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Radiotherapy (RT) is one of the primary treatments of head and neck squamous cell carcinoma (HNSCC), which has a high-risk of locoregional failure (LRF). Presently, there is no reliable predictive biomarker of radioresistance in HNSCC. Here, we found that mutations in NFE2L2, which encodes Nrf2, are associated with a significantly higher rate of LRF in patients with oral cavity cancer treated with surgery and adjuvant (chemo)radiotherapy but not in those treated with surgery alone. Somatic mutation of NFE2L2 led to Nrf2 activation and radioresistance in HNSCC cells. Tumors harboring mutant Nrf2E79Q were substantially more radioresistant than tumors with wild-type Nrf2 in immunocompetent mice, whereas the difference was diminished in immunocompromised mice. Nrf2E79Q enhanced radioresistance through increased recruitment of intratumoral polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) and reduction of M1-polarized macrophages. Treatment with the glutaminase inhibitor CB-839 overcame the radioresistance induced by Nrf2E79Q or Nrf2E79K. RT increased expression of PMN-MDSC–attracting chemokines, including CXCL1, CXLC3, and CSF3, in Nrf2E79Q-expressing tumors via the TLR4, which could be reversed by CB-839. This study provides insights into the impact of NFE2L2 mutations on radioresistance and suggests that CB-839 can increase radiosensitivity by switching intratumoral myeloid cells to an antitumor phenotype, supporting clinical testing of CB-839 with RT in HNSCC with NFE2L2 mutations.Significance:NFE2L2 mutations are predictive biomarkers of radioresistance in head and neck cancer and confer sensitivity to glutaminase inhibitors to overcome radioresistance.

The relationship between NFE2L2 mutation and radiation resistance in OC cancer. Kaplan-Meier analysis of PFS and OSin OC patients treated with surgery and postoperative (chemo)radiotherapy.

CB-839 overcomes the Nrf2E79Q-induced radiation resistance through regulating TLR4-mediated cytokine changes.

Mutational landscape and details of NFE2L2 gene mutation in a cohort of oral cavity cancer patients treated with surgery and postoperative (chemo)radiotherapy at Stanford University.

Nrf2 mutation leads to extrinsic radiation resistance through recruitment of PMN-MDSC in tumors.

Supplementary Figures related to Figures 1, 2, 3, and 4.

Table S2: Surveillance plasma sample ctDNA metrics. Table S3: Baseline plasma sample ctDNA metrics. Table S4: Surveillance plasma sample variants in ctDNA detected samples. Table S5: Baseline plasma variants in available samples. Table S6: Tumor variants detected by whole exome and targeted sequencing. Table S7: Canonical genes implicated in clonal hematopoiesis.

Supplemental Table 1 shows patients distribution in OC cohorts from Stanford University. Supplemental Table 2 shows primers for mutagenesis. Supplemental Table 3 shows primers for real-time PCR. Supplemental Table 4 shows gene mutations identified by targeted next generation sequencing in a cohort of oral cavity cancer patients treated with surgery and postoperative (chemo)radiotherapy at Stanford University. Supplemental Table 5 shows tumor growth delay of indicated MOC1 xenografts using 1000mm3 tumor size as a proxy.

Table S1 shows summary patient demographics, pathologic features, and treatment details

Radiotherapy (RT) is one of the primary treatments of head and neck squamous cell carcinoma (HNSCC), which has a high-risk of locoregional failure (LRF). Presently, there is no reliable predictive biomarker of radioresistance in HNSCC. Here, we found that mutations in NFE2L2, which encodes Nrf2, are associated with a significantly higher rate of LRF in patients with oral cavity cancer treated with surgery and adjuvant (chemo)radiotherapy but not in those treated with surgery alone. Somatic mutation of NFE2L2 led to Nrf2 activation and radioresistance in HNSCC cells. Tumors harboring mutant Nrf2E79Q were substantially more radioresistant than tumors with wild-type Nrf2 in immunocompetent mice, whereas the difference was diminished in immunocompromised mice. Nrf2E79Q enhanced radioresistance through increased recruitment of intratumoral polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) and reduction of M1-polarized macrophages. Treatment with the glutaminase inhibitor CB-839 overcame the radioresistance induced by Nrf2E79Q or Nrf2E79K. RT increased expression of PMN-MDSC–attracting chemokines, including CXCL1, CXLC3, and CSF3, in Nrf2E79Q-expressing tumors via the TLR4, which could be reversed by CB-839. This study provides insights into the impact of NFE2L2 mutations on radioresistance and suggests that CB-839 can increase radiosensitivity by switching intratumoral myeloid cells to an antitumor phenotype, supporting clinical testing of CB-839 with RT in HNSCC with NFE2L2 mutations.Significance:NFE2L2 mutations are predictive biomarkers of radioresistance in head and neck cancer and confer sensitivity to glutaminase inhibitors to overcome radioresistance.

