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Supplementary Figure Legends S1-S5

Purpose: Hyperactivation of AKT is common and associated with endocrine resistance in estrogen receptor–positive (ER+) breast cancer. The allosteric pan-AKT inhibitor MK-2206 induced apoptosis in PIK3CA-mutant ER+ breast cancer under estrogen-deprived condition in preclinical studies. This neoadjuvant phase II trial was therefore conducted to test the hypothesis that adding MK-2206 to anastrozole induces pathologic complete response (pCR) in PIK3CA mutant ER+ breast cancer.Experimental Design: Potential eligible patients with clinical stage II/III ER+/HER2− breast cancer were preregistered and received anastrozole (goserelin if premenopausal) for 28 days in cycle 0 pending tumor PIK3CA sequencing. Patients positive for PIK3CA mutation in the tumor were eligible to start MK-2206 (150 mg orally weekly, with prophylactic prednisone) on cycle 1 day 2 (C1D2) and to receive a maximum of four 28-day cycles of combination therapy before surgery. Serial biopsies were collected at preregistration, C1D1 and C1D17.Results: Fifty-one patients preregistered and 16 of 22 with PIK3CA-mutant tumors received study drug. Three patients went off study due to C1D17 Ki67 >10% (n = 2) and toxicity (n = 1). Thirteen patients completed neoadjuvant therapy followed by surgery. No pCRs were observed. Rash was common. MK-2206 did not further suppress cell proliferation and did not induce apoptosis on C1D17 biopsies. Although AKT phosphorylation was reduced, PRAS40 phosphorylation at C1D17 after MK-2206 persisted. One patient acquired an ESR1 mutation at surgery.Conclusions: MK-2206 is unlikely to add to the efficacy of anastrozole alone in PIK3CA-mutant ER+ breast cancer and should not be studied further in the target patient population. Clin Cancer Res; 23(22); 6823–32. ©2017 AACR.

Fig S1 Study Flowchart Fig S2 PIK3CA somatic mutation pattern Fig S3 Lack of apoptotic effect by anastrozole monotherapy (C1D1) and in combination with MK-2206 (C1D17 and surgery) Fig S4 CDH1 somatic mutation pattern Fig S5 ESR1 somatic mutation pattern

