++ + + ++++ Class 1 alteration (n = 58) Class 1 1.59 1.04, 2.41 ++ + Class 2 alteration (n = 52) + Sex 0.6 ++++ Female -- -- 0.75 + ++ ++ ++ ++++++++ Male 0.93 0.70, 1.25 ++ ++++++ + +++ p <0.001 Age (10 years) 1.33 1.13, 1.55 <0.001 + ++ + Smoking status 0.7 + ++++ Never smoker -- -- +++ + + + Former light (<15 pack-year) 1.03 0.49, 2.16 ++++ 0.50 ++++ ++++ Former heavy (>15 pack year) 1.12 0.59, 2.14 + ++ + + + Current smoker 0.88 0.43, 1.78 ++ + + + +++ Histology 0.13 + + ++++++++++ Adenocarcinoma -- -- ++++++ + Overall survival probability Overall + Non-adenocarcinoma 1.61 0.90, 2.90 0.25 + ++ + Tumor mutation burden (TMB) 0.97 0.95, 1.00 0.023 + STK11 0.017 Negative -- -- ++ Positive 1.51 1.08, 2.11 + KEAP1 0.10 0.00 Negative -- -- Positive 1.34 0.95, 1.89 Downloaded0 6 from clincancerres.aacrjournals.org 12 18 24 on 30September 36 25, 2021. © 2020 American Association for Cancer Months Research. Author Manuscript Published OnlineFirst on July 24, 2020; DOI: 10.1158/1078-0432.CCR-20-1825 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

Figure 4 A. B. C. p = 0.03 100 p < 0.01 100 1.00 ++++ SMARCA4 altered: ++++ + Did not receive ICI (n = 205) ++ + + Received ICI (n = 87) 75 80 0.75 ++++ + p = 0.01 ++ + 50-100% +++++ 60 0.50 +++ ++ 50 1-49% +++++++ +++

+++++++++ b ++ TMB/M 40 0.25 ++ + ++++ +++ 0%

+++ + Frequenc y ++++++ +++++++ ++ + + + +++++++++ + 25 0.00 + + + 20 0 6 12 18 24 30 36 42 48 54 60 Overall survival probability Overall Months 0 0 SMARCA4 WT Class 1 Class 2 SMARCA4 WT Class 1 Class 2 (n=996) (n=149) (n=143) (n=294) (n=39) (n=54)

D. E. F. 1.00 Mutation Status: 1.00 + +++ Mutation Status: 100 + Wild type (n=325) ++ + Wild type (n=482) + Class 1 alteration (n=41) + + Class 1 alteration (n=50) Class 2 alteration (n=33) + + + + + Class 2 alteration (n=37) + 0.75 + +++ 75 0.75 ++ ORR +++ ++++++++ p = 0.35 +++++++++ +++++++++ p = 0.027 p = 0.74 ++++++++ 50 +++++++ 0.50 +++++ 0.50 +++ ++++++ +++++++++++ % of patient s +++ 25 + + ++++++++ + + + ++ +++++++++ + + + + +++++++ +++++++++ 0.25 + 0.25 ++++ + ++++++++++++++ 0 ++++++ survival probability Overall ++ ++++ + + + + +++++ ++ ++ + SMARCA4 WT Class 1 Class 2 + ++++ ++ + Progression−free su rvival probability +++++ +++++++ + ++++++++++ + (n=358) (n=50) (n=37) 0.00 0.00 0 6 12 18 24 30 36 0 6 12 18 24 30 36 Months from start of IO Months from start of IO

The Genomic Landscape of SMARCA4 Alterations and Associations with Outcomes in Patients with Lung Cancer

Adam J Schoenfeld, Chaitanya Bandlamudi, Jessica A Lavery, et al.

Clin Cancer Res Published OnlineFirst July 24, 2020.

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