Large-scale Pan-cancer Cell Line Screening Identifies Actionable and Effective Drug Combinations

Oncology drug combinations can improve therapeutic responses and increase treatment options for patients. The number of possible combinations is vast and responses can be context-specific. Systematic screens can identify clinically relevant, actionable combinations in defined patient subtypes. We present data for 109 anticancer drug combinations from AstraZeneca's oncology small molecule portfolio screened in 755 pan-cancer cell lines. Combinations were screened in a 7 × 7 concentration matrix, with more than 4 million measurements of sensitivity, producing an exceptionally data-rich resource. We implement a new approach using combination Emax (viability effect) and highest single agent (HSA) to assess combination benefit. We designed a clinical translatability workflow to identify combinations with clearly defined patient populations, rationale for tolerability based on tumor type and combination-specific "emergent" biomarkers, and exposures relevant to clinical doses. We describe three actionable combinations in defined cancer types, confirmed in vitro and in vivo, with a focus on hematologic cancers and apoptotic targets.

SIGNIFICANCE

We present the largest cancer drug combination screen published to date with 7 × 7 concentration response matrices for 109 combinations in more than 750 cell lines, complemented by multi-omics predictors of response and identification of "emergent" combination biomarkers. We prioritize hits to optimize clinical translatability, and experimentally validate novel combination hypotheses. This article is featured in Selected Articles from This Issue, p. 695.

A PKPD Case Study: Achieving Clinically Relevant Exposures of AZD5991 in Oncology Mouse Models

Capturing human equivalent drug exposures preclinically is a key challenge in the translational process. Motivated by the need to recapitulate the pharmacokinetic (PK) profile of the clinical stage Mcl-1 inhibitor AZD5991 in mice, we describe the methodology used to develop a refined mathematical model relating clinically relevant concentration profiles to efficacy. Administration routes were explored to achieve target exposures matching the clinical exposure of AZD5991. Intravenous infusion using vascular access button (VAB) technology was found to best reproduce clinical target exposures of AZD5991 in mice. Exposure-efficacy relationships were evaluated, demonstrating that dissimilar PK profiles result in differences in target engagement and efficacy outcomes. Thus, these data underscore the importance of accurately ascribing key PK metrics in the translational process to enable clinically meaningful predictions of efficacy.

Abstract 4024: Combining selumetinib with BH3 mimetics enhances activity in MAPK-activated acute myeloid leukemia

Mitogen-activated protein kinase (MAPK) pathway alterations comprise some of the most frequent mutations in newly diagnosed acute myeloid leukemia (AML). Moreover, MAPK pathway alterations are also emerging as potential mechanisms of resistance to targeted therapy in AML including FLT3 inhibitors and venetoclax. In an ex vivo pharmacologic analysis of primary AML samples, sensitivity to the MEK inhibitor selumetinib (ARRY-142886) was enriched in patient samples resistant to venetoclax. Clinical activity of MAPK pathway inhibitors such as selumetinib has been explored in AML but monotherapy responses were modest. Another MEK inhibitor, cobimetinib, is currently being tested in combination with venetoclax in AML. We sought to understand whether combining selumetinib with BH3 mimetics such as venetoclax would improve efficacy in AML models. We evaluated combination activity of selumetinib plus venetoclax or the MCL1 inhibitor AZD5991 in a panel of AML cell lines. Cells were exposed to a 6x6 matrix of both agents for 72hrs and then viability assessed using CellTiter-Glo. Combination benefit was assessed using highest single agent (HSA) analysis. Selumetinib+AZD5991 demonstrated strong combination benefit (HSA score >0.1, Emax >0.5) in 4/19 AML cell lines. Selumetinib+venetoclax showed strong combination activity in 6/19 lines. Three lines showed benefit with both combinations. Many of these cell lines harbor MAPK pathway mutations including OCI-AML5 (SOS1N233Y, NF1K1385R), ML-2 (KRASA146T), HL-60 (NRASQ61L), and Nomo-1 (KRASG13D). Selumetinib treatment also led to robust BIM induction in vitro. Nomo-1 xenografts were evaluated for in vivo sensitivity to venetoclax (100 mg/kg qd PO), 5-azacytidine (1mg/kg BID q8h 3days on/4days off IP), AZD5991 (30mpk bid q2h qw IV), selumetinib (10 mg/kg bid q8h PO), as well as combinations of venetoclax+5-aza, AZD5991+selumetinib, and venetoclax+selumetinib. Venetoclax and venetoclax+5-aza treatment were ineffective. Selumetinib monotherapy led to 63% tumor growth inhibition (TGI) but tumors eventually grew out through treatment. The combination of selumetinib+venetoclax slightly improved efficacy (81% TGI) but markedly delayed tumor outgrowth (selumetinib monotherapy arm reached mean tumor volume >1000 mm3 on day 17, selumetinib+venetoclax reached average of ~966 mm3 on day 28). Reducing venetoclax dose (30mg/kg qd) or frequency (100mg/kg 3days on/4days off) maintained most of the combination efficacy. Selumetinb+AZD5991 also strongly improved efficacy compared to either monotherapy (88% TGI, mean tumor volume did not exceed ~400mm3 by day 28). Together these data suggest potential for combining MEK inhibitors with BH3 mimetics in AML. Work is ongoing to further understand how scheduling impacts combination efficacy, evaluate the triple combination of selumetinib+BH3 mimetic+azacytidine, and assess efficacy in disseminated models.

Citation Format: Courtney L. Andersen, Azadeh Cheraghchi-Bashi, Patricia Jaaks, Elizabeth A. Coker, Kathleen Burke, Justin Cidado, Paul Smith, Corinne Reimer, Raoul Tibes, Mathew Garnett, Jerome Mettetal. Combining selumetinib with BH3 mimetics enhances activity in MAPK-activated acute myeloid leukemia [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 4024.

