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Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up To Cancer-Mark Foundation cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including (1) favorable (for example, ATM altered) and unfavorable (for example, TERT amplified) genomic subgroups, (2) a prominent association between expression of inducible components of the immunoproteasome and response and (3) a dedifferentiated tumor-intrinsic subtype with enhanced response to checkpoint blockade. Taken together, results from this cohort demonstrate the complexity of biological determinants underlying immunotherapy outcomes and reinforce the discovery potential of integrative analysis within large, well-curated, cancer-specific cohorts.

Purpose: This first-in-human study aimed to determine the MTD and safety of MEDI3617, a selective anti–angiopoietin-2 (Ang2) mAb, alone and combined with bevacizumab or cytotoxic chemotherapy.Patients and Methods: This phase I/Ib, multicenter, open-label, dose-escalation and dose-expansion study evaluated patients with advanced solid tumors. Patients received intravenous MEDI3617 as monotherapy [5–1,500 mg every 3 weeks (Q3W)] or with bevacizumab every 2 weeks (Q2W) or Q3W, weekly paclitaxel, or carboplatin plus paclitaxel Q3W. Dose expansions included a monotherapy cohort in platinum-resistant ovarian cancer and a bevacizumab combination cohort in bevacizumab-refractory malignant glioma. Safety/tolerability, pharmacokinetics, pharmacodynamics, and clinical activity were assessed.Results: We enrolled 116 patients. No formal MTD was identified (monotherapy or combination therapy). MEDI3617 demonstrated linear pharmacokinetics and maximal accumulation of peripheral Ang2 binding at doses above 300 mg Q3W. MEDI3617 monotherapy safety profile was acceptable, except in advanced ovarian cancer [prolonged grade 3 edema-associated adverse events (AE) occurred]. Otherwise, MEDI3617 combined with chemotherapy or bevacizumab was well tolerated. The AE profiles of MEDI3617 and bevacizumab were largely non-overlapping. Overall response rates in ovarian cancer and glioma monotherapy dose-expansion arms were 6% and 0%, respectively.Conclusions: Recommended MEDI3617 monotherapy dosage is 1,500 mg Q3W or 1,000 mg Q2W, except in ovarian cancer. Although peripheral edema has occurred with other Ang2 inhibitors, the severity and duration seen here in ovarian cancer potentially identifies a new, clinically significant safety signal for this class of agents. On the basis of limited clinical activity, MEDI3617 development was discontinued. Clin Cancer Res; 24(12); 2749–57. ©2018 AACR.

PDF file - 76K, Examples of negative results with the NanoString assay for kinase fusions.

SUPPLEMENTARY TABLES Supplementary Table 1. Treatment-emergent grade 3/4 adverse events in the safety population (n=116) Supplementary Table 2. MEDI3617 pharmacokinetic parameters Supplementary Table 3. Treatment outcome: objective response and progression-free survival, by cohort

PDF - 278K, Supplementary Methods and Materials, QTc prolongation results. Supplementary Figure 1 - QTc prolongation compared with serum U3-1287 concentration. Supplementary Figure 2 - U3-1287-mediated pancreatic xenograft growth inhibition)

PDF file - 308K, Complete list of target sequences for NanoString probes

Background: The mutually exclusive pattern of the major driver oncogenes in lung cancer suggests that other mutually exclusive oncogenes exist. We conducted a systematic search for tyrosine kinase fusions by screening all tyrosine kinases for aberrantly high RNA expression levels of the 3′ kinase domain (KD) exons relative to more 5′ exons.Methods: We studied 69 patients (including five never smokers and 64 current or former smokers) with lung adenocarcinoma negative for all major mutations in KRAS, EGFR, BRAF, MEK1, HER2, and for ALK fusions (termed “pan-negative”). A NanoString-based assay was designed to query the transcripts of 90 tyrosine kinases at two points: 5′ to the KD and within the KD or 3′ to it. Tumor RNAs were hybridized to the NanoString probes and analyzed for outlier 3′ to 5′ expression ratios. Presumed novel fusion events were studied by rapid amplification of cDNA ends (RACE) and confirmatory reverse transcriptase PCR (RT-PCR) and FISH.Results: We identified one case each of aberrant 3′ to 5′ ratios in ROS1 and RET. RACE isolated a GOPC-ROS1 (FIG-ROS1) fusion in the former and a KIF5B-RET fusion in the latter, both confirmed by RT-PCR. The RET rearrangement was also confirmed by FISH. The KIF5B-RET patient was one of only five never smokers in this cohort.Conclusion: The KIF5B-RET fusion defines an additional subset of lung cancer with a potentially targetable driver oncogene enriched in never smokers with “pan-negative” lung adenocarcinomas. We also report in lung cancer the GOPC-ROS1 fusion originally discovered and characterized in a glioma cell line. Clin Cancer Res; 18(24); 6599–608. ©2012 AACR.