Purpose:Treatment with PD-(L)1 blockade can produce remarkably durable responses in patients with non–small cell lung cancer (NSCLC). However, a significant fraction of long-term responders ultimately progress and predictors of late progression are unknown. We hypothesized that circulating tumor DNA (ctDNA) analysis of long-term responders to PD-(L)1 blockade may differentiate those who will achieve ongoing benefit from those at risk of eventual progression.Experimental Design:In patients with advanced NSCLC achieving long-term benefit from PD-(L)1 blockade (progression-free survival ≥ 12 months), plasma was collected at a surveillance timepoint late during/after treatment to interrogate ctDNA by Cancer Personalized Profiling by Deep Sequencing. Tumor tissue was available for 24 patients and was profiled by whole-exome sequencing (n = 18) or by targeted sequencing (n = 6).Results:Thirty-one patients with NSCLC with long-term benefit to PD-(L)1 blockade were identified, and ctDNA was analyzed in surveillance blood samples collected at a median of 26.7 months after initiation of therapy. Nine patients also had baseline plasma samples available, and all had detectable ctDNA prior to therapy initiation. At the surveillance timepoint, 27 patients had undetectable ctDNA and 25 (93%) have remained progression-free; in contrast, all 4 patients with detectable ctDNA eventually progressed [Fisher P < 0.0001; positive predictive value = 1, 95% confidence interval (CI), 0.51–1; negative predictive value = 0.93 (95% CI, 0.80–0.99)].Conclusions:ctDNA analysis can noninvasively identify minimal residual disease in patients with long-term responses to PD-(L)1 blockade and predict the risk of eventual progression. If validated, ctDNA surveillance may facilitate personalization of the duration of immune checkpoint blockade and enable early intervention in patients at high risk for progression.

CB-839 overcomes RT resistance in Nrf2E79Q MOC1 cells through regulating the tumor microenvironment.

Somatic mutation of NFE2L2 leads to Nrf2 activation and promotes intrinsic radiation resistance in human head and neck squamous cell carcinoma (HNSCC).

NFE2L2 mutation leads to extrinsic radiation resistance.

Several microRNAs have been implicated in human breast cancer but none to date have been validated or utilized consistently in clinical management. MicroRNA-301 (miR-301) overexpression has been implicated as a negative prognostic indicator in lymph node negative (LNN) invasive ductal breast cancer, but its potential functional impact has not been determined. Here we report that in breast cancer cells, miR-301 attenuation decreased cell proliferation, clonogenicity, migration, invasion, tamoxifen resistance, tumor growth, and microvessel density, establishing an important oncogenic role for this gene. Algorithm-based and experimental strategies identified FOXF2, BBC3, PTEN, and COL2A1 as candidate miR-301 targets, all of which were verified as direct targets through luciferase reporter assays. We noted that miR-301 is located in an intron of the SKA2 gene which is responsible for kinetochore assembly, and both genes were found to be coexpressed in primary breast cancer samples. In summary, our findings define miR-301 as a crucial oncogene in human breast cancer that acts through multiple pathways and mechanisms to promote nodal or distant relapses. Cancer Res; 71(8); 2926–37. ©2011 AACR.

Supplementary Table 1 from MicroRNA-301 Mediates Proliferation and Invasion in Human Breast Cancer

Supplementary Figures 1-6 from MicroRNA-301 Mediates Proliferation and Invasion in Human Breast Cancer

Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based tests could increase screening uptake. Here we introduce improvements to cancer personalized profiling by deep sequencing (CAPP-Seq)5, a method for the analysis of circulating tumour DNA (ctDNA), to better facilitate screening applications. We show that, although levels are very low in early-stage lung cancers, ctDNA is present prior to treatment in most patients and its presence is strongly prognostic. We also find that the majority of somatic mutations in the cell-free DNA (cfDNA) of patients with lung cancer and of risk-matched controls reflect clonal haematopoiesis and are non-recurrent. Compared with tumour-derived mutations, clonal haematopoiesis mutations occur on longer cfDNA fragments and lack mutational signatures that are associated with tobacco smoking. Integrating these findings with other molecular features, we develop and prospectively validate a machine-learning method termed 'lung cancer likelihood in plasma' (Lung-CLiP), which can robustly discriminate early-stage lung cancer patients from risk-matched controls. This approach achieves performance similar to that of tumour-informed ctDNA detection and enables tuning of assay specificity in order to facilitate distinct clinical applications. Our findings establish the potential of cfDNA for lung cancer screening and highlight the importance of risk-matching cases and controls in cfDNA-based screening studies.