Targeting MCL-1 dysregulates cell metabolism and leukemia-stroma interactions and resensitizes acute myeloid leukemia to BCL-2 inhibition

MCL-1 and BCL-2 are both frequently overexpressed in acute myeloid leukemia (AML) and critical for the survival of AML cells and AML stem cells. MCL-1 is a key factor in venetoclax resistance. Using genetic and pharmacological approaches, we discovered that MCL-1 regulates leukemia cell bioenergetics and carbohydrate metabolisms, including the TCA cycle, glycolysis and pentose phosphate pathway and modulates cell adhesion proteins and leukemia-stromal interactions. Inhibition of MCL-1 sensitizes to BCL-2 inhibition in AML cells and AML stem/progenitor cells, including those with intrinsic and acquired resistance to venetoclax through cooperative release of pro-apoptotic BIM, BAX, and BAK from binding to anti-apoptotic BCL- 2 proteins and inhibition of cell metabolism and key stromal microenvironmental mechanisms. The combined inhibition of MCL-1 by MCL-1 inhibitor AZD5991 or CDK9 inhibitor AZD4573 and BCL-2 by venetoclax greatly extended survival of mice bearing patient-derived xenografts established from an AML patient who acquired resistance to venetoclax/decitabine. These results demonstrate that co-targeting MCL-1 and BCL-2 improves the efficacy of and overcomes pre-existing and acquired resistance to BCL-2 inhibition. Activation of metabolomic pathways and leukemia-stroma interactions are newly discovered functions of MCL-1 in AML, which are independent from canonical regulation of apoptosis by MCL-1. Our data provide new mechanisms of synergy and a rationale for co-targeting MCL-1 and BCL-2 clinically in patients with AML and potentially other cancers.

Discovery of AZD4573, a Potent and Selective Inhibitor of CDK9 That Enables Short Duration of Target Engagement for the Treatment of Hematological Malignancies

A CDK9 inhibitor having short target engagement would enable a reduction of Mcl-1 activity, resulting in apoptosis in cancer cells dependent on Mcl-1 for survival. We report the optimization of a series of amidopyridines (from compound 2), focusing on properties suitable for achieving short target engagement after intravenous administration. By increasing potency and human metabolic clearance, we identified compound 24, a potent and selective CDK9 inhibitor with suitable predicted human pharmacokinetic properties to deliver transient inhibition of CDK9. Furthermore, the solubility of 24 was considered adequate to allow i.v. formulation at the anticipated effective dose. Short-term treatment with compound 24 led to a rapid dose- and time-dependent decrease of pSer2-RNAP2 and Mcl-1, resulting in cell apoptosis in multiple hematological cancer cell lines. Intermittent dosing of compound 24 demonstrated efficacy in xenograft models derived from multiple hematological tumors. Compound 24 is currently in clinical trials for the treatment of hematological malignancies.

AZD4320, A Dual Inhibitor of Bcl-2 and Bcl-xL, Induces Tumor Regression in Hematologic Cancer Models without Dose-limiting Thrombocytopenia

PURPOSE

Targeting Bcl-2 family members upregulated in multiple cancers has emerged as an important area of cancer therapeutics. While venetoclax, a Bcl-2-selective inhibitor, has had success in the clinic, another family member, Bcl-x_L, has also emerged as an important target and as a mechanism of resistance. Therefore, we developed a dual Bcl-2/Bcl-x_L inhibitor that broadens the therapeutic activity while minimizing Bcl-x_L-mediated thrombocytopenia.

EXPERIMENTAL DESIGN

We used structure-based chemistry to design a small-molecule inhibitor of Bcl-2 and Bcl-x_L and assessed the activity against in vitro cell lines, patient samples, and in vivo models. We applied pharmacokinetic/pharmacodynamic (PK/PD) modeling to integrate our understanding of on-target activity of the dual inhibitor in tumors and platelets across dose levels and over time.

RESULTS

We discovered AZD4320, which has nanomolar affinity for Bcl-2 and Bcl-x_L, and mechanistically drives cell death through the mitochondrial apoptotic pathway. AZD4320 demonstrates activity in both Bcl-2- and Bcl-x_L-dependent hematologic cancer cell lines and enhanced activity in acute myeloid leukemia (AML) patient samples compared with the Bcl-2-selective agent venetoclax. A single intravenous bolus dose of AZD4320 induces tumor regression with transient thrombocytopenia, which recovers in less than a week, suggesting a clinical weekly schedule would enable targeting of Bcl-2/Bcl-x_L-dependent tumors without incurring dose-limiting thrombocytopenia. AZD4320 demonstrates monotherapy activity in patient-derived AML and venetoclax-resistant xenograft models.

CONCLUSIONS

AZD4320 is a potent molecule with manageable thrombocytopenia risk to explore the utility of a dual Bcl-2/Bcl-x_L inhibitor across a broad range of tumor types with dysregulation of Bcl-2 prosurvival proteins.

Abstract 1801: Sequential inhibition of BCL-XL and MCL1 elicits massive apoptosis in anaplastic thyroid cancer cells

Despite advancements in cancer therapy, anaplastic thyroid cancer (ATC) remains a lethal disease. In fact, the effect of both current chemoradiation regimens and of investigative targeted therapies is at best cytostatic, as shown by the systematic lack of durable responses and the rarity even of achieving stable disease. While efficient induction of apoptosis would be the ideal and definitive therapeutic approach for this aggressive tumor, ATC cells are remarkably resistant to therapy-induced apoptotic stimuli, thanks to the high rate of TP53 loss, hallmark EMT, and frequent overexpression of anti-apoptotic BCL2 family members.

BH3 mimetics are small molecules that bind to anti-apoptotic BCL2 proteins in the docking site where the BH3 domains of the death-promoting members of the family bind, thus releasing the latter from sequestration to induce apoptosis. This concept has been successfully applied to hematological malignancies, with the recent approval of venetoclax, a BCL2 inhibitor, for the treatment of chronic lymphocytic leukemia and acute myeloid leukemia.

Solid tumors have instead proven very refractory to these approaches, and the clinical activity of BH3 mimetics is extremely limited.

To determine the effect of targeting key anti-apoptotic proteins that protect ATC cells from apoptosis, we have studied the response of a large panel of ATC cell lines to novel MCL1 (AZD5991) and BCL-2/BCL-XL (AZD4320) inhibitors.

We found that every cell line tested was modestly sensitive to each inhibitor in monotherapy, and that the AZD5991 and AZD4320 showed identical or quite similar EC50s in the low micromolar range. These data strongly suggest that ATC cells are in fact co-addicted to MCL1 and BCL-XL, and that both proteins are essential to buffer the pro-apoptotic signals induced with the transformed state. This notion, however, cannot be readily translated into a therapeutic opportunity because concomitant treatment at doses that exhibit monotherapy activity results in rapid lethal toxicity.