PDF file - 32K, Clinicopathological characteristics of study cohort

Purpose: HER3 is a key dimerization partner for other HER family members, and its expression is associated with poor prognosis. This first-in-human study of U3-1287 (NCT00730470), a fully human anti-HER3 monoclonal antibody, evaluated its safety, tolerability, and pharmacokinetics in patients with advanced solid tumor.Experimental Design: The study was conducted in 2 parts: part 1—sequential cohorts received escalating doses (0.3–20 mg/kg) of U3-1287 every 2 weeks, starting 3 weeks after the first dose; part 2—additional patients received 9, 14, or 20 mg/kg U3-1287 every 2 weeks, based on observed tolerability and pharmacokinetics from part 1. Recommended phase II dose, adverse event rates, pharmacokinetics, and tumor response were determined.Results: Fifty-seven patients (part 1: 26; part 2: 31) received U3-1287. As no dose-limiting toxicities were reported, the maximum-tolerated dose was not reached. The maximum-administered dose was 20 mg/kg every 2 weeks. The most frequent adverse events related to U3-1287 were fatigue (21.1%), diarrhea (12.3%), nausea (10.5%), decreased appetite (7.0%), and dysgeusia (5.3%). No patient developed anti-U3-1287 antibodies. In these heavily pretreated patients, stable disease was maintained 9 weeks or more in 19.2% in part 1 and 10 weeks or more in 25.8% in part 2.Conclusion: U3-1287 treatment was well tolerated, and some evidence of disease stabilization was observed. Pharmacokinetic data support U3-1287 dosing of 9 to 20 mg/kg every 2 to 3 weeks. Combination studies of U3-1287 are ongoing. Clin Cancer Res; 19(11); 3078–87. ©2013 AACR.

Background: Chimeric antigen receptor T cell therapy (CAR T) has demonstrated remarkable clinical efficacy in hematological malignancies. However, compromised T cell effector function, proliferation, and persistence can limit CAR T from reaching their full curative potential. Interleukin-2 (IL-2) is a potent stimulator of T cells, however therapeutic use of IL-2 is limited by systemic toxicity due its pleiotropy. Therefore, to provide a selective IL-2 signal to engineered T cells, we have developed a human orthogonal ligand/receptor system consisting of a half-life extended pegylated IL-2 mutein (STK-009) and a mutated IL-2 Receptor Beta (hoRb) that responds to STK-009 but not wild type IL-2. SYNCAR-001 is an autologous CAR T co-expressing a CD19 CAR and hoRb on the T cell surface. In mouse models of refractory lymphoma, STK-009 treatment led to expansion and activation of SYNCAR-001 cells with a maintenance of stem cell memory and effector T cell phenotypes. When added to SYNCAR-001, STK-009 increased complete response rate and durable responses in a dose dependent manner. In non-human primate studies, STK-009 alone demonstrated no significant biological activity in IL-2 sensitive populations (T cells or NK cells) and was tolerable without toxicity. Methods: This is a first-in-human, open-label, dose escalation study of combination SYNCAR-001 + STK-009 in adults with relapsed or refractory (r/r) CD19+ hematologic malignancies. The objectives of this study are to evaluate the safety, preliminary efficacy, pharmacokinetics, immunogenicity, and pharmacodynamics of SYNCAR-001 + STK-009. Dose escalation follows a standard 3+3 design with STK-009 being escalated while SYNCAR-001 is held at a single fixed dose. A dose extension will enroll a cohort of patients treated at a selected dose level and indication based on dose escalation findings. SYNCAR-001 is dosed intravenously (IV) once at Day 0 and STK-009 is dosed subcutaneously (SC) over the course of the study. Participants receive a single safety lead-in dose of STK-009 prior to lymphodepletion and subsequent SYNCAR-001 infusion. After SYNCAR-001 initiation, STK-009 is dosed SC weekly for 12 weeks and then monthly for 3 months. Eligible participants include individuals with r/r chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) and selected r/r B-cell non-Hodgkin lymphoma (NHL subtypes of large B cell, mantle cell, and indolent lymphoma). Prior CD19 CAR use is excluded. The primary endpoint of safety includes outcomes such as adverse events and dose-limiting toxicities. Secondary endpoints include assessments of response, pharmacokinetics, and immunogenicity. Exploratory endpoints include assessment of immune cell populations, and relevant gene/protein expression, as well as persistence, phenotype, and functionality of SYNCAR-001 in the peripheral blood and/or bone marrow in response to STK-009. Citation Format: Maria Lia Palomba, Matthew G. Mei, Paolo F. Caimi, Matthew Cortese, Marco Davila, Greg Yadnik, Nestor Huang, David Mou, Martin Oft, Paul-Joseph Aspuria, Anita Mehta-Damani, Navneet Ratti, Naiyer Rizvi, Alex Azrilevich, Ran Reshef. A Phase 1 study to evaluate the safety and tolerability of a combination autologous CD19 CAR T cell therapy (SYNCAR-001) and orthogonal IL-2 (STK-009) in subjects with relapsed or refractory CD19 expressing hematologic malignancies (NCT05665062) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT125.