Circulating tumor DNA (ctDNA) molecular residual disease (MRD) following curative-intent treatment strongly predicts recurrence in multiple tumor types, but whether further treatment can improve outcomes in patients with MRD remains unclear. We applied CAPP-Seq ctDNA analysis to 218 samples from 65 patients receiving chemoradiation therapy (CRT) for locally advanced NSCLC, including 28 patients receiving consolidation immune checkpoint inhibition (CICI). Patients with undetectable ctDNA after CRT had excellent outcomes whether or not they received CICI. Among such patients, one died from CICI-related pneumonitis, highlighting the potential utility of only treating patients with MRD. In contrast, patients with MRD after CRT who received CICI had significantly better outcomes than patients who did not receive CICI. Furthermore, the ctDNA response pattern early during CICI identified patients responding to consolidation therapy. Our results suggest that CICI improves outcomes for NSCLC patients with MRD and that ctDNA analysis may facilitate personalization of consolidation therapy.

8534 Background: The current standard of care for patients with inoperable stage III non-small cell lung cancer (NSCLC) includes chemoradiation (CRT) followed by up to 1 year of checkpoint inhibitor (CPI) therapy. However, many patients are not able to complete 1 year of treatment and the optimal duration of consolidation therapy remains unknown. Identifying minimal residual disease (MRD) via detection of circulating tumor DNA (ctDNA) may help inform the optimal duration of treatment. Here we report the results of a preplanned correlative study evaluating the association between detectable ctDNA and survival outcomes from the BTCRC LUN 16-081 phase 2 trial of consolidation nivolumab or nivolumab plus ipilimumab following CRT in patients with unresectable Stage III NSCLC (NCT03285321). Methods: Following CRT, patients with unresectable stage IIIA/B NSCLC were randomized 1:1 to receive nivolumab 480 mg IV Q4weeks for up to 6 cycles or nivolumab 240 mg IV Q2weeks plus ipilimumab 1 mg/kg IV Q6weeks for up to 4 cycles. Plasma samples for ctDNA analysis were collected after completion of CRT, prior to C2D1 of CPI, and at the end of treatment or withdrawal from the study. Tumor genotyping and ctDNA analysis were performed using CAPP-Seq with a panel targeting 260 genes recurrently mutated in NSCLC. Patient-specific tumor variants were identified using tumor tissue or baseline plasma and matched leukocyte DNA samples. Tumor variants were then monitored in plasma samples using a tumor mutation-informed bioinformatic strategy. Results: Thirty-nine patients received either nivolumab (n = 25; cycles: median = 6, range 1-6), or nivolumab plus ipilimumab (n = 14; cycles; median = 2, range = 1-6). Patients with detectable ctDNA MRD after completion of CRT demonstrated significantly inferior progression free survival (PFS) than patients who were MRD-negative (12-month 29% vs 76%, 24-month 29% vs 68%, P = 0.003), prior to C2D1 of CPI (12-month 0% vs 85%, 24-month 0% vs 72%, P < 0.0001) and at the end of CPI (12-month 14% vs 90%, 24-month 14% vs 79%, P < 0.0001). Patients with undetectable ctDNA MRD at the end of CPI (median cycles = 5.5; range 1-6) demonstrated 24-month overall survival of 91%. Additionally, patients with decreasing or undetectable ctDNA levels after one cycle of CPI had improved outcomes compared to patients with increasing ctDNA levels (24-month PFS 73% vs 0%, P < 0.0001). Progression of disease occurred within 10.8 months of starting CPI in all patients with increasing ctDNA levels at C2D1. Conclusions: Detectable ctDNA before, during, and after consolidation CPI is strongly associated with inferior survival outcomes. Furthermore, less than 12 months of CPI consolidation can result in MRD negativity and high rates of long term PFS. Clinical trial information: NCT03285321.

Purpose: Treatment with PD-(L)1 blockade can produce remarkably durable responses in patients with non–small cell lung cancer (NSCLC). However, a significant fraction of long-term responders ultimately progress and predictors of late progression are unknown. We hypothesized that circulating tumor DNA (ctDNA) analysis of long-term responders to PD-(L)1 blockade may differentiate those who will achieve ongoing benefit from those at risk of eventual progression. Experimental Design: In patients with advanced NSCLC achieving long-term benefit from PD-(L)1 blockade (progression-free survival ≥ 12 months), plasma was collected at a surveillance timepoint late during/after treatment to interrogate ctDNA by Cancer Personalized Profiling by Deep Sequencing. Tumor tissue was available for 24 patients and was profiled by whole-exome sequencing (n = 18) or by targeted sequencing (n = 6). Results: Thirty-one patients with NSCLC with long-term benefit to PD-(L)1 blockade were identified, and ctDNA was analyzed in surveillance blood samples collected at a median of 26.7 months after initiation of therapy. Nine patients also had baseline plasma samples available, and all had detectable ctDNA prior to therapy initiation. At the surveillance timepoint, 27 patients had undetectable ctDNA and 25 (93%) have remained progression-free; in contrast, all 4 patients with detectable ctDNA eventually progressed [Fisher P < 0.0001; positive predictive value = 1, 95% confidence interval (CI), 0.51–1; negative predictive value = 0.93 (95% CI, 0.80–0.99)]. Conclusions: ctDNA analysis can noninvasively identify minimal residual disease in patients with long-term responses to PD-(L)1 blockade and predict the risk of eventual progression. If validated, ctDNA surveillance may facilitate personalization of the duration of immune checkpoint blockade and enable early intervention in patients at high risk for progression.