To begin exploring how to mitigate this toxicity, we hypothesized that inhibition of one critical anti-apoptotic protein (i.e. BCL-XL), in co-addicted cells, might shift the cells' dependence on the other protein (i.e. MCL1). Thus, we have tested whether intermittent and sequential dosing in vitro could improve efficacy compared to monotherapy, providing an opportunity for a therapeutic margin.

Strikingly, pre-treatment with a dose of the BCL-2/BCL-XL inhibitor that has no effect in monotherapy resulted in an approximately 50-fold decrease in EC50 for the MCL1 inhibitor, and in massive caspase 3-mediated apoptosis occurring within 6-8 hours from MCL1 inhibition.

These results provide a compelling proof-of-principle suggesting that ATC cells can be effectively killed using a rationally designed drug administration strategy that targets critical components of the cells' antiapoptotic machinery.

Citation Format: Xhesika Shanja-Grabarz, Justin Cidado, Antonio Di Cristofano. Sequential inhibition of BCL-XL and MCL1 elicits massive apoptosis in anaplastic thyroid cancer cells [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 1801.

Abstract 56: AZD0466, a nanomedicine of a potent dual Bcl-2/Bcl-xL inhibitor, exhibits anti-tumor activity in a range of hematological and solid tumor models

The induction of apoptosis in tumor cells represents a promising approach to the treatment of cancer. In tumor cells, the B cell lymphoma 2 (Bcl-2) protein family promotes cell survival through upregulation of anti-apoptotic Bcl-2 proteins, such as Bcl-2, Bcl-xL, Mcl-1 and Bcl-w. Clinical activity of the Bcl-2 inhibitor venetoclax has validated the approach of targeting this class of molecules, but additional value remains in jointly targeting Bcl-2 with other family members. AZD0466 is a novel drug-dendrimer conjugate, where the active moiety, AZD4320, is chemically conjugated to Starpharma's DEP® dendrimer platform, a 5-generation PEGylated poly-lysine dendrimer via a hydrolytically labile linker. AZD4320 is a potent dual Bcl-2/Bcl-xL inhibitor, with nanomolar affinity for both proteins1. AZD0466 has been optimized to maintain efficacy whilst mitigating anticipated on-target toxicities of AZD4320. The active moiety, AZD4320, was profiled in an unbiased 72 h cell proliferation screen of 764 cancer cell lines. The greatest degree of sensitivity to AZD4320 (IC50 value ≤0.1 µM) was observed in hematological and small cell lung cancer (SCLC) cell lines. AZD0466 demonstrated greater monotherapy activity than platinum/etoposide chemotherapy regimen or venetoclax monotherapy in 6 out of 11 SCLC PDX models. AZD0466 was also evaluated at different doses in the RS4;11 B-ALL xenograft model. Weekly intravenous dose of AZD0466 resulted in complete tumor regression at 34 and 103 mg/kg doses. Administration of a single dose of AZD0466 produced dose dependent induction of cleaved caspase 3 in tumors as measured by MSD ELISA, which was consistent with the concentrations of released AZD4320 measured in the tumor. All treatments were well tolerated. Anti-tumor activity of AZD0466 was also evaluated in the disseminated luciferase-tagged Ri-1-DLBCL tumor model. AZD0466 dosed weekly IV at 34 mg/kg showed approximately 82% inhibition of bioluminescence compared to vehicle treated animals, whereas 103 mg/kg and 340 mg/kg showed complete inhibition of bioluminescence. In the SUDHL-4 GCB DLBCL model, 103 mg/kg AZD0466 with 10 mg/kg Rituximab resulted in complete and durable regressions in 5/6 animals. Finally, combination of 103 mg/kg AZD0466 with 12.5 mg/kg BID Acalabrutinib, a Bruton's Tyrosine kinase inhibitor, was investigated in OCI-LY10 DLBCL model. While neither agent showed any demonstrable monotherapy activity the combination resulted in complete regressions in 8/8 mice in this model. These data show that AZD0466 has monotherapy activity and a differentiated response from Venetoclax in SCLC models. AZD0466 also has therapeutic potential as monotherapy and a combinatorial agent to increase the depth and duration of response to standard of care and BTK inhibitors in hematological tumors. 1Cidado, J; et al. AACR (2018)

Citation Format: Srividya B. Balachander, Areya Tabatabai, Shenghua Wen, Francis D. Gibbons, Giulia Fabbri, Guangnong Sunny Zhang, Justin Cidado, Lorraine Graham, Marianne Ashford, Barry Davies. AZD0466, a nanomedicine of a potent dual Bcl-2/Bcl-xL inhibitor, exhibits anti-tumor activity in a range of hematological and solid tumor models [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 56.

Abstract 3075: Anti-leukemic activity of BCL-2/BCL-XL dual inhibitor - AZD0466 in T-acute lymphoblastic leukemia preclinical models

Upregulation of BCL-2 family proteins, such as BCL-2 and BCL-XL, leads to imbalanced ratio between pro-death and pro-survival proteins that favors leukemic survival, tumorigenesis, and is an important driver of chemoresistance. B- and T-ALL JAK-STAT signaling pathway is positively correlated with increased BCL-2 family function. Importantly, this pathway plays an important role in the switch between BCL-2 and BCL-XL dependencies in normal developing T-cells. However, recent studies have shown that co-expression of BCL-2 and BCL-XL is linked with higher therapeutic resistance in different types of ALL. In this study, we tested BCL-2 and BCL-XL dependencies among different subtypes of ALL and the potential to revert these using AZD0466, a novel drug-dendrimer conjugate, of a BCL-2/ BCL-XL inhibitor AZD4320 and an FDA-approved BCL-2 inhibitor, ABT-199 (Venetoclax). The analysis of protein expression patterns in ALL cell lines revealed increased levels of BCL-2 in B-ALL cell lines, and of BCL-XL in Ph-like B-ALL and T-ALL cell lines. The analysis of cell viability assay revealed most B-ALL cell lines show sensitivity to both ABT-199 and AZD4320, except NALM6 which lacks the expression of the executioner Bax protein. Ph-like B-ALL and T-ALL cell lines on the other hand are most sensitive to the BCL-2/BCL-XL dual inhibitor, AZD4320. Additionally, Ph-like B-ALL and T-ALL PDX cells responded greater to dual inhibitor. The analysis of BH3 profiling of ALL cell lines demonstrated BCL-2 and BCL-XL codependence in Ph-like B-ALL and T-ALL cell lines while major BCL-2 dependence was seen in B-ALL cell lines. Our pre-clinical studies in T-ALL PDX models showed moderate response to ABT-199 and significantly prolonged survival and decreased leukemic burden mice treated with dual BCL-2/BCL-XL inhibitor AZD0466 (30mg/kg/weekly/IV). Importantly, AZD0466 treated cohorts did not show any significant change in the body weight and platelet counts when compared to control animals. Comparison of pharmacological response to dual inhibitor AZD0466 treatments in B-ALL PDX models demonstrated lower therapeutic efficacy than observed in T-ALL PDX, while in the same T-ALL PDX ABT-199 (100mg/kg/daily/oral) showed reduced efficacy. Further studies including BH3 profiling to measure the dynamic response of mitochondria and determine prior BH3 domain dependencies are in progress and will be reported. Our findings suggest that the novel dual BCL-2/BCL-XL inhibitor AZD0466 outperforms single BCL-2 inhibition by ABT-199 in T-ALL and Ph-like B-ALL. These findings will facilitate translation of AZD0466 dual BCL-2/BCL-XL inhibitor into ALL clinical trials, alone or in combination with standard chemotherapy and monoclonal antibodies.

