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Supplementary Figure 7. In vivo tolerance study

Supplementary Figure 3. H524 cytotoxicity

Most small cell lung cancer (SCLC) patients are initially responsive to cytotoxic chemotherapy, but almost all undergo fatal relapse with progressive disease, highlighting an urgent need for improved therapies and better patient outcomes in this disease. The proapoptotic BH3 mimetic ABT-737 that targets BCL-2 family proteins demonstrated good single-agent efficacy in preclinical SCLC models. However, so far clinical trials of the BH3 mimetic Navitoclax have been disappointing. We previously demonstrated that inhibition of a PI3K/BMX cell survival signaling pathway sensitized colorectal cancer cells to ABT-737. Here, we show that SCLC cell lines, which express high levels of BMX, become sensitized to ABT-737 upon inhibition of PI3K in vitro, and this is dependent on inhibition of the PI3K-BMX-AKT/mTOR signaling pathway. Consistent with these cell line data, when combined with Navitoclax, PI3K inhibition suppressed tumor growth in both an established SCLC xenograft model and in a newly established circulating tumor cell–derived explant (CDX) model generated from a blood sample obtained at presentation from a chemorefractory SCLC patient. These data show for the first time that a PI3K/BMX signaling pathway plays a role in SCLC cell survival and that a BH3 mimetic plus PI3K inhibition causes prolonged tumor regression in a chemorefractory SCLC patient–derived model in vivo. These data add to a body of evidence that this combination should move toward the clinic. Mol Cancer Ther; 15(6); 1248–60. ©2016 AACR.

Supplementary Figure 6. Statistics for knockdown experiments

Supplementary Figure 5. Bcl2 family expression

Supplementary Figure 2. Cyotoxicity assays

Supplementary Figure 1. BMX expression in SCLC

Supplementary Figure 8. PI3K signaling in CDX2

Materials and methods, Supplementary figure legends; Supplementary Table 1:BMX, MCL-1 and non-targeting siRNAs target sequence.

Supplementary Figure 4. GI50 tables

Gene list for customized mini-screen

An increasingly recognized component of resistance to tyrosine kinase inhibitors (TKI) involves persistence of a drug-tolerant subpopulation of cancer cells that survive despite effective eradication of the majority of the cell population. Multiple groups have demonstrated that these drug-tolerant persister cells undergo transcriptional adaptation via an epigenetic state change that promotes cell survival. Because this mode of TKI drug tolerance appears to involve transcriptional addiction to specific genes and pathways, we hypothesized that systematic functional screening of EGFR TKI/transcriptional inhibitor combination therapy would yield important mechanistic insights and alternative drug escape pathways. We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib + THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting. As expected, suppression of multiple genes associated with transcriptional complexes (EP300, CREBBP, and MED1) enhanced erlotinib/THZ1 synergy. Unexpectedly, we uncovered nearly every component of the recently described ufmylation pathway in the synergy suppressor group. Loss of ufmylation did not affect canonical downstream EGFR signaling. Instead, absence of this pathway triggered a protective unfolded protein response associated with STING upregulation, promoting protumorigenic inflammatory signaling but also unique dependence on Bcl-xL. These data reveal that dysregulation of ufmylation and ER stress comprise a previously unrecognized TKI drug tolerance pathway that engages survival signaling, with potentially important therapeutic implications.Significance: These findings reveal a novel function of the recently described ufmylation pathway, an ER stress survival signaling in drug-tolerant persister cells, which has important biological and therapeutic implications. Cancer Res; 78(4); 1044–57. ©2017 AACR.

Figure S1 Preparation experiments for CRIPSR screening. Figure S2 Quality control of the result of CRISPR screening. Figure S3 Validation experiments with PC9 or HCC827 cells transduced sgRNAs targeting ufmylation. Figure S4 ER stress pathway response involve in the phenotypic change of the PC9 cells in the abcense of ufmylation. Figure S5 Inflammation pathway activation affect the status of cancer cells through modifying the apoptosis pathway. Figure S6 Bcl-xL dependency in the cells with increased ER stress

Supplementary Methods for detailed screening methods and the materials used.