Insights into mutational burden of the airway epithelium, the field of cancerization, may play important role in stratifying individuals at different levels of risk for lung cancer. We hypothesized that cytologically normal bronchial epithelium of patients with lung cancer and those at high risk for lung cancer harbor driver mutations. We performed next generation sequence-based targeted CAPP-Seq (CAncer Personalized Profiling by deep Sequencing) and whole exome sequencing (WES) of DNA from the bronchial epithelial cells from the bronchial brushings of individuals at-risk for lung cancer and patients with lung cancer as well as matched lung tumor tissues. We used the Tammemagi risk model to calculate the risk for lung cancer. Both CAPPSeq and WES data analyses showed higher mutation burden in lung tumor tissues compared to bronchial brushings. Using targeted CAPPSeq, a total of 129 nonsynonymous mutations were identified in bronchial brushings. Among individuals without lung cancer, 9 oncogenic driver mutations were identified in 5 out of 13 high risk and 2 out of 7 low risk individuals. Among individuals with cancer, 13 out of 22 brushings harbored 11 driver mutations, of which mutations in TP53 and PTEN were identified in both tumor and brushing matched samples. Mutations detected in the brushings of individuals with and without cancer were TP53, PIK3CA, NOTCH1, KRAS, MET, CUL3, and NF1. Using WES on the DNA from the same brushings (low risk, n=9; high risk, n=8 and lung cancer, n=17), we identified 19478 mutations total, and 90 of that were also identified by CAPPSeq. WES identified 80% of the mutations that were identified by CAPPSeq with >5% variant allelic frequencies (VAF). Mutations identified by CAPPSeq had VAF as low as 0.2% and vast majority of the mutations identified by WES had VAF >5%. Out of 9 mutations in TP53 identified in the brushings by CAPPSeq, 4 were identified by WES. Mutation in KMT2D, a histone methylation enzyme and believed to be a tumor suppressor, was identified by WES in the brushings and the tumor tissues of patients with lung cancer as well as in one high risk brushings. Mutational signature profiling identified tobacco mutational signature in the bronchial epithelium and tobacco, APOBEC and DNA-DSB repair signatures in the tumor tissues. Copy number variation (CNV) data analysis revealed significantly higher CNV levels in tumor samples than brushing samples. Genome-wide CNA profiling identified regions significantly influenced by CNV, such as deletions in chromosome region 19p13.3, which was previously reported to be related to lung cancer. We identified mutations in cancer driver genes in the bronchial brushings of individuals with and without lung cancer. This field of cancerization effect may provide a tool for risk assessment for lung cancer. This research was funded by U01CA196405 to PPM. Citation Format: SM Jamshedur Rahman, Shilin Zhao, Shih-Kai Chu, Yong Zou, Angela B. Hui, Thomas P. Stricker, Chen Heidi, Maximilian Diehn, Pierre P. Massion. Mutational landscape of the bronchial epithelium of individuals at high risk for lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2536.

8533 Background: Lung cancer is the leading cause of cancer death world-wide, and chemotherapy and radiation remain backbones of therapy for patients with locoregionally advanced and metastatic disease. However, the genetic mechanisms that mediate resistance to chemotherapy and radiation are largely unclear due to a lack of available tissue at the time of relapse. We hypothesized that circulating tumor DNA (ctDNA) analysis could identify emergent mutations after chemotherapy and radiation that may lead to treatment resistance. Methods: To identify emergent mutations at the time of progression following an initial response to chemotherapy and/or radiation therapy for lung cancer, we utilized CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) to analyze plasma samples and matched leukocytes collected pre-treatment and at the time of relapse. We analyzed a targeted panel enriched for lung cancer drivers and recurrently mutated genes for 27 patients treated with chemoradiation therapy for locoregionally advanced lung cancer. In addition, we performed ultra-deep whole exome sequencing ( > 2000X deduped depth) of pre-treatment and relapse cell-free DNA for 5 patients treated with combination chemotherapy for metastatic lung cancer. Functional enrichment analysis was performed on emergent mutation gene lists to identify significantly enriched pathways. Results: We identified emergent variants in 6 out of 27 patients using targeted sequencing after chemoradiation therapy. Emergent mutations after chemoradiation were enriched for plasma membrane adhesion molecules such as PCDH17, PCDH10, and FAT3 (adjusted P = 0.03). Using ultra-deep whole exome sequencing, we observed emergent mutations in 3 out of 5 patients treated with combination chemotherapy. After combination chemotherapy, there was a trend towards enrichment in mutations in ATP-binding cassette transporters, including ABCA13 and ABCB4 (adjusted P = 0.057). Notably, there were no recurrent emergent mutations within our cohort. Conclusions: Our results suggest that ultra-deep whole exome sequencing can non-invasively identify emergent mutations at the time of progression. Resistance to cytotoxic therapy is likely multi-factorial and analysis in expanded cohorts will be helpful to identify recurrently mutated pathways that may contribute to disease progression after an initial response to therapy.