Citation Format: Sankaranarayanan Kannan, Sanaz Ghotbaldini, Julia E. Wells, Qi Zhang, Srividya Balachander, Justin Cidado, Marina Konopleva. Anti-leukemic activity of BCL-2/BCL-XL dual inhibitor - AZD0466 in T-acute lymphoblastic leukemia preclinical models [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 3075.

The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells

Overexpression of anti-apoptotic proteins MCL1 and Bcl-xL are frequently observed in many cancers. Inhibitors targeting MCL1 are in clinical development, however numerous cancer models are intrinsically resistant to this approach. To discover mechanisms underlying resistance to MCL1 inhibition, we performed multiple flow-cytometry based genome-wide CRISPR screens interrogating two drugs that directly (MCL1i) or indirectly (CDK9i) target MCL1. Remarkably, both screens identified three components (CUL5, RNF7 and UBE2F) of a cullin-RING ubiquitin ligase complex (CRL5) that resensitized cells to MCL1 inhibition. We find that levels of the BH3-only pro-apoptotic proteins Bim and Noxa are proteasomally regulated by the CRL5 complex. Accumulation of Noxa caused by depletion of CRL5 components was responsible for re-sensitization to CDK9 inhibitor, but not MCL1 inhibitor. Discovery of a novel role of CRL5 in apoptosis and resistance to multiple types of anticancer agents suggests the potential to improve combination treatments.

Abstract 2500: Transient CDK9 inhibition with AZD4573 modulates Bfl-1 in preclinical lymphoma models

AZD4573 is a selective cyclin-dependent kinase 9 (CDK9) inhibitor under clinical development in patients with hematological malignancies. Transient CDK9 inhibition serves as an orthogonal approach for targeting Mcl-1, a labile anti-apoptotic protein essential for the survival of cancer cells. Across-broad hematological cancer models, anti-tumor responses with AZD4573 strongly correlate with selective Mcl-1 inhibitors, such as AZD5991 (R2=0.8). Despite compelling evidence for an Mcl-1 dependent mechanism of action, we also observed a subset of lymphoma models more sensitive to CDK9 inhibition compared to Mcl-1 inhibition, suggesting acute CDK9 inhibition could be targeting other labile proteins beyond Mcl-1 to induce apoptosis. We identified Bfl-1 as one such potential target and demonstrate lymphoma models expressing Bfl-1 are highly sensitive to CDK9 inhibition.

Bfl-1 belongs to the Bcl-2 family of anti-apoptotic proteins and was detected in over 20% of lymphoma cell lines evaluated (n=33). Cycloheximide experiments indicate Bfl-1 has a short protein half-life (<1h), similar to Mcl-1. Therefore, treatment with 100nM of AZD4573 in diffuse large B-cell lymphoma cell lines OCILY10 and TMD8 caused rapid down-regulation of both Mcl-1 and Bfl-1 by 4h, resulting in caspase cleavage by 6h. Evaluation of caspase activation following 6h treatment revealed an average maximum effect of 87% for AZD4573 compared to 45% with Mcl-1 inhibition, suggesting these cell lines are not exclusively Mcl-1-dependent. The hypothesis that survival of lymphoma cells may be co-dependent on both Mcl-1 and Bfl-1 was evaluated by siRNA knockdown. Following a dose-dependent suppression of Bfl-1 protein (>80%) in OCILY10 and TMD8 cells, viability loss was minimal (<30% reduction relative to control). However, when Bfl-1 knockdown cells were treated for 6h with an Mcl-1 inhibitor, the maximum caspase activation increased to over 90% in both cell lines, phenocopying a similar magnitude achieved with AZD4573-mediated CDK9 inhibition. In these models, depletion of both Bfl-1 and Mcl-1 was necessary to induce maximum apoptosis, with studies ongoing to evaluate single-gene Bfl-1 dependency in additional lymphoma models.

Consistent with the in vitro phenotype, intermittent dosing of the ABC-DLBCL xenografts OCILY10 and TMD8 with AZD4573 caused robust tumor regressions (198 and 184% TGI, respectively). AZD4573-mediated anti-tumor activity was associated with pharmacodynamic reductions of pSer2-RNAPII, Mcl-1 and Bfl-1, followed by caspase activation. Collectively, these findings support the ability to target Bfl-1 via CDK9 inhibition. Given the current absence of clinical small molecule Bfl-1 inhibitors and expanded monotherapy activity compared to selective Mcl-1 inhibition in a subset of preclinical models, CDK9 inhibitors have tremendous therapeutic potential in the treatment of patients with Bfl-1-expressing lymphoma.

Citation Format: Scott Boiko, Theresa Proia, Maryann San Martin, Lisa Drew, Wenlin Shao, Justin Cidado. Transient CDK9 inhibition with AZD4573 modulates Bfl-1 in preclinical lymphoma models [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 2500.

