Development of a prognostic scoring system for patients with advanced cancer enrolled in immune checkpoint inhibitor phase 1 clinical trials

Background:

We sought to develop a prognostic scoring system to aid in patient selection for immune checkpoint inhibitor (ICI) phase 1 clinical trials.

Methods:

Clinical data from patients treated in phase 1 ICI clinical trials at MD Anderson (MDA) Center were analysed. Seventeen clinical factors were studied. Recursive partitioning analysis, a tree-based model, was used to develop a regression tree and identify optimal cut-points based on differences in survival for each clinical factor. A Cox proportional hazards regression model was then used to identify factors independently affecting overall survival. A prognostic scoring system was subsequently developed.

Results:

A total of 172 patients (105 CTLA4- and 67 PD1-based) were analysed. Seven factors were independently associated with worse overall survival (OS): age>52 years (hazard ratio (HR) 1.59, 95% confidence interval (CI) 1.1–2.4), Eastern Cooperative Oncology Group performance status>1 (HR 2.81, 95%CI 1.3–6.3), lactate dehydrogenase >466 (which is 0.75 × the upper limit of normal at our institution) (HR 2.1, 95% CI 1.4–3.2), platelet count >300 × 10³μL⁻¹ (HR 1.8, 95% CI 1.2–2.8), absolute neutrophil count >4.9 × 10³μL⁻¹ (HR 2.3, 95% CI 1.5–3.5), absolute lymphocyte count <1.8 × 10³μL⁻¹ (HR 3.3, 95% CI 1.9–5.7), and liver metastases (HR 1.8, 95% CI 1.2–2.6). An index was created by dividing the cohort into risk groups based on the number of factors present: 0–2, 3, 4, or 5–6. Median OS was 24.2 months, 11.6 months, 8.0 months, and 3.8 months for patients with 0–2, 3, 4, or 5–6 risk factors, respectively; log-rank test, P<0.0001. The Harrell c-index of this scoring system was 0.72, indicating better predictability than the Royal Marsden Hospital score (c-index 0.67) and MDA score (c-index 0.61).

Conclusions:

We have developed a novel ‘MDA-ICI’ prognostic scoring system for patients treated in phase 1 ICI clinical trials. Prospective evaluation and external validation is warranted and may help aid patient selection for future clinical trials.

Liquid Biopsies Using Plasma Exosomal Nucleic Acids and Plasma Cell-Free DNA Compared with Clinical Outcomes of Patients with Advanced Cancers

Purpose: Blood-based liquid biopsies offer easy access to genomic material for molecular diagnostics in cancer. Commonly used cell-free DNA (cfDNA) originates from dying cells. Exosomal nucleic acids (exoNAs) originate from living cells, which can better reflect underlying cancer biology.Experimental Design: Next-generation sequencing (NGS) was used to test exoNA, and droplet digital PCR (ddPCR) and BEAMing PCR were used to test cfDNA for BRAF^V600, KRAS^G12/G13, and EGFR^{exon19del/L858R} mutations in 43 patients with progressing advanced cancers. Results were compared with clinical testing of archival tumor tissue and clinical outcomes.Results: Forty-one patients had BRAF, KRAS, or EGFR mutations in tumor tissue. These mutations were detected by NGS in 95% of plasma exoNA samples, by ddPCR in 92% of cfDNA samples, and by BEAMing in 97% cfDNA samples. NGS of exoNA did not detect any mutations not present in tumor, whereas ddPCR and BEAMing detected one and two such mutations, respectively. Compared with patients with high exoNA mutation allelic frequency (MAF), patients with low MAF had longer median survival (11.8 vs. 5.9 months; P = 0.006) and time to treatment failure (7.4 vs. 2.3 months; P = 0.009). A low amount of exoNA was associated with partial response and stable disease ≥6 months (P = 0.006).Conclusions: NGS of plasma exoNA for common BRAF, KRAS, and EGFR mutations has high sensitivity compared with clinical testing of archival tumor and testing of plasma cfDNA. Low exoNA MAF is an independent prognostic factor for longer survival. Clin Cancer Res; 24(1); 181-8. ©2017 AACR.