Introduction: Despite evidence that a subset of patients with locoregionally advanced non-small cell lung cancer (NSCLC) can be cured with radiation doses less than 60 Gy, there are currently no validated approaches to identify patients that could benefit from radiation dose de-escalation. Normal tissue changes including inflammation and fibrosis can be difficult to distinguish from residual disease on standard imaging during and following chemoradiation therapy (CRT), making assessment of treatment response and identification of favorable responders challenging. We hypothesized that circulating tumor DNA (ctDNA) kinetics during CRT could be used as a surrogate of response to identify genomic predictors of rapid response to treatment. Methods: We applied cancer personalized profiling by deep sequencing (CAPP-Seq) ctDNA analysis to 61 patients treated with CRT for Stage II-III NSCLC. We quantified ctDNA concentrations pre-CRT and a median of 21 days into CRT (mid-CRT) to determine the log-fold change in ctDNA concentration and identify “rapid responders.” The association between ctDNA log-fold change as a continuous variable with progression-free survival (PFS) was analyzed using univariable and multivariable regression, including gender, age, and stage as co-variables. The prevalence of driver gene single nucleotide variants in rapid responders versus slow responders was compared for each gene using Fisher’s exact tests with P-values adjusted using the Benjamini-Hochberg procedure. Results: Mid-CRT ctDNA log-fold change was significantly associated with progression-free survival as a continuous variable on both univariable (P=0.02) and multivariable analysis (P=0.03). Among patients whose ctDNA log-fold change was more negative than -2.15, 10/11 (91%) did not recur within the radiation field. We defined ctDNA rapid responders as the 10 patients with the largest decrease in ctDNA concentration mid-CRT without local progression. Compared with slow responders, ctDNA rapid responders had a trend towards more TP53 mutations (P=0.12), but no driver mutations were significantly enriched in rapid responders. Notably, mutations in common driver genes KEAP1, NFE2L2, KRAS, and EGFR were observed in 36% of slow responders and 0% of rapid responders (P=0.03). Conclusions: Our results suggest that ctDNA kinetics during CRT can identify patients responding favorably to treatment. Additional molecular characterization of ctDNA rapid responders may enable identification of patients who could benefit from treatment de-escalation. Citation Format: Everett J. Moding, Yufei Liu, Angela B. Hui, Jianzhong He, Yawei Qiao, Ting Xu, Luyang Yao, Saumil Gandhi, Zhongxing Liao, Millie Das, Kavitha J. Ramchandran, Sukhmani K. Padda, Joel W. Neal, Heather A. Wakelee, Billy W. Loo, Steven H. Lin, Ash A. Alizadeh, Maximilian Diehn. Circulating tumor DNA kinetics to identify genomic predictors of rapid response to chemoradiation in non-small cell lung cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-069.

Summary Although treatment of non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICIs) can produce remarkably durable responses, most patients develop early disease progression. Furthermore, initial response assessment by conventional imaging is often unable to identify which patients will achieve durable clinical benefit (DCB). Here, we demonstrate that pre-treatment circulating tumor DNA (ctDNA) and peripheral CD8 T cell levels are independently associated with DCB. We further show that ctDNA dynamics after a single infusion can aid in identification of patients who will achieve DCB. Integrating these determinants, we developed and validated an entirely noninvasive multiparameter assay (DIREct-On, Durable Immunotherapy Response Estimation by immune profiling and ctDNA-On-treatment) that robustly predicts which patients will achieve DCB with higher accuracy than any individual feature. Taken together, these results demonstrate that integrated ctDNA and circulating immune cell profiling can provide accurate, noninvasive, and early forecasting of ultimate outcomes for NSCLC patients receiving ICIs.