Responders to checkpoint blockade in Non Small Cell Lung Cancer (NSCLC) often feature an inflamed microenvironment prior to therapy. However, the complete set of molecular drivers connecting this histologic observation to enhanced tumor clearance remain enigmatic. In updated analysis of the Stand Up 2 Cancer-Mark Foundation (SU2C-MARK) Cohort - a collection of 393 patients with whole exome and/or RNA sequencing along with matched checkpoint blockade response annotation - we identify a prominent predictive role for inducible components of the immunoproteasome, a non-canonical peptide processing complex upstream of antigen presentation. Notably, these subunits are enriched as predictors relative to interferon-inducible genes as well as proteasome components in general, and are consistently associated with objective response, progression-free survival and overall survival. Expression of Immunoproteasome subunits associates positively with TCR (but not BCR) burden, supporting a mechanistic model in which enhanced immunoproteasome processivity leads to superior T-cell recognition. Furthermore, although they are known to be targets of interferon gamma (IFNɣ), we demonstrate that their expression is better modeled via a combination of IFNɣ and tumor necrosis factor-α (TNFα) levels, suggesting they may act as integrators of multiple cytokine cascades. Given the fact that the immunoproteasome can alter both antigen quantity as well as quality (including peptide cleavage site preference), the enhanced expression of this complex in the setting of checkpoint blockade response may have important implications for modeling of antigen presentation. These data also suggest novel strategies to enhance immune checkpoint blockade. Citation Format: Vivek Naranbhai, Arvind Ravi, Matthew Hellmann, Monica Arniella, Mark Holton, Samuel Freeman, Chip Stewart, Ignaty Leshchiner, Jaegil Kim, Yo Akiyama, Aaron Griffin, Natalie Vokes, Mustafa Sakhi, Vashine Kamesan, Hira Rizvi, Biagio Ricciuti, Patrick Forde, Valsamo Anagnostou, Jonathan Riess, Don Gibbons, Nathan Pennell, Vamsidhar Velcheti, Subba Digumarthy, Mari Mino-Kenudson, Andrea Califano, John Heymach, Roy Herbst, Julie Brahmer, Kurt Schalper, Victor Velculescu, Brian Henick, Naiyer Rizvi, Pasi Janne, Mark Awad, Andrew Chow, Benjamin Greenbaum, Marta Luksza, Alice Shaw, Jedd Wolchok, Nir Hacohen, Gad Getz, Justin Gainor. Immunoproteasome expression and checkpoint blockade response in advanced non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3468.