Gene Methylation Biomarkers in Sputum and Plasma as Predictors for Lung Cancer Recurrence

Detection of methylated genes in exfoliated cells from the lungs of smokers provides an assessment of the extent of field cancerization, is a validated biomarker for predicting lung cancer, and provides some discrimination when interrogated in blood. The potential utility of this 8-gene methylation panel for predicting tumor recurrence has not been assessed. The Eastern Cooperative Oncology Group initiated a prevention trial (ECOG-ACRIN5597) that enrolled resected stage I non-small cell lung cancer patients who were randomized 2:1 to receive selenized yeast versus placebo for 4 years. We conducted a correlative biomarker study to assess prevalence for methylation of the 8-gene panel in longitudinally collected sputum and blood after tumor resection to determine whether selenium alters their methylation profile and whether this panel predicts local and/or distant recurrence. Patients (N = 1,561) were enrolled into the prevention trial; 565 participated in the biomarker study with 122 recurrences among that group. Assessing the association between recurrence and risk of gene methylation longitudinally for up to 48 months showed a 1.4-fold increase in OR for methylation in sputum in the placebo group independent of location (local or distant). Kaplan-Meier curves evaluating the association between number of methylated genes and time to recurrence showed no increased risk in sputum, while a significant HR of 1.5 was seen in plasma. Methylation detection in sputum and blood is associated with risk for recurrence. Cancer Prev Res; 10(11); 635-40. ©2017 AACR.

Insurance Clearance for Early-Phase Oncology Clinical Trials Following the Affordable Care Act

Purpose: The Affordable Care Act (ACA) required that private insurance plans allow clinical trial participation and cover standard-of-care costs, but the impact of this provision has not been well-characterized. We assessed rates of insurance clearance for trial participation within our large early-phase clinical trials program, before and after implementation of the requirement.Experimental Design: We analyzed the departmental database for the Clinical Center for Targeted Therapy (CCTT) at MD Anderson Cancer Center (Houston, TX). Among patients referred for sponsored trials, we described rates of insurance clearance and prolonged time to clearance (at least 14 days) from July 2012 to June 2013 (baseline), July 2013-December 2013 (following CCTT staffing changes in July 2103), and January 2014-June 2015 (following implementation of the ACA). We used multivariable logistic regression models to compare rates across these time periods.Results: We identified 2,404 referrals for insurance clearance. Among privately insured patients, insurance clearance rates were higher for those referred from January 2014 to June 2015 than for those referred from July 2012 to June 2013 (OR, 4.72; 95% CI, 2.96-7.51). There was no association between referral period and clearance rates for Medicare/Medicaid patients (P = 0.25). Referral from January 2014 to June 2015 was associated with lower rates of prolonged clearance among both privately insured (OR 0.57; 95% CI, 0.38-0.86) and Medicare/Medicaid patients (OR 0.39; 95% CI, 0.19-0.83).Conclusions: Within our large early-phase clinical trials program, insurance clearance rates among privately insured patients improved following implementation of the ACA's requirement for coverage of standard-of-care costs. Clin Cancer Res; 23(15); 4155-62. ©2017 AACR.

Gene methylation biomarkers in sputum as a classifier for lung cancer risk

CT screening for lung cancer reduces mortality, but will cost Medicare ∼2 billion dollars due in part to high false positive rates. Molecular biomarkers could augment current risk stratification used to select smokers for screening. Gene methylation in sputum reflects lung field cancerization that remains in lung cancer patients post-resection. This population was used in conjunction with cancer-free smokers to evaluate classification accuracy of a validated eight-gene methylation panel in sputum for cancer risk. Sputum from resected lung cancer patients (n=487) and smokers from Lovelace (n=1380) and PLuSS (n=718) cohorts was studied for methylation of an 8-gene panel. Area under a receiver operating characteristic curve was calculated to assess the prediction performance in logistic regressions with different sets of variables. The prevalence for methylation of all genes was significantly increased in the ECOG-ACRIN patients compared to cancer-free smokers as evident by elevated odds ratios that ranged from 1.6 to 8.9. The gene methylation panel showed lung cancer prediction accuracy of 82–86% and with addition of clinical variables improved to 87–90%. With sensitivity at 95%, specificity increased from 25% to 54% comparing clinical variables alone to their inclusion with methylation. The addition of methylation biomarkers to clinical variables would reduce false positive screens by ruling out one-third of smokers eligible for CT screening and could increase cancer detection rates through expanding risk assessment criteria.