Although treatment of non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICI) can produce remarkably durable responses, most patients develop early disease progression. Furthermore, initial response assessment by conventional imaging is often unable to identify which patients will achieve durable clinical benefit (DCB). Here, we analyze 211 samples from 99 patients and demonstrate that pre-treatment circulating tumor DNA (ctDNA) and circulating immune profiles are independently associated with DCB. We further show that ctDNA dynamics after a single ICI infusion can identify the majority of patients who will achieve DCB. Integrating these determinants, we describe an entirely noninvasive multi-analyte assay (DIREct-On, Durable Immunotherapy Response Estimation by immune profiling and ctDNA- On-treatment) that robustly predicted DCB, and that was validated in two independent cohorts (AUC = 0.89-0.93, PPV = 92-100%, HR = 0.04-0.11). Taken together, these results demonstrate that integrated ctDNA and circulating immune cell profiling can provide accurate, noninvasive, and early forecasting of ultimate outcomes for NSCLC patients receiving ICI. Citation Format: Barzin Y. Nabet, Mohammad S. Esfahani, Emily G. Hamilton, Jacob J. Chabon, Everett J. Moding, Hira Rizvi, Chloe B. Steen, Aadel A. Chaudhuri, Chih Long Liu, Angela B. Hui, Henning Stehr, Linda Goljenola, Michael C. Jin, Young-Jun Jeon, Diane Tseng, Taha Merghoub, Joel W. Neal, Heather A. Wakelee, Sukhmani K. Padda, Kavitha J. Ramchandran, Millie Das, Rene F. Bonilla, Christopher Yoo, Emily L. Chen, Ryan B. Ko, Aaron M. Newman, Matthew D. Hellmann, Ash A. Alizadeh, Maximilian Diehn. A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5666.

9067 Background: Small cell lung cancer (SCLC) is an aggressive disease, characterized by inevitable chemotherapy resistance and rapid progression. We hypothesized that circulating tumor DNA (ctDNA) analysis can rapidly identify sensitivity to platinum-based therapy. Methods: Patients with SCLC at Memorial Sloan Kettering Cancer Center underwent serial plasma collections, including prior to the start of treatment and prior to Cycle 2 Day 1 of therapy (C2D1). Tumor mutations were identified from pre-treatment biopsies by MSK-IMPACT and/or pre-treatment plasma by CAncer Personalized Profiling by deep Sequencing (CAPP-Seq). Median variant allele fraction (VAF) of all mutations was monitored on subsequent blood draws using CAPP-Seq. Progression free survival (PFS) was measured from the time of first pre-treatment blood draw. Results: Plasma was collected from 19 patients treated with carboplatin and etoposide, including three who received concurrent atezolizumab. Seven were female, and mean age was 64.5 years. ctDNA was detected in 17 patients (89%), including in the two patients in our series with limited stage disease. The most common mutations were in TP53 and RB1 in 14 and 6 patients, respectively. Fourteen patients had available plasma at C2D1. At baseline prior to treatment, median VAF did not differ significantly between radiologic responders and non-responders (9.4% versus 30.3%, p = 0.35). After one cycle of chemotherapy, the VAF percent decrease was significantly more in responders versus non-responders (-96.9% versus -10.3%, p < 0.001). Median VAF was therefore significantly lower by C2D1 in patients who responded compared to non-responders (0.51% versus 27.2%, p = 0.02). Those who ultimately responded to therapy all had a > 2 fold decrease in VAF by C2D1. With a median follow-up of 180 days, PFS was significantly longer in patients with > 2 fold decrease in VAF by C2D1 (6.4 versus 1.9 months, log rank p < 0.001). Conclusions: A 2-fold decrease in plasma VAF by C2D1 predicted platinum-sensitivity in SCLC and was associated with longer PFS. ctDNA may permit early assessment of benefit and expedite alternative treatment options for those without significant decrease in median VAF after one cycle of therapy.