Background: Diffuse large B-cell lymphomas (DLBCL) are a heterogeneous group of aggressive B-cell non-Hodgkin lymphomas (NHL). Primary mediastinal B-cell lymphoma (PMBCL) is often grouped and managed as DLBCL, yet PMBCL is biologically and clinically different. Although about two-third of patients are cured with initial therapy, those who are refractory or progress within the first two years do poorly and will die from their disease. There is an unmet need for effective therapeutic approaches in this patient population. Evasion of the host immune responses is an important mechanism for inducing resistance to cancer therapy. Strategies to block molecular and cellular mediators of cancer induced immunosuppression such as programmed death -1 receptor (PD-1) have been explored. Targeting PD-1 immune checkpoints has the potential to play a major role in cancer therapy by reversing tumor immune escape. Trials using PD-1 blockers in advanced hematological malignancies demonstrated remarkable activity in Hodgkin lymphoma. Unfortunately, results in the DLBCL cohort with nivolumab were marginal and short lived. A phase 1b trial in heavily pre-treated relapsed/refractory (RR) PMBCL using pembrolizumab (a PD-1 blocker) showed that it was safe and active with an ORR of 41%. In recent years, several signaling pathways implicated in DLBCL pathogenesis have been targeted, including the PI3K-AKT-mTOR pathway. Copanlisib, a pan-PI3K inhibitor, with particularly potent PI3K-α/PI3K-δ inhibition, showed activity in both indolent and aggressive NHL, with a safer toxicity profile than the FDA-approved agent idelalisib. In a preclinical DLBCL mouse model, treatment with copanlisib resulted in effective down regulation of tumor‐infiltrating T-regulatory cells (Tregs). In the same model, copanlisib, when combined with a surrogate anti‐mouse PD‐1, showed in vivo responses in 75% vs 0% in the monotherapy groups. These data support the rational for the combination of copanlisib and checkpoint blockade in DLBCL. We developed a phase 2 prospective study with two RR cohorts (DLBCL and PMBCL), treated with the combination of copanlisib and nivolumab. Study Design: copanlisib hydrochloride 60 mg is given IV on days 1, 8 and 15 of cycles 1-8 and days 1 and 15 of subsequent cycles. Nivolumab 240 mg IV is given on days 1 and 15 of cycles 1-8 and 480 mg on day 1 of subsequent cycles. Cycles repeat every 28 days for up to 2 years in the absence of disease progression or unacceptable toxicity. Copanlisib dose will be determined using a safety cohort in 6 patients. The primary outcome is to assess ORR defined as complete and partial responses (CR+PR). Secondary outcomes are to evaluate safety of the combination; to assess progression free survival (PFS), duration of response (DOR), CR rate, and overall survival (OS). Exploratory objectives are to characterize the effects of the copanlisib and nivolumab combination regimen on tumor cells, tumor microenvironment and the immune response in RR DLBCL and PMBCL. We will also do Lymph3CX assay as an integrated biomarker to distinguish between DLBCL and PMBCL. Key inclusion criteria: adult patients with RR DLBCL and PMBCL who have measurable disease with at least one lesion that is >15mm in the longest diameter on cross-sectional imaging; After failure of ASCT or after failure of frontline therapy in subjects who declined or are not ASCT candidates; and have appropriate organ function. Key exclusion criteria: High grade B-cell lymphomas; Active, known or suspected autoimmune disease or patients on any prohibited therapies; History of active CNS involvement or leptomeningeal involvement This study is expected to enroll a maximum of 96 (6 safety cohort, 44 DLBCL and 46 PMBCL) evaluable patients. We anticipate accruing 10 additional patients to account for ineligibility, cancellation, or other reasons. Therefore, the study is expected to accrue a maximum of 106 patients. The largest success proportion where the proposed treatment regimen would be considered ineffective in DLBCL is 25% and 30% in PMBCL. The smallest success proportion that would warrant subsequent studies with the proposed regimen is 45% in DLBCL and 50% in PMBCL. This design has a 90% power with a 1-sided 10% level test. This study is conducted through NCI-CTEP (NCI Protocol #10193; NCT03484819) and is funded by Bayer. The study is to open in fall of 2019 at 11 ECTCN sites, and is available to interested sites to join in. Figure. Disclosures Bennani: Kite Pharma: Other: Advisory board; Seattle Genetics: Other: Advisory board; Purdue Pharma: Other: Advisory board; Seattle Genetics: Other: Advisory board; Bristol-Myers Squibb: Research Funding; Purdue Pharma: Other: Advisory board; Adicet Bio: Other: Advisory board; Adicet Bio: Other: Advisory board; Purdue Pharma: Other: Advisory board; Bristol-Myers Squibb: Research Funding; Bristol-Myers Squibb: Research Funding; Kite Pharma: Other: Advisory board; Kite Pharma: Other: Advisory board; Seattle Genetics: Other: Advisory board; Adicet Bio: Other: Advisory board. Nowakowski:Celgene: Consultancy, Research Funding; Selvita: Membership on an entity's Board of Directors or advisory committees; NanoString: Research Funding; MorphoSys: Consultancy, Research Funding; Genentech, Inc.: Research Funding; F. Hoffmann-La Roche Ltd: Research Funding; Curis: Research Funding; Bayer: Consultancy, Research Funding. Rimsza:NanoSting: Patents & Royalties: Named inventor on a patent licensed to NanoSting [Institution]. Ansell:Bristol-Myers Squibb: Research Funding; Mayo Clinic Rochester: Employment; Seattle Genetics: Research Funding; Seattle Genetics: Research Funding; Regeneron: Research Funding; Bristol-Myers Squibb: Research Funding; LAM Therapeutics: Research Funding; Regeneron: Research Funding; Regeneron: Research Funding; Mayo Clinic Rochester: Employment; Affimed: Research Funding; Bristol-Myers Squibb: Research Funding; Seattle Genetics: Research Funding; Trillium: Research Funding; Regeneron: Research Funding; Bristol-Myers Squibb: Research Funding; LAM Therapeutics: Research Funding; Regeneron: Research Funding; Bristol-Myers Squibb: Research Funding; Trillium: Research Funding; Trillium: Research Funding; Regeneron: Research Funding; Mayo Clinic Rochester: Employment; Trillium: Research Funding; LAM Therapeutics: Research Funding; Mayo Clinic Rochester: Employment; Affimed: Research Funding; LAM Therapeutics: Research Funding; Regeneron: Research Funding; LAM Therapeutics: Research Funding; Bristol-Myers Squibb: Research Funding; Trillium: Research Funding; Affimed: Research Funding; Seattle Genetics: Research Funding; LAM Therapeutics: Research Funding; Bristol-Myers Squibb: Research Funding; Trillium: Research Funding; LAM Therapeutics: Research Funding; Mayo Clinic Rochester: Employment; Seattle Genetics: Research Funding; Trillium: Research Funding; Mayo Clinic Rochester: Employment; Affimed: Research Funding; Trillium: Research Funding; Mayo Clinic Rochester: Employment; Mayo Clinic Rochester: Employment; Mayo Clinic Rochester: Employment; Seattle Genetics: Research Funding; Affimed: Research Funding; Trillium: Research Funding; Seattle Genetics: Research Funding; Affimed: Research Funding; Seattle Genetics: Research Funding; Regeneron: Research Funding; Affimed: Research Funding; LAM Therapeutics: Research Funding; Bristol-Myers Squibb: Research Funding; Affimed: Research Funding; LAM Therapeutics: Research Funding; Bristol-Myers Squibb: Research Funding; Affimed: Research Funding; Regeneron: Research Funding; Seattle Genetics: Research Funding.