SUMMARYAnti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). While our understanding of the biology underlying immune checkpoint blockade in NSCLC is still incomplete, studies to date have established predictive roles for PD-L1 tumor expression and tumor mutational burden (TMB). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up 2 Cancer - Mark Foundation (SU2C-MARK) Cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including: 1) favorable (e.g., ATM altered), and unfavorable (e.g., TERT amplified) genomic subgroups, 2) distinct immune infiltration signatures associated with wound healing (unfavorable) and immune activation (favorable), and 3) a novel de-differentiated tumor-intrinsic subtype characterized by expression of endodermal lineage genes, immune activation, and enhanced response rate. Taken together, results from this cohort extend our understanding of NSCLC-specific predictors, providing a rich set of molecular and immunologic hypotheses with which to further our understanding of the biology of checkpoint blockade in NSCLC.

Although immunotherapy can offer profound clinical benefit for patients with a variety of difficult-to-treat cancers, many tumors either do not respond to upfront treatment with immune checkpoint inhibitors (ICIs) or progressive/recurrent disease occurs after an interval of initial control. Improved response rates have been demonstrated with the addition of ICIs to cytotoxic therapies, leading to approvals from the US Food and Drug Administration and regulatory agencies in other countries for ICI−chemotherapy combinations in a number of solid tumor indications, including breast, head and neck, gastric, and lung cancer. Designing trials for patients with tumors that do not respond or stop responding to treatment with immunotherapy combinations, however, is challenging without uniform definitions of resistance. Previously, the Society for Immunotherapy of Cancer (SITC) published consensus definitions for resistance to single-agent anti-programmed cell death protein 1 (PD-1). To provide guidance for clinical trial design and to support analyses of emerging molecular and cellular data surrounding mechanisms of resistance to ICI-based combinations, SITC convened a follow-up workshop in 2021 to develop consensus definitions for resistance to multiagent ICI combinations. This manuscript reports the consensus clinical definitions for combinations of ICIs and chemotherapies. Definitions for resistance to ICIs in combination with targeted therapies and with other ICIs will be published in companion volumes to this paper.

The introduction of checkpoint blockade therapy, specifically anti-PD-1/PD-L1 agents, has transformed the treatment landscape of advanced Non-Small Cell Lung Cancer (NSCLC). While our understanding of the biology underlying immunotherapy in NSCLC is still incomplete, studies to date have established central roles for Tumor Mutation Burden (TMB) and PD-L1 Tumor Proportion Score (PDL1-TPS). In order to expand our understanding of the molecular features underlying response in NSCLC, we describe here the first joint analysis of the Stand Up 2 Cancer-Mark Foundation (SU2C-MARK) Cohort, a collection of 393 patients with whole exome and/or RNA sequencing along with matched checkpoint blockade response annotation. We identify a number of significant associations between molecular features and response, including: 1) favorable and unfavorable genomic subgroups; 2) distinct immune infiltration signatures associated with wound healing (unfavorable) and immune activated (favorable) microenvironments; and 3) a novel de-differentiated tumor-intrinsic subtype characterized by high TMB, immune activation, and enhanced response rate. Taken together, results from this cohort extend our understanding of NSCLC-specific predictors, providing a rich set of molecular and immunologic hypotheses with which to further our understanding of the biology of checkpoint blockade in NSCLC. Citation Format: Arvind Ravi, Justin Gainor, Monica Arniella, Chip Stewart, Sam Freeman, Mark M. Awad, Patrick Forde, Valsamo Anagnostou, Brian Henick, Jonathan W. Riess, Don Gibbons, Nathan Pennell, Vamisdhar Velcheti, Ignaty Leshchiner, Jaegil Kim, Subba Digumarthy, Mari Mino-Kenudson, John Heymach, Natalie Vokes, Andrew Griffin, Biagio Ricciuti, Naiyer Rizvi, Roy Herbst, Victor Velculescu, Julie Brahmer, Kurt Schalper, Pasi Janne, Jedd Wolchok, Alice Shaw, Nir Hacohen, Gad Getz, Matthew D. Hellmann. Integrative genomics of checkpoint blockade response in advanced non-small cell lung cancer [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 3580.