2547 Background: Detection of molecular residual disease via circulating tumor DNA (ctDNA) analysis after chemoradiation (CRT) in localized non-small cell lung cancer (NSCLC) predicts risk of relapse. We explored the hypotheses that (1) patients with undetectable ctDNA after CRT may not require consolidation immunotherapy (CI) and (2) ctDNA analysis could monitor the effectiveness of CI in patients with residual ctDNA after CRT. Methods: We applied CAPP-Seq ctDNA analysis to 88 plasma and matched leukocyte samples collected pre-CRT, post-CRT but pre-CI, and mid-CI in 22 patients with Stage IIB-IIIB NSCLC treated with CRT followed by CI. Identification of patient-specific tumor variants was performed using tumor tissue or pretreatment plasma, and ctDNA was quantified using a tumor mutation-informed bioinformatic strategy. Freedom from progression (FFP) defined radiographically by RECIST 1.1 criteria was compared in patients with ctDNA detected or not detected at pre-CI and mid-CI landmarks. Results: Median follow up from the start of CRT was 11 months. ctDNA detection was associated with inferior rates of FFP when compared to patients with ctDNA not detected both pre-CI (12-month 33% vs. 76%, P = 0.015, HR 7.51, 95% CI 1.47-38.24) and mid-CI (12-month 0% vs. 86%, P < 0.0001, HR 123.3, 95% CI 16.21-937.8). In patients with undetectable ctDNA after CRT, FFP was similar to a historical cohort of patients with undetectable ctDNA after CRT alone (12-month 88% vs. 87%, P = 0.56, HR 0.55, 95% CI 0.07-4.18), suggesting that such patients may not benefit from CI. All patients with detectable ctDNA pre-CI in whom ctDNA increased mid-CI developed progressive disease. Finally, in 2 patients with ctDNA detected after CRT, CI led to elimination of ctDNA at the mid-CI timepoint. One of these patients developed an isolated local recurrence 22 months after CRT and the other patient is currently disease free at 11 months, suggesting clinical benefit from CI. Conclusions: Our results suggest that ctDNA analysis may allow personalization and response monitoring of CI following CRT for NSCLC. Validation in more patients followed by prospective testing in clinical trials will be required to establish clinical utility of such an approach.

Several microRNAs have been implicated in human breast cancer but none to date have been validated or utilized consistently in clinical management. MicroRNA-301 (miR-301) overexpression has been implicated as a negative prognostic indicator in lymph node negative (LNN) invasive ductal breast cancer, but its potential functional impact has not been determined. Here we report that in breast cancer cells, miR-301 attenuation decreased cell proliferation, clonogenicity, migration, invasion, tamoxifen resistance, tumor growth, and microvessel density, establishing an important oncogenic role for this gene. Algorithm-based and experimental strategies identified FOXF2, BBC3, PTEN, and COL2A1 as candidate miR-301 targets, all of which were verified as direct targets through luciferase reporter assays. We noted that miR-301 is located in an intron of the SKA2 gene which is responsible for kinetochore assembly, and both genes were found to be coexpressed in primary breast cancer samples. In summary, our findings define miR-301 as a crucial oncogene in human breast cancer that acts through multiple pathways and mechanisms to promote nodal or distant relapses. Cancer Res; 71(8); 2926–37. ©2011 AACR.

Introduction: Head and neck cancer (HNC) is a challenging disease due to its heterogeneity and complexity. Despite continued advances in therapeutic options, treatment-associated toxicities and overall clinical outcomes have remained disappointing. Even with radiation therapy (RT), which remains the primary curative modality for HNC, the most effective regimens achieve local control rates of 50-70%, with disease free survival rates of only 30-40% for patients with locally advanced HNSCC. Thus, the development of novel strategies to enhance tumor cell killing, while minimizing damage to the surrounding normal tissues, is critical for improving cure rates with RT. Methods: A siRNA-based high-throughput screen (HTS) was performed for the large-scale identification of novel genes that will selectively sensitize HNC cells to ionizing radiation (IR). The Dharmacon Protein Kinase and Druggable Genome siRNA Libraries were screened using FaDu cells (human hypopharyngeal squamous cell cancer). Radiosensitizing targets were subjected to functional validation studies and in vitro characterization of mechanisms for radiosensitization. In vivo validation studies including tumor formation assays and the treatment of established HNC xenograft models were also conducted. Results: The HTS identified 67 target sequences with potential radiosensitizing effects; the validity of the screen was corroborated by the identification of known radiosensitizing targets (e.g. ATM, ATR, AURKA). Targets reducing the surviving fraction by >50% at 2 Gy relative to their un-irradiated counterparts were selected for further evaluation. A key regulator of the heme biosynthetic pathway was thus identified as a novel tumor-selective radiosensitizing target. Down-regulation of the enzyme plus IR induced caspase-mediated apoptosis and cell cycle arrest in vitro, while delaying tumor growth in vivo. Radiosensitization appeared to be mediated via enhancement of tumor oxidative stress from perturbation of iron homeostasis and increased reactive oxygen species production. This radiosensitizing target was significantly over-expressed in HNC patient biopsies, wherein lower pre-RT mRNA levels correlated with improved survival, suggesting that this enzyme could also be a potential predictor for radiation response. Down-regulation of the enzyme also radiosensitized several different human cancer models, while sparing normal cells. Conclusion: We have successfully developed an RNAi-based radiosensitizer HTS, and uncovered a key regulator of heme biosynthesis as a potent sensitizer for RT, with potentially broad implications in the management of many human malignancies. Citation Format: Emma Ito, Shijun Yue, Eduardo H. Moriyama, Angela B. Hui, Inki Kim, Wei Shi, Nehad M. Alajez, Nirmal Bhogal, GuoHua Li, Alessandro Datti, Aaron D. Schimmer, Brian C. Wilson, Peter P. Liu, Daniel Durocher, Benjamin G. Neel, Brian O'Sullivan, Bernard Cummings, Rob Bristow, Fei-Fei Liu. An RNAi screen identifies a heme biosynthetic mediator as a novel radiosensitizing target for head and neck cancer [abstract]. In: Proceedings of the AACR 101st Annual Meeting 2010; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr SSY01-03