Conventional chemotherapy is still of great utility in oncology and rationally constructing combinations with it remains a top priority. Drug-induced mitochondrial apoptotic priming, measured by dynamic BH3 profiling (DBP), has been shown in multiple cancers to identify drugs that promote apoptosis in vivo. We therefore hypothesized that we could use DBP to identify drugs that would render cancers more sensitive to conventional chemotherapy. We found that targeted agents that increased priming of non-small cell lung cancer (NSCLC) tumor cells resulted in increased sensitivity to chemotherapy in vitro. To assess whether targeted agents that increase priming might enhance the efficacy of cytotoxic agents in vivo as well, we carried out an efficacy study in a PC9 xenograft mouse model. The BH3 mimetic navitoclax, which antagonizes BCL-xL, BCL-w, and BCL-2, consistently primed NSCLC tumors in vitro and in vivo. The BH3 mimetic venetoclax, which electively antagonizes BCL-2, did not. Combining navitoclax with etoposide significantly reduced tumor burden compared to either single agent, while adding venetoclax to etoposide had no effect on tumor burden. Next, we assessed priming of primary patient NSCLC tumor cells on drugs from a clinically relevant oncology combination screen (CROCS). Results confirmed for the first time the utility of BCL-xL inhibition by navitoclax in priming primary NSCLC tumor cells and identified combinations that primed further. This is a demonstration of the principle that DBP can be used as a functional precision medicine tool to rationally construct combination drug regimens that include BH3 mimetics in solid tumors like NSCLC.

Key Points Adding venetoclax to FluBu2 reduced-intensity conditioning transplant did not impair engraftment or induce excessive graft-versus-host disease.Monitoring measurable residual disease by ultra-sensitive duplex sequencing revealed complex clonal dynamics before and after transplant., Visual Abstract, Adding the selective BCL-2 inhibitor venetoclax to reduced-intensity conditioning chemotherapy (fludarabine and busulfan [FluBu2]) may enhance antileukemic cytotoxicity and thereby reduce the risk of posttransplant relapse. This phase 1 study investigated the recommended phase 2 dose (RP2D) of venetoclax, a BCL-2 selective inhibitor, when added to FluBu2 in adult patients with high-risk acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and MDS/myeloproliferative neoplasms (MPN) undergoing transplant. Patients received dose-escalated venetoclax (200-400 mg daily starting day −8 for 6-7 doses) in combination with fludarabine 30 mg/m2 per day for 4 doses and busulfan 0.8 mg/kg twice daily for 8 doses on day −5 to day −2 (FluBu2). Transplant related–toxicity was evaluated from the first venetoclax dose on day −8 to day 28. Twenty-two patients were treated. At study entry, 5 patients with MDS and MDS/MPN had 5% to 10% marrow blasts, and 18 (82%) of 22 had a persistent detectable mutation. Grade 3 adverse events included mucositis, diarrhea, and liver transaminitis (n = 3 each). Neutrophil/platelet recovery and acute/chronic graft-versus-host-disease rates were similar to those of standard FluBu2. No dose-limiting toxicities were observed. The RP2D of venetoclax was 400 mg daily for 7 doses. With a median follow-up of 14.7 months (range, 8.6-24.8 months), median overall survival was not reached, and progression-free survival was 12.2 months (95% confidence interval, 6.0-not estimable). In patients with high-risk AML, MDS, and MDS/MPN, adding venetoclax to FluBu2 was feasible and safe. To further address relapse risk, assessment of maintenance therapy after venetoclax plus FluBu2 transplant is ongoing. This study was registered at clinicaltrials.gov as #NCT03613532.

Currently, malignant pleural mesothelioma (MPM) is mainly treated with conventional therapies such as surgery, chemotherapy and radiation, and patients often suffer from the lack of second line therapy options. In this study, we aimed to identify efficacious drug combinations in primary MPM patient samples and novel MPM patient-derived xenograft (PDX) models to provide better therapeutic options for MPM patients. BH3 profiling is a functional assay that measures mitochondrial priming of the cell. It uses BH3 peptides derived from the BH3 domain of pro-apoptotic BH3-only Bcl-2 family members to provoke a response from viable mitochondria. When tumor cells are treated with drugs prior to BH3 profiling, early changes in their apoptosis signaling can be captured before frank apoptosis occurs. This method is termed dynamic BH3 profiling (DBP), which has been applied in multiple cancer types to identify efficacious drugs. Here, we used high throughput dynamic BH3 profiling (HTDBP) to assess hundreds of drug treatments simultaneously to identify drug combinations that increased apoptotic priming in primary MPM cells ex vivo. Next, we created novel MPM PDX models and tested these drug combinations to determine the ones that primed MPM PDX cells. The HTDBP result from MPM PDX cells recapitulated the chemical vulnerabilities of the primary MPM cells. Moreover, one of the top combination candidates that comprised of navitoclax (BCL-xL, BCL-2 and BCL-w antagonist) and AZD8055 (mTORC1/2 inhibitor) was shown to be safe and efficacious in vivo in our CPDM_011x MPM PDX model. Finally, on the molecular level, we revealed that treatment with navitoclax drove the anti-apoptotic dependence of MPM cell lines towards MCL-1, whose level was downregulated by AZD8055 treatment. In this study, we identified a novel drug combination for MPM with HTDBP that consists of navitoclax and AZD8055. In addition, our results further corroborated that DBP, as a functional assay, can be used to rationally construct novel drug combinations to improve treatment outcomes for cancer patients. Citation Format: Danielle S. Potter, Ruochen Du, Kin-Hoe Chow, Keith L. Ligon, Raphael Bueno, Anthony Letai. Dynamic BH3 profiling identifies novel combinations in malignant pleural mesothelioma with in vivo efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3691.