Background: High dose intravenous (IV) interleukin-2 (IL-2) induces complete responses in certain cancers, but its use is limited due to toxicities including severe hypotension and capillary leak syndrome (CLS), and the requirement for inpatient administration. Recent approaches to develop IL-2 therapies with an expanded therapeutic index have targeted the dimeric form (β/γ) of the IL-2 receptor, which is predominantly expressed on naïve T cells and NK cells, rather than the high affinity trimeric form (α/β/γ), predominantly expressed on antigen activated T cells and Tregs. Preclinical data support the hypothesis that this “non-α” approach favors activating cells that serve as principal mediators of toxicity (NK cells) over antitumor activity (antigen activated T cells). STK-012 is a pegylated, α/β-IL-2R selective partial agonist engineered to preferentially stimulate antigen-activated CD25+ T cells and avoid systemic NK and naïve T cell activation. In syngeneic tumor models, subcutaneously (SQ) injected STK-012 mouse surrogate demonstrated reduced toxicities and improved efficacy relative to mouse wild-type IL-2 or a non-α IL-2. In cynomolgus monkeys, acute lung inflammation was induced by aldesleukin and non-α-IL-2, but not by STK-012. STK-012 is in development as monotherapy and in combination with pembrolizumab for the treatment of advanced solid tumors. Methods: This is a first-in-human, open-label, dose escalation and expansion study in adults with advanced solid tumors (NCT05098132). The objectives of this study are to evaluate the safety, pharmacokinetics, immunogenicity, preliminary efficacy, and pharmacodynamics of STK-012 as monotherapy and in combination with pembrolizumab. Dose escalation will follow a standard 3+3 design for STK-012 monotherapy and in combination with pembrolizumab. STK-012 will be dosed SQ weekly, and pembrolizumab will be dosed IV every 3 weeks. Eligible participants for dose escalation include individuals with non-small cell lung cancer, head and neck squamous cell cancer, malignant melanoma, renal cell carcinoma, ovarian cancer, cervical cancer and microsatellite instability-high or mismatch repair deficient cancers who are relapsed/refractory to, intolerant to, or refuse standard of care treatment. Expansion cohorts will enroll participants at selected dose(s) and indications on the basis of dose escalation findings. The primary endpoint of safety includes outcomes such as adverse events and dose-limiting toxicities. Efficacy, a secondary endpoint, will include assessments of tumor response according to RECIST v1.1. Exploratory biomarker assessments will include peripheral and tumor measures of immune cell populations and relevant gene/protein expression. Enrollment in STK-012 monotherapy dose escalation has been initiated. Citation Format: David Spigel, Alexander Spira, Dmitriy Zamarin, David F. McDermott, Jason Luke, John V. Heymach, Rebecca Previs, Ryan Sullivan, Leena Gandhi, Alex Azrilevich, Naiyer Rizvi, Martin Oft, Natalie Busby, Benjamin Izar. A phase 1a/1b study of STK-012, an α/β IL-2 receptor selective partial agonist as monotherapy and in combination with pembrolizumab in advanced solid tumors (NCT05098132) [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 CT244.

2519 Background: Resistance to immune checkpoint blockade (ICB) can manifest as disease progression either at the initiation of treatment (primary resistance) or after some initial response (acquired resistance). To better understand the mechanisms underlying acquired resistance, the imCORE Network is conducting a study (NCT03333655) to examine changes in tumor biology from pre-treatment to disease progression across cancer types. Methods: Eligible patients included those experiencing clinical benefit on ICB (defined as objective response or stable disease longer than 6 months) and had evaluable tissue samples from both pre-treatment and within 30 days of progression. Samples were subjected to whole exome sequencing (WES), RNA sequencing (RNA-Seq), and immunohistochemistry (IHC). Whole blood samples or adjacent normal tissue were used as a reference for tumor variant calling. Results: As of December 3rd, 2021, 24 enrolled patients have complete sample pairs. Of those, melanoma, bladder, and lung were most common (n = 7, 6 and 5 pairs, respectively), but our cohort also included patients with breast cancer, squamous head & neck, and renal cell carcinoma. IHC data unexpectedly showed a modest, but consistent increase in tumor infiltrating CD8+ T cells at progression. In addition, IHC evidence of a decrease in MHC-I proteins (HLA-A and B2M) suggest that in 5 out of 24 cases, key proteins needed for antigen presentation are lost. Global differential gene expression analysis showed that immune gene expression was significantly increased at progression, including numerous chemokines and significant enrichment in gene sets responsible for antigen presentation machinery. Protein-altering mutations at progression appeared in B2M in one patient, and CXCL9 in another. However, in most cases it is unclear what genetic alterations are responsible. We do not observe evidence of consistent IFNγ and Jak/stat signaling loss or antigen presentation loss. Conclusions: While ICB resistance is thought to be associated with a lack of immune response within the TME, we found that acquired resistance is usually associated with either maintenance or an increase in immune infiltration. Multiple alterations that are unique to individual patients also continue to emerge. Our data shows ICB resistance is multifactorial and associated with dynamic changes to markers amid immune activation and inhibition. Clinical trial information: NCT03333655.