Systems such as aircraft and consumer electronics have included embedded computers in their designs for several decades now. In these systems, software was usually treated as a component inside a box much the same way you would treat a circuit card assembly or a power supply. Requirements would flow down to the box specification and the box specification would then flow down to the components inside the box. But recently, several trends are changing the relationship between embedded software and the system as a whole. Many embedded computer systems now use network protocols and infrastructures similar to information systems deployed on commodity hardware. Systems with embedded computers now have expectations and requirements for extensibility similar to those of information systems where methodologies for extensibility are well established. But unlike information systems, systems with embedded software often have complex non-software elements and the software is not loosely coupled with the hardware. These systems require a synthesis of approaches.

Flavopiridol, a Cdk inhibitor, potentiates irinotecan-induced apoptosis. In a phase I trial of sequential irinotecan and flavopiridol, 2 patients with advanced hepatocellular carcinoma (HCC) had stable disease (SD) for ≥14 months. We thus studied the sequential combination of irinotecan and flavopiridol in patients with HCC.Patients with advanced HCC naïve to systemic therapy, Child-Pugh ≤B8, and Karnofsky performance score (KPS) ≥70% received 100 mg/m(2) irinotecan followed 7 hours later by flavopiridol 60 mg/m(2) weekly for 4 of 6 weeks. The primary end point was an improvement in progression-free survival at 4 months (PFS-4) from 33% to 54%, using a Simon's two-stage design. Tumors were stained for p53.Only 16 patients in the first stage were enrolled: median age, 64 years; median KPS, 80%; Child-Pugh A, 87.5%; and stage III/IV, 25%/75%. The primary end point was not met; PFS-4 was 20%, leading to early termination of the study. Ten patients were evaluable for response: 1 had SD1 year and 9 had disease progression. Grade 3 fatigue, dehydration, diarrhea, neutropenia with or without fever, lymphopenia, anemia, hyperbilirubinemia, and transaminitis occurred in ≥10% of the patients. Of the 9 patients who progressed, 5 had mutant p53 and 4 had wild-type p53. The patient with stable disease had wild-type p53.Sequential irinotecan and flavopiridol are ineffective and poorly tolerated in patients with advanced HCC. Despite our limited assessments, it is possible that the presence of wild-type p53 is necessary but not sufficient to predict response in HCC.

Abstract 3729 The serine/threonine kinase Akt plays a critical signaling role downstream of phosphatidylinositol-3-kinase (PI3K) and is important in promoting cell survival and inhibiting apoptosis. Indeed, Akt activation and overexpression is often associated with resistance to chemotherapy or radiotherapy. Previous studies demonstrated the potential therapeutic value of targeting the PI3K pathway in lymphoma, as both the selective PI3Kδ inhibitor CAL-101, and everolimus and temsirolimus, which target PI3K and mTOR, produce clinical responses in a variety of lymphomas. We evaluated the effect of the novel allosteric Akt inhibitor, MK-2206, in a panel of lymphoma cell lines and primary lymphoma cells. We found that Akt, and activated pAkt, are highly expressed in lymphoma cells. After 72 hours of incubation, the Akt inhibitor MK-2206 demonstrated antiproliferative activity in a variety of lymphoma cell lines, with an IC50 ranging between 0.1 and 5μM. There was no correlation between pre-treatment levels of pAKT, PI3K isoforms, or PTEN protein expression and sensitivity to MK-2206. Within the diffuse large B cell lymphoma cell lines, those of GCB cell of origin were more sensitive to MK-2206, compared with the ABC-derived cell lines. Resistant cell lines tended to had weak or absent expression of p-GSK3 and p-4EBPI. Mechanistically, MK-2206 treatment decreased the level of p-Akt (Ser473), and p-Akt (Thr308), irrespective of drug sensitivity. Furthermore, MK-2206 decreased the phosphorylation level of Akt downstream targets, including p-GSK3 beta and p-PRAS40, upregulated p27. and dephosphorylated p70S6K. Moreover, MK-2206 treatment decreased HIF-1 alpha and VEGF expression. Depending on the cell of origin, the antiproliferative effect resulted from cycle arrest at the G0/G1 phase, autophagy, orapoptosis. MK-2206 showed synergistic effect in combination with the HDAC inhibitor, Vorinostat. Using pathway-specific protein arrays focusing on apoptosis, kinases, and transcription factors, the combination of MK-2206 and Vorinostat effectively altered p53 and p27 levels, which were associated with increased PARP cleavage and induction of apoptosis. Our data demonstrate that AKT is a promising target for the treatment of lymphoma, and provide a rationale for an ongoing trial, evaluating MK-2206 for the treatment of patients with relapsed lymphoma. Disclosures: No relevant conflicts of interest to declare.