Abstract 311: AZD4320 is a potent, dual Bcl-2/xLinhibitor that rapidly induces apoptosis in preclinical hematologic tumor models

Apoptosis is a normal cellular process that is regulated by the dynamic interaction of pro- and anti-apoptotic proteins of the B-cell lymphoma 2 (Bcl-2) family. Cancers, however, have evolved mechanisms to hijack this process and tip the balance in favor of anti-apoptotic proteins, conferring a survival advantage for tumor cells as well as a means of resistance to anti-cancer therapies. Indeed, the Bcl-2 family are some of the most frequently amplified genes and over-expressed proteins across various tumor types. As a result, tumor cells can become addicted to Bcl-2 family members and, hence, vulnerable to targeted BH3 mimetics. Clinical validation of this concept has been demonstrated by venetoclax with its approval for treatment of R/R CLL patients with 17p deletion. Given the great potential that directly targeting the apoptotic machinery holds in treating cancer, developing BH3 mimetics is an attractive proposition.

To that end, we have developed a potent small molecule, AZD4320,1 that has nanomolar affinity for Bcl-2 and Bcl-xL, similar to navitoclax, but has physicochemical properties suitable for IV administration. This will help mitigate toxicities observed with oral administration of navitoclax (e.g. allow recovery of platelets), thus improving therapeutic index. AZD4320 also displays the hallmarks of a bona fide BH3 mimetic, most notably the ability to disrupt the complex formation of Bcl-2 with BH3-only proteins and the necessity for intact BAK and BAX to propagate the apoptotic cascade. A kinetic study was also conducted to explore apoptosis induction in the Bcl-2-addicted B-ALL cell line, RS4;11, which revealed both a dose- and time-dependent increase in cleaved caspase-3 (CC3) and corresponding reduction in cell viability. In an expanded panel of human cancer cell lines, AZD4320 rapidly induced CC3 (6h) and loss of viability (24h) in a diverse set of hematological lines with a median EC50 of 182nM. Solid tumor cell lines, however, were much less responsive (median EC50 >30μM). A comparison to venetoclax from the same cell line panel screen revealed that many more hematological tumor cell lines were sensitive to AZD4320, highlighting the utility and promise of a dual Bcl-2/xL inhibitor. Furthermore, in a venetoclax-resistant derived ABC-DLBCL cell line, AZD4320 was equally potent when compared to the parental cell line whereas venetoclax exhibited a >20-fold reduction in activity. Lastly, for in vivo efficacy studies with RS4;11 xenograft tumors, regressions with corresponding induction of CC3 were observed following a single dose of AZD4320.

Together, these results highlight the therapeutic potential of a dual Bcl-2/xL inhibitor to be used as a foundation therapy across a broad range of hematological tumor types as well as combat resistance to other BH3 mimetics and targeted therapies.

1Hennessy, E; et al. ACS National Meeting 24 (2015).

Citation Format: Justin Cidado, J Paul Secrist, Francis D. Gibbons, Edward J. Hennessy, Stephanos Ioannidis, Edwin A. Clark. AZD4320 is a potent, dual Bcl-2/xLinhibitor that rapidly induces apoptosis in preclinical hematologic tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 311.

Abstract 297: AZD4573: Mechanistic PKPD model linking CDK9 inhibition to Mcl1 depletion and induction of apoptosis in preclinical AML model

Cyclin-dependent kinase 9 (CDK9) regulates elongation of transcription through phosphorylation of RNA polymerase II (pSer2-RNAPII), and its short-term inhibition results in the selective downregulation of genes with short-lived transcripts and labile proteins - including the anti-apoptotic protein Mcl1. AZD4573 is a selective inhibitor of CDK9 with short pharmacokinetic (PK) half-life. Intermittent dosing of AZD4573 in mouse MV411 (AML cell line) xenograft models results in progressive reduction in tumor volume with the mechanism of action believed to be via induction of apoptosis following depletion of Mcl1. The aim of this work was to derive a quantitative understanding of the relationships between extent and duration of CDK9 inhibition, depletion of Mcl1 and rate of induction of apoptosis in MV411 tumor cells.

A mechanistic model has been established that quantitatively and dynamically connects AZD4573 plasma and tumor PK to the rate and extent of modulation of pSer2-RNAPII and Mcl1 in the tumor and rate of induction of cell death (as measured by reduction in tumor volume). Tumor pSer2-RNAPII and Mcl1 pharmacodynamics were modeled using a series of linked indirect response models. Production rate of pSer2-RNAPII was modeled as being directly inhibited by AZD4573 concentration in the tumor. Production rate of Mcl1 was linked to pSer2-RNAPII via a series of transit compartments to capture the transcription/translation driven delay in onset of response. Induction of intrinsic apoptosis in the MV411 tumor cells was modelled as being inhibited by Mcl1.

Tumor pSer2-RNAPII exhibited a rapid, dose-dependent decrease following IP dosing of AZD4573 in mice. The free concentration of AZD4573 that resulted in half-maximal inhibition of pSer2-RNAPII production rate was estimated to be in the range 11-21 nM. Following a brief delay, tumor Mcl1 also exhibited a relatively rapid decrease that was proportional to the pSer2-RNAPII response. Mcl1 protein half-life was estimated to be 0.3 hr. Rate of induction of apoptosis could be decribed as a saturable first-order process (Kmax ~ 0.2 hr-1) and appeared to exhibit a steep response to the depletion of Mcl1, with reduction of Mcl1 to 25% (of the baseline value) being estimated to result in half-maximal rate of induction of apoptosis in the MV411 cells.

The described MV411 PKPD/efficacy model has been assumed to be representative of AML in human patients and was used to derive preliminary predictions of clinical efficacy at a range of possible IV dosing regimens.

Citation Format: Douglas Ferguson, Theresa Proia, Justin Cidado, Scott Boiko, Maryann San Martin, Steven Criscione, Wenlin Shao, Lisa Drew. AZD4573: Mechanistic PKPD model linking CDK9 inhibition to Mcl1 depletion and induction of apoptosis in preclinical AML model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 297.

Structure-Based Design of Selective Noncovalent CDK12 Inhibitors

Cyclin-dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA-damage-response genes and sensitizes BRCA wild-type cells to poly(ADP-ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we sought a potent, selective CDK12 inhibitor. Crystal structures and modeling informed hybridization between dinaciclib and SR-3029, resulting in lead compound 5 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-ethyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Further structure-guided optimization delivered a series of selective CDK12 inhibitors, including compound 7 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-isopropyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Profiling of this compound across CDK9, 7, 2, and 1 at high ATP concentration, single-point kinase panel screening against 352 targets at 0.1 μm, and proteomics via kinase affinity matrix technology demonstrated the selectivity. This series of compounds inhibits phosphorylation of Ser2 on the C-terminal repeat domain of RNA polymerase II, consistent with CDK12 inhibition. These selective compounds were also acutely toxic to OV90 as well as THP1 cells.