Figure S2. An example of the relationship between PD-L1 expression and predicted TGFB1 expression using Weka 3 algorithms for all patients in the dataset. Similar trends were seen when comparing the PD-L1 expression level to the other 13 predicted molecules. For this, the number of gene mutations identified for each patient ranged from 2 to 36 with a total of 264 unique genes between all patients. This categorical data was preprocessed and expanded into a gene vector of length 264 to represent each of the unique genes. For each gene in the vector, the data was represented in binary; a 1 was assigned if the patient had a mutation in this gene, a 0 otherwise. Two datasets, one including gene mutations (Molecules and Gene Mutations) and one without (Molecules), were both used to learn prediction models. The Discovery and Validation datasets were determined based on the split provided to allow for comparable results. The performance of a subset of these models on the testing and training sets for both Molecules and Molecules and Gene Mutations datasets are shown. The SMO support vector machine with a normalized polynomial kernel had the best performance when applied to the molecule dataset. This model correctly identified 24 out of 29 patients whereas the simulation models correctly identified 25 of 29. This was only a difference of one match between the two prediction methods. Still, several other methods, while not performing as well overall, were able to identify 9 patients in the test dataset accurately. This was near the computational simulation model prediction capability in which 10 patients were successfully identified in the test dataset. In general, adding the gene mutation data to the molecule data either maintained or decreased the performance of a model. (DOCX 4114Â kb)

SITC NSCLC CIG Bibliography. (DOCX 62Â kb)

Figure S1. A schematic pyramid showing the levels of information used to develop the validated, cancer network. This network was created from published reports on cell receptors, signaling pathways, pathway signaling intermediates, activation factors, transcription factors, and enzyme kinetics. Information on each pathway node, its functionality, and its links with other genes, proteins, and pathways was manually researched, analyzed, curated, and aggregated to construct the integrated network maze. Every process or reaction was modeled mathematically using Michaelis Menton kinetics, mass action kinetics, and variations of these representations using ordinary differential equations (ODEs). Modeled events included but were not limited to interactions at the cell surface (e.g., binding of ligands to receptors, etc.), metabolic and cell signaling (e.g., signal pathway events, cross talk interactions among pathways, feedback control, etc.), activation and regulation of genes (e.g., activation links of transcription factors, etc.), intracellular processes such as proteasomal degradation, endoplasmic reticulum (ER) stress, oxidative stress, DNA damage and repair pathways, and cell cycle pathways. Time-dependent changes in signaling pathway fluxes of every biological reaction modeled utilizing modified ODEs were solved with a proprietary solver. Models were validated with a series of internal control analysis checks on predictions. These checks included assessing the effects of pathway molecule over-expression or knockdown on pathway predictions; effects of drugs on pathway predictions; and activation, regulation, and cross-talk interactions among pathway intermediates on pathway predictions. (DOCX 53Â kb)

Table S6. Comparisons of clinical and predicated responses and match scores. We used a cross-validation approach to assess the match scores in Table 1 of the PD-1 predicted responses against the PD-1 clinical responses in the Rizvi et al. 2015 Discovery dataset vs. the Validation dataset. We then pooled and re-partitioned the dataset into two new Training and Test datasets. We then used a similar cross-validation approach to assess the match scores of the PD-1 predicted responses vs. the PD-1 clinical responses. (DOCX 17Â kb)

Table S4. Creation of the dendritic cell infiltration index for the patient SA97V5-specific simulation model. Chemokines CCL11, CCL20, CCL2, CCL3, CCL4, CCL5, CCL7, CX3CL1, and CXCL14, capable of trafficking of dendritic cells into the tumor microenvironment, were used to create the index. Individual chemokine percent expression (with respect to non-tumorigenic baseline controls) was predicted and given weightage so as to normalize the total to 1. The index was then calculated to be the sum of each prediction % change * weightage. (DOCX 16Â kb)

Comments from Member Open Review. (DOCX 14Â kb)