Cancer cells have differential metabolic dependencies compared to their non-malignant counterparts. However, few metabolism-targeting compounds have been successful in clinical trials. Here, we investigated the metabolic vulnerabilities of triple-negative breast cancer (TNBC), in particular those metabolic perturbations that increased mitochondrial apoptotic priming and sensitivity to BH3 mimetics (drugs that antagonize anti-apoptotic proteins). We used high throughput-dynamic BH3 profiling (HT-DBP) to screen a library of metabolism-perturbing small molecules, which revealed inhibitors of the enzyme nicotinamide phosphoribosyltransferase (NAMPT) as top candidates. In some TNBC cells but not in non-malignant cells, NAMPT inhibitors increased overall apoptotic priming and induced dependencies on specific anti-apoptotic BCL-2 family members. Treatment of TNBC cells with NAMPT inhibitors sensitized them to subsequent treatment with BH3 mimetics. The combination of a NAMPT inhibitor (FK866) and an MCL-1 antagonist (S63845) reduced tumor growth in a TNBC patient-derived xenograft model in vivo. We found that NAMPT inhibition reduced NAD(+) concentrations below a critical threshold that resulted in depletion of adenine, which was the metabolic trigger that primed TNBC cells for apoptosis. These findings demonstrate a close interaction between metabolic and mitochondrial apoptotic signaling pathways and reveal that exploitation of a tumor-specific metabolic vulnerability can sensitize some TNBC to BH3 mimetics.

An increasingly recognized component of resistance to tyrosine kinase inhibitors (TKI) involves persistence of a drug-tolerant subpopulation of cancer cells that survive despite effective eradication of the majority of the cell population. Multiple groups have demonstrated that these drug-tolerant persister cells undergo transcriptional adaptation via an epigenetic state change that promotes cell survival. Because this mode of TKI drug tolerance appears to involve transcriptional addiction to specific genes and pathways, we hypothesized that systematic functional screening of EGFR TKI/transcriptional inhibitor combination therapy would yield important mechanistic insights and alternative drug escape pathways. We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib + THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting. As expected, suppression of multiple genes associated with transcriptional complexes (EP300, CREBBP, and MED1) enhanced erlotinib/THZ1 synergy. Unexpectedly, we uncovered nearly every component of the recently described ufmylation pathway in the synergy suppressor group. Loss of ufmylation did not affect canonical downstream EGFR signaling. Instead, absence of this pathway triggered a protective unfolded protein response associated with STING upregulation, promoting protumorigenic inflammatory signaling but also unique dependence on Bcl-xL. These data reveal that dysregulation of ufmylation and ER stress comprise a previously unrecognized TKI drug tolerance pathway that engages survival signaling, with potentially important therapeutic implications. Significance: These findings reveal a novel function of the recently described ufmylation pathway, an ER stress survival signaling in drug-tolerant persister cells, which has important biological and therapeutic implications. Cancer Res; 78(4); 1044–57. ©2017 AACR.

Mitochondrial priming is regulated by the B-cell lymphoma 2 (BCL-2) family of proteins and determines a cell's "readiness" for apoptosis. A highly primed cell will undergo apoptosis more easily than an unprimed cell in response to apoptotic stimuli via the intrinsic apoptotic pathway. Priming can be measured via BH3 profiling, which uses BH3 peptides derived from the BH3 domain of pro-apoptotic BH3-only BCL-2 family members to provoke a response from viable mitochondria. BH3 profiling can be performed on tumor cells and can identify mechanisms a cell uses to evade apoptosis and anti-apoptotic dependency to the anti-apoptotic BCL-2 family members. Priming correlates with chemosensitivity of patients in multiple cancers. Therapeutics that enhances priming of patient tumor cells ex vivo could be used to aid therapeutic decisions for patients in the future.