PIK3CA mutations and TP53 alterations cooperate to increase cancerous phenotypes and tumor heterogeneity

BACKGROUND/PURPOSE

The combined contributions of oncogenes and tumor suppressor genes toward carcinogenesis remain poorly understood. Elucidation of cancer gene cooperativity can provide new insights leading to more effective use of therapies.

EXPERIMENTAL DESIGN/METHODS

We used somatic cell genome editing to introduce singly and in combination PIK3CA mutations (E545K or H1047R) with TP53 alterations (R248W or knockout), to assess any enhanced cancerous phenotypes. The non-tumorigenic human breast epithelial cell line, MCF10A, was used as the parental cell line, and resultant cells were assessed via various in vitro assays, growth as xenografts, and drug sensitivity assays using targeted agents and chemotherapies.

RESULTS

Compared to single-gene-targeted cells and parental controls, cells with both a PIK3CA mutation and TP53 alteration had increased cancerous phenotypes including cell proliferation, soft agar colony formation, aberrant morphology in acinar formation assays, and genomic heterogeneity. Cells also displayed varying sensitivities to anti-neoplastic drugs, although all cells with PIK3CA mutations showed a relative increased sensitivity to paclitaxel. All cell lines remained non-tumorigenic.

CONCLUSIONS

This cell line panel provides a resource for further elucidating cooperative genetic mediators of carcinogenesis and response to therapies.

Ki-67 is required for maintenance of cancer stem cells but not cell proliferation

Ki-67 expression is correlated with cell proliferation and is a prognostic marker for various cancers; however, its function is unknown. Here we demonstrate that genetic disruption of Ki-67 in human epithelial breast and colon cancer cells depletes the cancer stem cell niche. Ki-67 null cells had a proliferative disadvantage compared to wildtype controls in colony formation assays and displayed increased sensitivity to various chemotherapies. Ki-67 null cancer cells showed decreased and delayed tumor formation in xenograft assays, which was associated with a reduction in cancer stem cell markers. Immunohistochemical analyses of human breast cancers revealed that Ki-67 expression is maintained at equivalent or greater levels in metastatic sites of disease compared to matched primary tumors, suggesting that maintenance of Ki-67 expression is associated with metastatic/clonogenic potential. These results elucidate Ki-67's role in maintaining the cancer stem cell niche, which has potential diagnostic and therapeutic implications for human malignancies.

TMSB4Y is a candidate tumor suppressor on the Y chromosome and is deleted in male breast cancer

Male breast cancer comprises less than 1% of breast cancer diagnoses. Although estrogen exposure has been causally linked to the development of female breast cancers, the etiology of male breast cancer is unclear. Here, we show via fluorescence in situ hybridization (FISH) and droplet digital PCR (ddPCR) that the Y chromosome was clonally lost at a frequency of ~16% (5/31) in two independent cohorts of male breast cancer patients. We also show somatic loss of the Y chromosome gene TMSB4Y in a male breast tumor, confirming prior reports of loss at this locus in male breast cancers. To further understand the function of TMSB4Y, we created inducible cell lines of TMSB4Y in the female human breast epithelial cell line MCF-10A. Expression of TMSB4Y resulted in aberrant cellular morphology and reduced cell proliferation, with a corresponding reduction in the fraction of metaphase cells. We further show that TMSB4Y interacts directly with β-actin, the main component of the actin cytoskeleton and a cell cycle modulator. Taken together, our results suggest that clonal loss of the Y chromosome may contribute to male breast carcinogenesis, and that the TMSB4Y gene has tumor suppressor properties.

Functional isogenic modeling of BRCA1 alleles reveals distinct carrier phenotypes

Clinical genetic testing of BRCA1 and BRCA2 is commonly performed to identify specific individuals at risk for breast and ovarian cancers who may benefit from prophylactic therapeutic interventions. Unfortunately, it is evident that deleterious BRCA1 alleles demonstrate variable penetrance and that many BRCA1 variants of unknown significance (VUS) exist. In order to further refine hereditary risks that may be associated with specific BRCA1 alleles, we performed gene targeting to establish an isogenic panel of immortalized human breast epithelial cells harboring eight clinically relevant BRCA1 alleles. Interestingly, BRCA1 mutations and VUS had distinct, quantifiable phenotypes relative to isogenic parental BRCA1 wild type cells and controls. Heterozygous cells with known deleterious BRCA1 mutations (185delAG, C61G and R71G) demonstrated consistent phenotypes in radiation sensitivity and genomic instability assays, but showed variability in other assays. Heterozygous BRCA1 VUS cells also demonstrated assay variability, with some VUS demonstrating phenotypes more consistent with deleterious alleles. Taken together, our data suggest that BRCA1 deleterious mutations and VUS can differ in their range of tested phenotypes, suggesting they might impart varying degrees of risk. These results demonstrate that functional isogenic modeling of BRCA1 alleles could aid in classifying BRCA1 mutations and VUS, and determining BRCA allele cancer risk.

Abstract 3558: Predicting response to Mcl-1 targeting agents in NSCLC and multiple myeloma

Mcl-1 is an anti-apoptotic member of the Bcl-2 family of proteins and is frequently amplified or over-expressed in both solid tumors and hematological malignancies, suggesting that its activity may be important for the survival of cancer cells. CDK9 inhibition results in the down regulation of Mcl-1 mRNA and subsequent protein levels by inhibiting transcription and represents an indirect approach to targeting Mcl-1. Mcl-1 can also be targeted directly using an inhibitor that disrupts the Mcl-1 complexes to induce apoptosis.