Purpose: Bryostatin-1 is a compound known to inhibit protein kinase C expression. Clinical trials have focused on administration schedules ranging from 1 hour to 72 hour infusions. Preclinical data suggest that the down regulation of the target PKC occurs only as long as the drug is being infused. Therefore we performed a phase 1 clinical trial to determine the safety and recommended dose of prolonged infusion Bryostatin-1. Experimental Design: Patients with advanced metastatic cancer were enrolled in this traditional phase 1 clinical trial utilizing prolonged infusion Bryostatin-1. The administration of Bryostatin-1 was initially begun at 96 hours and extended to 14 days. Doses were escalated using the 96 hour infusion time and then duration of infusion was increased. All patients underwent extensive sampling for determination of PKC levels as well as other key biologic end points. The determination of maximum tolerated dose and recommended phase two dose were based on toxicity. Results: 38 patients were...

This study was designed as a multicenter, randomized, double-blind, placebo-controlled trial. Patients were randomized by center to placebo (16 patients, 31%), oral bexarotene 300 mg/m2/day (21 patients, 40%), or oral bexarotene 600 mg/m2/day (15 patients, 29%) following demonstration of stable or responsive disease after first-line chemotherapy. The study was prematurely terminated because of slow accrual after 54 patients enrolled. Median time to progression (TTP) from the beginning of study drug treatment was 56 days for placebo, 82 days for moderate-dose bexarotene (300 mg/m2/day), and 128 days for high-dose bexarotene (600 mg/m2/day) (P = 0.56, log-rank test). For prior chemotherapy responders only, median TTP from the beginning of study drug treatment was 56 days for placebo, 146 days for moderate-dose bexarotene, and 177 days for high-dose bexarotene. Of note, there were more chemotherapy responders randomized to the placebo group (63%) than the bexarotene treatment arms (48% and 47%), further supporting a bexarotene-related improvement in TTP. Bexarotene-related toxicity was manageable and consisted primarily of elevated serum triglycerides and asthenia, skin toxicity (dryness, peeling, flaking), thyroid dysfunction, and headache. Because this study was closed prematurely, it does not have the statistical power to detect differences among the treatment groups. This study shows that patients can tolerate bexarotene at initial doses up to 600 mg/m2/day after platinum-based chemotherapy and that bexarotene may have the potential to delay disease progression in patients with advanced non–small-cell lung cancer with previously stable or responsive disease following platinum-based chemotherapy.

Preclinical data suggest that the combination of inhibitors of topoisomerases I and II may be synergistic when administered together. The optimal sequence of such combinations is uncertain, but initial administration of a topoisomerase I inhibitor upregulates topoisomerase II. Several combinations of these inhibitors have been evaluated, but have not clearly demonstrated synergy. Thus, we have started a phase I study of the combination of irinotecan (CPT-11, Camptosar) and epirubicin (Ellence). Typical eligibility criteria for phase I studies were employed. Patients with a history of congestive heart failure,240 mg/m2 of prior doxorubicin, or10% weight loss in the prior 4 weeks were excluded. Irinotecan and epirubicin were administered on days 1 and 8, every 28 days. Initially, patients were treated with irinotecan at 100 mg/m2 and epirubicin at 40 mg/m2 (dose level 1). After substantial toxicity at this level, the doses to be evaluated were changed to irinotecan: 50--75--100 mg/m2, and epirubicin: 20--25--30 mg/m2. Dose-limiting toxicities were noted in 2/4 patients (2 neutropenic fever, 1 thrombocytopenia) on dose level 1; 0/3 on dose level 1A; 1/8 (neutropenia) on dose level 2A; and 1/3 (neutropenia) on dose level 3A. This is the first combination of irinotecan and epirubicin to be evaluated in humans. The toxicity, primarily myelosuppression, noted to date has exceeded the expected toxicity for the doses of the irinotecan and epirubicin alone, suggesting the possibility of a synergistic interaction of the agents on this schedule, at least in the bone marrow. Other toxicities were acceptable and non-dose-limiting. Accrual of patients continues, at level 3A (irinotecan at 75 mg/m2, epirubicin at 25 mg/m2).