Mutation-Enrichment Next-Generation Sequencing for Quantitative Detection of KRAS Mutations in Urine Cell-Free DNA from Patients with Advanced Cancers

Purpose: Tumor-derived cell-free DNA (cfDNA) from urine of patients with cancer offers noninvasive biological material for detection of cancer-related molecular abnormalities such as mutations in Exon 2 of KRASExperimental Design: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA was developed, and results were compared with clinical testing of archival tumor tissue and plasma cfDNA from patients with advanced cancer.Results: With 90 to 110 mL of urine, the KRASG12/G13 cfDNA test had an analytical sensitivity of 0.002% to 0.006% mutant copies in wild-type background. In 71 patients, the concordance between urine cfDNA and tumor was 73% (sensitivity, 63%; specificity, 96%) for all patients and 89% (sensitivity, 80%; specificity, 100%) for patients with urine samples of 90 to 110 mL. Patients had significantly fewer KRASG12/G13 copies in urine cfDNA during systemic therapy than at baseline or disease progression (P = 0.002). Compared with no changes or increases in urine cfDNA KRASG12/G13 copies during therapy, decreases in these measures were associated with longer median time to treatment failure (P = 0.03).Conclusions: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA had good concordance with testing of archival tumor tissue. Changes in mutated urine cfDNA were associated with time to treatment failure. Clin Cancer Res; 23(14); 3657-66. ©2017 AACR.

Abstract 5687: Detection and monitoring of IDH mutations in unamplified plasma cell-free DNA in patients with advanced cancers treated with IDH inhibitors

Background: Cell-free (cf) DNA from plasma of patients with advanced cancers offers an easily obtainable material for detection of IDH mutations, which can be used for diagnostics and monitoring purposes.

Methods: Plasma was serially collected from patients with advanced cancers with IDH1 R132 or IDH2 R172 mutations, who were enrolled to clinical trials with IDH1, IDH2 or pan-IDH inhibitors. cfDNA was purified and up to 16 ng of each DNA was tested for mutations in the R132 hotspot of IDH1 and R172 hotspot of IDH2 using the QX200 Droplet Digital PCR™ platform (Bio-Rad). Results (mutation allele frequency [MAF] in the wild-type background or the number of IDH-mutant copies/mL of plasma) were compared both to treatment outcomes and to the results of mutation analysis of either archival primary or metastatic tumor tissue obtained at different points of clinical care from a CLIA-certified laboratory.

Results: Of the 28 patients (cholangiocarcinoma, 24; other cancers, 4) with IDH1 R132 mutations (N=25) or IDH2 R172 mutations (N=3) in the tumor tissue, IDH mutations were detected in 26 (93%) of plasma cfDNA samples even though median time from tissue to plasma sampling was 16.5 months (3.5-71.1 months). Quantity (&lt; median vs. &gt; median MAF or copies/mL) of IDH-mutant cfDNA was not associated with survival (median not reached vs. 11.1 months, P=0.26). The best radiological response to treatment with IDH inhibitors was stable disease for &gt; 4 months (5/28, 18%) and the median progression-free survival was 1.8 months (95% CI 1.4-2.2). The median quantity of IDH-mutant cfDNA (MAF and copies/mL) at baseline, on therapy and at disease progression did not differ (P=0.16). Changes in quantity (MAF and copies/mL) of IDH-mutant cfDNA within first 3 weeks of therapy were not associated with response on radiographic imaging (P&gt;0.65) or progression-free survival (P&gt;0.12).

Conclusions: Detection of IDH mutations in a small amount of unamplified plasma cfDNA using ddPCR has excellent sensitivity compared to conventional clinical IDH mutation testing of archival specimens. Quantity and change in IDH-mutant cfDNA did not correspond with treatment outcomes.

Citation Format: Filip Janku, Helen J. Huang, Rachna T. Shroff, Milind Javle, Anthony P. Conley, Anjali Raina, Veronica R. Holley, Aung Naing, Daniel D. Karp, David Fogelman, Ahmed O. Kaseb, Rajyalakshmi Luthra, George A. Karlin-Neumann, Funda Meric-Bernstam. Detection and monitoring of IDH mutations in unamplified plasma cell-free DNA in patients with advanced cancers treated with IDH inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5687. doi:10.1158/1538-7445.AM2017-5687

Abstract 3261: Gene methylation biomarkers in sputum as a classifier for lung cancer risk