Using both molecular and pharmacological approaches, we sought to identify predictive biomarkers of Mcl1 dependency in sensitive NSCLC and multiple myeloma cell lines. Here we demonstrate that NSCLC cell lines lacking MCL1 gene copy number gains are not sensitive to siRNA mediated knockdown of Mcl-1 or Mcl-1 inhibition (cell line sensitivity to CDK9 or Mcl-1 inhibition is defined by potency and extent of caspase activation). However, the presence of a copy number alteration does not predict sensitivity to Mcl-1 inhibition. To better understand what the drivers of sensitivity are, we developed quantitative assays on the Peggy platform (a capillary based immunoassay platform by Protein Simple) to measure both Mcl-1 and Bcl-xL protein levels. Using these assays, we show a correlation between sensitivity to a CDK9 or Mcl1 inhibitor and Mcl-1 levels, as well as to the ratio of Mcl-1 to Bcl-xL protein in a NSCLC cell line panel.

These findings were then extended into a panel of multiple myeloma cell lines. While somewhat broad activity for CDK9 or Mcl-1 inhibition is seen across the cell lines tested, a subset of the sensitive lines have MCL1 amplification and express high levels of Mcl-1 protein. Mcl-1 levels alone, however, do not predict for sensitivity across the panel and, similar to NSCLC, the ratio of Mcl1 to Bcl-xL expression has greater positive predictive value.

These results provide the rationale for exploring Mcl-1 copy number alterations and Mcl-1 and Bcl-xL protein levels as predictive biomarkers for tumor response when treating with a CDK9 or Mcl-1 inhibitor in both NSCLC and multiple myeloma.

Citation Format: Kristen McEachern, Greg O’Connor, Justin Cidado, Matthew Belmonte, Evan Barry, Hannah Dry, Paul Secrist, Lisa Drew. Predicting response to Mcl-1 targeting agents in NSCLC and multiple myeloma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3558.

ESR1 Mutations in Circulating Plasma Tumor DNA from Metastatic Breast Cancer Patients

PURPOSE

Mutations in the estrogen receptor (ER)α gene, ESR1, have been identified in breast cancer metastases after progression on endocrine therapies. Because of limitations of metastatic biopsies, the reported frequency of ESR1 mutations may be underestimated. Here, we show a high frequency of ESR1 mutations using circulating plasma tumor DNA (ptDNA) from patients with metastatic breast cancer.

EXPERIMENTAL DESIGN

We retrospectively obtained plasma samples from eight patients with known ESR1 mutations and three patients with wild-type ESR1 identified by next-generation sequencing (NGS) of biopsied metastatic tissues. Three common ESR1 mutations were queried for using droplet digital PCR (ddPCR). In a prospective cohort, metastatic tissue and plasma were collected contemporaneously from eight ER-positive and four ER-negative patients. Tissue biopsies were sequenced by NGS, and ptDNA ESR1 mutations were analyzed by ddPCR.

RESULTS

In the retrospective cohort, all corresponding mutations were detected in ptDNA, with two patients harboring additional ESR1 mutations not present in their metastatic tissues. In the prospective cohort, three ER-positive patients did not have adequate tissue for NGS, and no ESR1 mutations were identified in tissue biopsies from the other nine patients. In contrast, ddPCR detected seven ptDNA ESR1 mutations in 6 of 12 patients (50%).

CONCLUSIONS

We show that ESR1 mutations can occur at a high frequency and suggest that blood can be used to identify additional mutations not found by sequencing of a single metastatic lesion.

A phosphoproteomic screen demonstrates differential dependence on HER3 for MAP kinase pathway activation by distinct PIK3CA mutations

The PIK3CA gene encodes for the p110 alpha isoform of PI3 kinase and is one of the most frequently mutated oncogenes in human cancers. However, the mechanisms by which PIK3CA mutations activate cell signaling are not fully understood. Here we used a phosphoproteomic approach to compare differential phosphorylation patterns between human breast epithelial cells and two isogenic somatic cell knock in derivatives, each harboring a distinct PIK3CA mutation. We demonstrated differential phosphorylation patterns between isogenic cell lines containing a PIK3CA helical domain mutation (E545K) compared to cells with a PIK3CA kinase domain mutation (H1047R). In particular, the receptor tyrosine kinase, HER3, showed increased phosphorylation at tyrosine 1328 in H1047R cells versus E545K cells. Genetic studies using shRNA demonstrated that H1047R cells have a profound decrease in growth factor independent proliferation upon HER3 knock down, but this effect was attenuated in E545K cells. In addition, HER3 knock down led to reductions in both PI3 kinase and MAP kinase pathway activation in H1047R cells, but in E545K cells only PI3 kinase pathway diminution was observed. These studies demonstrate the power of using paired isogenic cell lines for proteomic analysis to gain new insights into oncogenic signal transduction pathways.

Analysis of BRCA2 loss of heterozygosity in tumor tissue using droplet digital polymerase chain reaction

Loss-of-heterozygosity (LOH) analysis of archival tumor tissue can aid in determining the clinical significance of BRCA variants. Here we describe an approach for assessing LOH in formalin-fixed, paraffin-embedded (FFPE) tissues using variant-specific probes and droplet digital polymerase chain reaction (ddPCR). We evaluated LOH in 2 related breast cancer patients harboring a rare missense BRCA2 variant of unknown clinical significance (c.6966G>T; M2322I). Conventional PCR followed by Sanger sequencing suggested a change in allelic abundance in the FFPE specimens. However, we found no evidence of LOH as determined by the allelic ratio (wild type-variant) for BRCA2 in both patients' archival tumor specimens and adjacent normal control tissues using ddPCR. In summary, these experiments demonstrate the utility of ddPCR to quickly and accurately assess LOH in archival FFPE tumor tissue.

Detection of cancer DNA in plasma of patients with early-stage breast cancer

PURPOSE

Detecting circulating plasma tumor DNA (ptDNA) in patients with early-stage cancer has the potential to change how oncologists recommend systemic therapies for solid tumors after surgery. Droplet digital polymerase chain reaction (ddPCR) is a novel sensitive and specific platform for mutation detection.

EXPERIMENTAL DESIGN

In this prospective study, primary breast tumors and matched pre- and postsurgery blood samples were collected from patients with early-stage breast cancer (n = 29). Tumors (n = 30) were analyzed by Sanger sequencing for common PIK3CA mutations, and DNA from these tumors and matched plasma were then analyzed for PIK3CA mutations using ddPCR.