Depsipeptide (FR901228) is a bicyclic peptide isolated from Chromobacterium violaceum that has demonstrated potent in vitro cytotoxic activity against human tumor cell lines and in vivo efficacy against human tumor xenografts. The primary mechanism of action is through inhibition of histone deacetylase. Initial development was halted due to significant cardiac toxicity. Subsequent studies performed at the National Cancer Institute demonstrated administration without cardiotoxicity was possible by varying the schedule of administration. A phase I trial was designed to determine the maximum tolerated dose and toxicity profile when administered as a 4-hour infusion weekly x 3 with one week rest. 33 Patients with advanced, incurable cancers were enrolled into this trial and treated with doses of Depsipeptide ranging from 1 mg/m2 to 17.7 mg/m2. At doses above 5 mg/m2, we observed common symptoms of nausea, vomiting, fatigue, and anorexia. Subtle changes in ECGs were seen in several patients. However, no cardiac enzyme abnormalities or reduction in ejection fraction were observed. The MTD was defined as 13.3 mg/m2 with dose limiting toxicities being grade 3 thrombocytopenia and fatigue. Depsipeptide can be safely administered when given as a 4-hour infusion and further clinical trials are warranted.

Bryostatin-1 is a compound known to inhibit protein kinase C expression. Clinical trials have focused on administration schedules ranging from 1 hour to 72 hour infusions. Preclinical data suggest that the down regulation of the target PKC occurs only as long as the drug is being infused. Therefore we performed a phase 1 clinical trial to determine the safety and recommended dose of prolonged infusion Bryostatin-1.Patients with advanced metastatic cancer were enrolled in this traditional phase 1 clinical trial utilizing prolonged infusion Bryostatin-1. The administration of Bryostatin-1 was initially begun at 96 hours and extended to 14 days. Doses were escalated using the 96 hour infusion time and then duration of infusion was increased. All patients underwent extensive sampling for determination of PKC levels as well as other key biologic end points. The determination of maximum tolerated dose and recommended phase two dose were based on toxicity.38 patients were enrolled in the study. The recommended phase two doses were 24 mcg/m2 over five days, 16 mcg/m2 over six days and 8 mcg/m2 over 14 days. At the higher dose levels we demonstrated consistent down regulation of PKC-alpha. This was not observed at the low dose level. Toxicities were limited to myalgias and fatigue and were dose-related. The results of downstream signaling effects were less clear. MMP expression was not altered by treatment with Bryostatin-1. Only limited evidence for alterations in PKC activity as measured by expression of phosphorylated MAPK was observed. No objective responses were observed with five patients having prolonged stabilization of disease.Bryostatin-1 is safely administered over prolonged infusion schedules. There appears to be a dose response for PKC inhibition. Bryostatin-1 is a complicated compound as is the target PKC and its related signaling pathways. There is only limited clinical activity with this compound as a single agent; future studies should focus on combinations with other cytotoxics or targeted therapies.

Both irinotecan (CPT-11, Camptosar) and epirubicin (Ellence) are significant chemotherapeutic agents that are used in the management of many different cancers. Each agent works through the inhibition of topoisomerases, and inhibition of topoisomerases I and II may possibly result in significant clinical synergy. This phase I clinical study represents an investigation of the first combination of irinotecan and epirubicin in patients with advanced cancer. Standard phase I eligibility was utilized, and recruitment proceeded in cohorts of three with escalating doses of irinotecan and epirubicin. The treatments were given on days 1 and 8 of a 28-day cycle. Our initial cohort of patients developed significant myelosuppression that required a modification in the initial dose-escalation scheme, and accrual to these lower doses is ongoing. Evidence of clinical activity has been observed. Accrual will continue until the maximum tolerated dose can be determined. Other schedules of the combination of irinotecan and epirubicin should be explored.

Supplementary Materials and Methods (DOCX 109Â kb)

Supplementary Materials and Methods (DOCX 109Â kb)

Table S1. Molecules with immunosuppressive functions used in simulation models to predict PD-1 drug responder status. (DOCX 55Â kb)

Table S2. Individual mutational profiles of patient drug responders (n = 11) and nonresponders (n = 18). (DOCX 19 kb)

Table S1. Molecules with immunosuppressive functions used in simulation models to predict PD-1 drug responder status. (DOCX 55Â kb)

Table S2. Individual mutational profiles of patient drug responders (n = 11) and nonresponders (n = 18). (DOCX 19 kb)