Background Head and neck cancer (HNC) is the 8 most common malignancy worldwide. Despite advances in therapeutic options over the last few decades, treatment toxicities and overall clinical outcomes have remained disappointing, underscoring a need to develop novel therapeutic approaches, particularly those that enhance tumor cell death, while minimizing damage to the surrounding normal tissues.

Head and neck cancer (HNC) is the eighth most common malignancy worldwide, comprising a diverse group of cancers affecting the head and neck region. Despite advances in therapeutic options over the last few decades, treatment toxicities and overall clinical outcomes have remained disappointing, thereby underscoring a need to develop novel therapeutic approaches in HNC treatment. Uroporphyrinogen decarboxylase (UROD), a key regulator of heme biosynthesis, was identified from an RNA interference-based high-throughput screen as a tumor-selective radiosensitizing target for HNC. UROD knockdown plus radiation induced caspase-mediated apoptosis and cell cycle arrest in HNC cells in vitro and suppressed the in vivo tumor-forming capacity of HNC cells, as well as delayed the growth of established tumor xenografts in mice. This radiosensitization appeared to be mediated by alterations in iron homeostasis and increased production of reactive oxygen species, resulting in enhanced tumor oxidative stress. Moreover, UROD was significantly overexpressed in HNC patient biopsies. Lower preradiation UROD mRNA expression correlated with improved disease-free survival, suggesting that UROD could potentially be used to predict radiation response. UROD down-regulation also radiosensitized several different models of human cancer, as well as sensitized tumors to chemotherapeutic agents, including 5-fluorouracil, cisplatin, and paclitaxel. Thus, our study has revealed UROD as a potent tumor-selective sensitizer for both radiation and chemotherapy, with potential relevance to many human malignancies.

Introduction: MicroRNAs (miRs) are ∼22-nucleotide, non-coding RNAs that regulate gene expression post-transcriptionally. Recent data have indicated that miRs are aberrantly expressed in almost all human malignancies, including cervical cancer. In order to better understand how miRs might mediate tumor progression in cervical cancer, dysregulated miRs were identified and functional studies performed for miR-196b. Experimental Procedures: miR expression was measured in 3 cervical cancer cell lines (SiHa, ME-180 and HT3) and 3 normal cervix tissues using a quantitative real-time PCR approach examining 365 miRs and 3 endogenous controls. SiHa cells were transfected with Pre-miR miRNA Precursor Molecules (Ambion) to determine the effects of miR-196b overexpression. Candidate miR-196b targets were elucidated using a tri-pronged approach combining in silico target prediction algorithms, clinical mRNA expression data, and in vitro mRNA expression data following transfection of cell lines. To test for direct binding of miR-196b to the HOXB7 3’ UTR, a luciferase reporter assay was performed. Reporter vectors were constructed containing either the HOXB7 3’ UTR sequence (pMIR-REPORT-HOXB7/UTR), or the HOXB7 3’ UTR sequence with a mutation in the predicted miR-196b binding site (pMIR-REPORT-HOXB7/mut). SiHa cells were serially transfected with: a) miR-196b pre-miR or negative control pre-miR, and b) pMIR-HOXB7/UTR or pMIR-HOXB7/mut, and luciferase activity was measured 24 hours later. To determine the effect of knocking down HOXB7, SiHa cells were transfected with siHOXB7 (Qiagen). Results: Twenty-seven miRs were observed to be downregulated in all three cell lines compared to normal cervix. One of the 27 downregulated miRs, miR-196b, was shown to inhibit cell growth and colony-forming ability when overexpressed in SiHa cells. HOXB7 was identified as one of the candidate targets of miR-196b using our tri-pronged approach. Knocking down HOXB7 recapitulated the inhibition in cell growth and clonogenicity that was observed following mir-196b overexpression. When the luciferase reporter assay was performed, miR-196b overexpression resulted in a significant reduction in luciferase activity in cells transfected with pMIR-HOXB7/UTR, but not in cells transfected with pMIR-HOXB7/mut, demonstrating direct and specific binding of miR-196b to the 3’ UTR of HOXB7. Conclusion: miR-196b is downregulated in cervical cancer and negatively regulates HOXB7. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2059.