RESULTS

Sequencing of tumors identified seven PIK3CA exon 20 mutations (H1047R) and three exon 9 mutations (E545K). Analysis of tumors by ddPCR confirmed these mutations and identified five additional mutations. Presurgery plasma samples (n = 29) were then analyzed for PIK3CA mutations using ddPCR. Of the 15 PIK3CA mutations detected in tumors by ddPCR, 14 of the corresponding mutations were detected in presurgical ptDNA, whereas no mutations were found in plasma from patients with PIK3CA wild-type tumors (sensitivity 93.3%, specificity 100%). Ten patients with mutation-positive ptDNA presurgery had ddPCR analysis of postsurgery plasma, with five patients having detectable ptDNA postsurgery.

CONCLUSIONS

This prospective study demonstrates accurate mutation detection in tumor tissues using ddPCR, and that ptDNA can be detected in blood before and after surgery in patients with early-stage breast cancer. Future studies can now address whether ptDNA detected after surgery identifies patients at risk for recurrence, which could guide chemotherapy decisions for individual patients.

Single copies of mutant KRAS and mutant PIK3CA cooperate in immortalized human epithelial cells to induce tumor formation

The selective pressures leading to cancers with mutations in both KRAS and PIK3CA are unclear. Here, we show that somatic cell knockin of both KRAS G12V and oncogenic PIK3CA mutations in human breast epithelial cells results in cooperative activation of the phosphoinositide 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) pathways in vitro, and leads to tumor formation in immunocompromised mice. Xenografts from double-knockin cells retain single copies of mutant KRAS and PIK3CA, suggesting that tumor formation does not require increased copy number of either oncogene, and these results were also observed in human colorectal cancer specimens. Mechanistically, the cooperativity between mutant KRAS and PIK3CA is mediated in part by Ras/p110α binding, as inactivating point mutations within the Ras-binding domain of PIK3CA significantly abates pathway signaling. In addition, Pdk1 activation of the downstream effector p90RSK is also increased by the combined presence of mutant KRAS and PIK3CA. These results provide new insights into mutant KRAS function and its role in carcinogenesis.

Needles in a haystack: finding recurrent genomic changes in breast cancer

Significant advances over the past decade have enabled scientists to obtain increasingly detailed molecular profiles of breast cancer. The recent analysis by The Cancer Genome Atlas published in the September 2012 issue of Nature is the most comprehensive description of breast cancer 'omics' to date. This study is impressive in its scope and scale, with the findings reconfirming the heterogeneity of breast cancer and highlighting the future challenges in translating these findings for clinical benefit.

Targeting the PI3K/Akt/mTOR pathway for breast cancer therapy

Recent advances in genetics and genomics have revealed new pathways that are aberrantly activated in many breast cancers. Chief among these genetic changes are somatic mutations and/or gains and losses of key genes within the phosphoinositide 3-kinase (PI3K) pathway. Since breast cancer cell growth and progression is often dependent upon activation of the PI3K pathway, there has been intense research interest in finding therapeutic agents that can selectively inhibit one or more constituents of this signaling cascade. Here we review key molecules involved with aberrant PI3K pathway activation in breast cancers and current efforts to target these components for therapeutic gain.

PIK3CA mutations and EGFR overexpression predict for lithium sensitivity in human breast epithelial cells

A high frequency of somatic mutations has been found in breast cancers within the gene encoding the catalytic p110α subunit of PI3K, PIK3CA. Using isogenic human breast epithelial cells, we have previously demonstrated that oncogenic PIK3CA "hotspot" mutations predict for response to the toxic effects of lithium. However, other somatic genetic alterations occur within this pathway in breast cancers, and it is possible that these changes may also predict for lithium sensitivity. We overexpressed the epidermal growth factor receptor (EGFR) into the non-tumorigenic human breast epithelial cell line MCF-10A, and compared these cells to isogenic cell lines previously created via somatic cell gene targeting to model Pten loss, PIK3CA mutations, and the invariant AKT1 mutation, E17K. EGFR overexpressing clones were capable of cellular proliferation in the absence of EGF and were sensitive to lithium similar to the results previously seen with cells harboring PIK3CA mutations. In contrast, AKT1 E17K cells and PTEN -/- cells displayed resistance or partial sensitivity to lithium, respectively. Western blot analysis demonstrated that lithium sensitivity correlated with significant decreases in both PI3K and MAPK signaling that were observed only in EGFR overexpressing and mutant PIK3CA cell lines. These studies demonstrate that EGFR overexpression and PIK3CA mutations are predictors of response to lithium, whereas Pten loss and AKT1 E17K mutations do not predict for lithium sensitivity. Our findings may have important implications for the use of these genetic lesions in breast cancer patients as predictive markers of response to emerging PI3K pathway inhibitors.

Analysis of cytokine functions in graft rejection by gene expression profiles

BACKGROUND

The function of interferon (IFN)gamma in the regulation of the immune response after allogeneic transplantation is still poorly understood. Previous studies have suggested that IFNgamma can promote rejection and be important in tolerance induction.

METHODS

To analyze the various IFNgamma-dependent functions in terms of T helpers 1 and 2 responses during rejection, we investigated mice deficient in the transcription factors (signal transducer of activated T cells [STAT]4 and 6) and IFNgamma in fully major histocompatibility complex-mismatched vascularized cardiac transplants. Serum levels of the cytokines tumor necrosis factor-alpha, IFNgamma, and interleukin (IL)-1beta were evaluated by enzyme-linked immunosorbent assay, and the graft-infiltrating cells were examined by immunohistochemical staining. To analyze a large panel of immune parameters, we determined the expression of chemokines, chemokine receptors, and clusters of differentiation markers by RNAase protection assays. The data were analyzed with algorithms that generated hierarchic clustering dendrograms. Also, the expression profiles of individual genes were determined with self-organizing maps.

RESULTS

Our data show that both the STAT4- and STAT6-deficient groups have statistically prolonged graft survival (P<0.04 and P<0.01). Despite the absence of prolongation of graft survival in the IFNgamma-deficient group, our analysis of variance data show that more genes (18) were modulated in the IFNgamma-deficient group compared with the other two STAT4- and STAT6-deficient groups (five each).

CONCLUSIONS

Our results indicate that IFNgamma plays a distinct role in the modulation of gene expression that includes STAT4-independent mechanisms. Our study identifies eight genes (IL-1beta, IL-1RA, macrophage inflammatory protein-1beta, monocyte chemoattractant protein-1, CC-chemokine receptor (CCR)-1, CCR2, CCR5, and F4/80) that are highly expressed in all of our experimental groups. Thus, these genes become candidates for essential functions during rejection.