Mitochondrial apoptotic priming (referred to as priming) determines a cell’s ‘readiness’ for cell death and is regulated by the B-cell lymphoma 2 (BCL-2) family of proteins. It has been shown in multiple disease settings such as acute lymphoblastic leukemia, acute myeloid leukemia, multiple myeloma and ovarian cancer, that chemosensitivity correlates with priming. Patients with highly primed tumors exhibited superior clinical response to chemotherapy. In contrast, chemoresistant cancers and normal tissues were poorly primed. Priming is relative and can be measured using BH3 profiling. BH3 profiling is a functional assay which uses BH3 peptides derived from the BH3 domain of pro-apoptotic BH3-only BCL-2 family members to provoke a response from viable mitochondria. To identify drugs that enhance priming, tumor cells can be incubated with drugs prior to BH3 profiling, a method called dynamic BH3 profiling (DBP). DBP is a functional approach to precision medicine and measures early changes in death signaling after drug perturbation. An increase in priming after short term drug treatment (8-24 hours) has been shown to result in cell death days later. Moreover, it has been shown to predict in vivo response to therapy. Therefore, DBP can predict efficacious therapies within 24 hours.We hypothesized that drugs that enhance priming would render cancers more sensitive to conventional chemotherapy. To determine whether drugs that increase priming enhanced sensitivity to docetaxel and etoposide in non-small cell lung cancer (NSCLC), we first identified agents that enhanced priming via DBP. We found that targeted agents that increased priming of NSCLC tumor cells resulted in increased chemosensitivity in vitro. To assess whether targeted agents that increase priming might enhance the efficacy of cytotoxic agents in vivo, we carried out an efficacy study in PC9 xenograft mouse model. The BH3 mimetic navitoclax, which inhibits BCL-xL, BCL-w and BCL-2, consistently primed NSCLC tumors in vitro and in vivo. The BH3 mimetic venetoclax, which inhibits BCL-2, did not. In vivo navitoclax reduced tumor burden whilst mice were treated but as soon as therapy was stopped tumors recovered comparable to vehicle treated mice. Etoposide as a single agent had no effect on tumors. However, combining navitoclax with etoposide significantly reduced tumor burden after treatment was stopped, increasing mouse survival. Adding venetoclax to etoposide had no effect on tumor burden. These data suggest that targeted agents that increase priming, increased chemosensitivity resulting in reduction of tumor burden in vivo. Citation Format: Danielle S. Potter, Anthony G. Letai. Dynamic BH3 profiling identifies active combinations with conventional chemotherapy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2496.

Most small cell lung cancer (SCLC) patients are initially responsive to cytotoxic chemotherapy, but almost all undergo fatal relapse with progressive disease, highlighting an urgent need for improved therapies and better patient outcomes in this disease. The proapoptotic BH3 mimetic ABT-737 that targets BCL-2 family proteins demonstrated good single-agent efficacy in preclinical SCLC models. However, so far clinical trials of the BH3 mimetic Navitoclax have been disappointing. We previously demonstrated that inhibition of a PI3K/BMX cell survival signaling pathway sensitized colorectal cancer cells to ABT-737. Here, we show that SCLC cell lines, which express high levels of BMX, become sensitized to ABT-737 upon inhibition of PI3K in vitro, and this is dependent on inhibition of the PI3K-BMX-AKT/mTOR signaling pathway. Consistent with these cell line data, when combined with Navitoclax, PI3K inhibition suppressed tumor growth in both an established SCLC xenograft model and in a newly established circulating tumor cell–derived explant (CDX) model generated from a blood sample obtained at presentation from a chemorefractory SCLC patient. These data show for the first time that a PI3K/BMX signaling pathway plays a role in SCLC cell survival and that a BH3 mimetic plus PI3K inhibition causes prolonged tumor regression in a chemorefractory SCLC patient–derived model in vivo. These data add to a body of evidence that this combination should move toward the clinic. Mol Cancer Ther; 15(6); 1248–60. ©2016 AACR.

Evasion of apoptosis is a hallmark of cancer, and reversing this process by inhibition of survival signaling pathways is a potential therapeutic strategy. Phosphoinositide 3-kinase (PI3K) signaling can promote cell survival and is upregulated in solid tumor types, including colorectal cancer (CRC), although these effects are context dependent. The role of PI3K in tumorigenesis combined with their amenability to specific inhibition makes them attractive drug targets. However, we observed that inhibition of PI3K in HCT116, DLD-1, and SW620 CRC cells did not induce apoptotic cell death. Moreover, these cells were relatively resistant to the Bcl-2 homology domain 3 (BH3) mimetic ABT-737, which directly targets the Bcl-2 family of apoptosis regulators. To test the hypothesis that PI3K inhibition lowers the apoptotic threshold without causing apoptosis per se, PI3K inhibitors were combined with ABT-737. PI3K inhibition enhanced ABT-737-induced apoptosis by 2.3- to 4.5-fold and reduced expression levels of MCL-1, the resistance biomarker for ABT-737. PI3K inhibition enhanced ABT-737-induced apoptosis a further 1.4- to 2.4-fold in CRC cells with small interfering RNA-depleted MCL-1, indicative of additional sensitizing mechanisms. The observation that ABT-737-induced apoptosis was unaffected by inhibition of PI3K downstream effectors AKT and mTOR, implicated a novel PI3K-dependant pathway. To elucidate this, an RNA interference (RNAi) screen of potential downstream effectors of PI3K signaling was conducted, which demonstrated that knockdown of the TEC kinase BMX sensitized to ABT-737. This suggests that BMX is an antiapoptotic downstream effector of PI3K, independent of AKT.