Lung cancer is the leading cause of cancer death primarily because it is often diagnosed at an advanced stage. Results from the National Lung Screening Trial (NLST) showed that CT screening can reduce lung cancer mortality by 20%, but the high number of false positives and need for additional testing suggest that better risk classification of smokers prior to screening could save more lives with less cost and improved efficiency. Furthermore, eligibility criteria for NLST were restricted to smokers ages of 55-74 with &gt;30 pack-years of smoking and &lt; 15y since smoking cessation, which captures only ~40% of incident lung cancer cases. Molecular biomarkers could augment current risk stratification used to select smokers for screening. We have shown that gene specific promoter hypermethylation detected in sputum provides an assessment of field cancerization within the lungs of smokers that in turn predicts lung cancer. The current study addressed whether our validated 8-gene methylation panel could be extended to improve the existing risk prediction model used to recommend people for a CT screen by evaluating methylation in 487 resected Stage I lung cancer patients from the ECOG-ACRIN5597 trial (field of injury remains), 1378 current and former smokers from the Lovelace Smokers cohort (LSC) and 718 current and former smokers from the PLuSS cohort. Our initial analysis was restricted to individuals from each cohort who met NLST criteria for CT screening (n=371 ECOG-ACRIN, n=466 LSC and n=597 PLuSS). The methylation prevalence of all 8 genes was significantly increased in resected lung cancer patients compared to cancer-free smokers (odds ratios 1.6 to 8.9). The area under the receiver operator characteristic curve (AUC) was used to evaluate classification accuracy of different logistic regression models. Classification accuracy for clinical risk factors alone was 74-76%, methylation alone, 82-86%; and clinical risk factors plus methylation, 87-90% (p&lt;10-9 - 10-16). Setting the sensitivity at 95% improved specificity from 25% to 54% with both methylation and clinical factors in the model. Assessment of the performance of the gene methylation panel in all of the cancer patients and smokers did not reduce classification accuracy or increase specificity. Implementation of gene methylation biomarkers for screening could be a paradigm shift for lung cancer management by providing a much improved risk assessment model that will allow for expanding the number of smokers considered for screening, decreasing by one-third the actual number referred, and reducing mortality through increasing the CT positive predictive value. (Supported largely by R01 CA095568 and in part P30 CA118100)

Citation Format: Maria A. Picchi, Shuguang Leng, Guodong Wu, Donna M. Klinge, Cynthia L. Thomas, Elia Casas, Christine A. Stidley, Sandra J. Lee, Seena Aisner, Jill M. Siegfried, Suresh Ramalingam, Fadlo R. Khuri, Daniel D. Karp, Steven A. Belinsky. Gene methylation biomarkers in sputum as a classifier for lung cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3261. doi:10.1158/1538-7445.AM2017-3261

Abstract 642: Detection of circulating antibodies against KRAS in patients with advanced cancers

Introduction: KRAS gene plays a major role in tumorigenesis, cell proliferation and survival. Yet, there has been no effective targeted therapy against KRAS mutation-mediated tumors. We hypothesized that KRAS can induce humoral-mediated immune response.

Methods: Plasma or serum samples from patients with progressing advanced cancers with or without KRAS mutations were tested for the presence of circulating KRAS antibodies. We used the Maverick Detection System (Genalyte, San Diego, CA), which can perform real-time detection of macromolecules in crude samples using biologically functionalized silicon photonic biosensors lithographically printed on disposable silicon chips.

Results: We collected serum or plasma samples from 213 patients with advanced cancers (KRAS-mutant, N=100; KRAS wild-type, N=113) and 50 (23%) were found to have circulating KRAS antibodies. There was no association between KRAS antibodies and tumor KRAS mutation status (21/100, 21% for KRAS-mutant vs. 29/113, 26% for KRAS wild-type; P=0.52). In addition, there was no difference in detection of KRAS antibodies in colorectal cancer (21/89, 24%) compared to other cancers (29/124, 23%; P=1.00). There was no difference in the median survival in patients with KRAS antibodies compared to patients without KRAS antibodies (9.0 months vs. 10.1 months; P= 0.825). Similarly, there was no difference in the median survival according to the presence of circulating KRAS antibodies in subgroups of patients with tumor KRAS mutations (P= 0.96) and without tumor KRAS mutations (P=0.63). On the contrary, the median survival of patients with tumor KRAS mutation was shorter compared to patients with KRAS wild-type (7.2 months vs. 11.5 months; P&lt;0.001).

Conclusion: Circulating KRAS antibodies can be detected in 23% of patients with advanced cancers. Biological implications of circulating KRAS antibodies remain to be understood.

Citation Format: Ed Kheder, Helen J. Huang, Alice Wu, David S. Hong, Sarina A. Piha-Paul, Daniel D. Karp, Siqing Fu, Vivek Subbiah, Apostolia M. Tsimberidou, Aung Naing, Adi Diab, Milind Javle, Scott Kopetz, Anil K. Sood, Jonathan M. Kurie, Funda Meric-Bernstam, Martin Gleeson, Filip Janku. Detection of circulating antibodies against KRAS in patients with advanced cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 642. doi:10.1158/1538-7445.AM2017-642

Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer

Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy.Experimental Design: We developed a highly sensitive ultradeep next-generation sequencing (NGS) assay using reagents from TruSeqNano library preparation and NexteraRapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools. The results were retrospectively compared with molecular testing of archival primary or metastatic tumor tissue obtained at different points of clinical care.Results: In a study of 55 patients with advanced cancer, the ultradeep NGS assay detected 82% (complete detection) to 87% (complete and partial detection) of the aberrations identified in discordantly collected corresponding archival tumor tissue. Patients with a low variant allele frequency (VAF) of mutant cfDNA survived longer than those with a high VAF did (P = 0.018). In patients undergoing systemic therapy, radiological response was positively associated with changes in cfDNA VAF (P = 0.02), and compared with unchanged/increased mutant cfDNA VAF, decreased cfDNA VAF was associated with longer time to treatment failure (TTF; P = 0.03).Conclusions: Ultradeep NGS assay has good sensitivity compared with conventional clinical mutation testing of archival specimens. A high VAF in mutant cfDNA corresponded with shorter survival. Changes in VAF of mutated cfDNA were associated with TTF. Clin Cancer Res; 23(18); 5648-56. ©2017 AACR.

Liquid biopsies of plasma exosomal nucleic acids, plasma cell-free DNA, and survival of patients with advanced cancers

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Background: Blood-based liquid biopsies offer easy accessible genomic material for molecular diagnostics in cancer. Commonly used cell-free DNA (cfDNA) originates from dying cells. In contrast exosomal nucleic acid (exoNA) originates from living cells, which can better reflect underlying cancer biology. Methods: We isolated exoNA (EXO52) and cfDNA (QIAamp Circulating Nucleic Acid kit) from plasma of patients with progressing advanced cancers and tested for BRAFV600, KRASG12/G13, and EGFRexon19del/L858R mutations using next-generation sequencing (EXO1000), droplet digital PCR (ddPCR, QX200) and BEAMing digital PCR. The results were compared to clinical testing of archival tumor tissue and correlated with survival. Results: Of the 43 patients (colorectal cancer, 20; melanoma, 8; non-small cell lung cancer, 6; ovarian cancer, 2; papillary thyroid cancer, 2; other cancers, 5) 41 had a mutation in the tumor tissue (20 [47%] BRAF mutation, 17 [40%] KRAS mutation and 4 [9%] EGFR mutation). Mutation testing of plasma exoNA from all 43 patients detected 39 (95%) of 41 mutations present in tumor tissue with 100% specificity. Mutation testing of plasma cfDNA from 39 patients using ddPCR detected 33 (89%) of 37 mutations present in tumor and testing of plasma cfDNA from 37 patients using BEAMing detected 34 (97%) of 35 mutations present in tumor tissue; however, both cfDNA methods reported an additional KRAS mutation not present in tumor tissue. Patients with high mutation allele frequency (MAF, > median) had shorter median survival compared to patients with low MAF ( < median) when using exoNA (5.9 vs. 11.8 months, P= 0.006), but not cfDNA ddPCR (6.0 vs. 7.4 months, P= 0.06) or cfDNA BEAMing (6.5 vs. 7.4 month, P= 0.07). High MAF in exoNA was an independent prognostic factor for survival in multicovariate analysis (HR 0.13, P= 0.017). Conclusions: Mutation testing of plasma exoNA for common BRAF, KRAS, and EGFR mutations has high sensitivity compared to clinical testing of archival tumor tissue and better specificity than PCR testing of plasma cfDNA. High MAF in exoNA is the independent prognostic factor for shorter survival.

SWI/SNF complex subunit aberrations in diverse cancers: Next-generation sequencing of 539 patients

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Background: The SWI/SNF complex is an ATP-dependent chromatin remodeler that is enriched at promoters and enhancers of active genes. It has been implicated as both an oncogene and tumor suppressor. Specific subunit mutations have even been associated with specific cancers with increased PRC2 component EZH2 activity. EZH2/ EED inhibitors are in early stage development to target SWI/SNF complex. Methods: We analyzed 539 consecutive patients with diverse malignancies who were referred for Phase 1 clinical trials and had CLIA certified targeted next-generation sequencing (Foundation one) for presence of aberrations in SWI/SNF complex genes (ARID1A, ARID2, PBRM1, SMARCA4, SMARCB1). Patient charts were reviewed for general demographics (sex, age at diagnosis and death, performance status), tumor histology, stage, metastatic sites, treatment history, outcomes and co-occurring alterations. Results: Fifty patients had mutations in SWI/SNF subunits. Median age at diagnosis was 56 (14-79 years) and M:F ratio 21:29. Kidney, colorectal, ovary and breast were the most common among 15 different cancers. Most were stage IV at diagnosis (68%), had a strong family history of cancer (80%) & were smokers (42%). The most common mutated subunit was ARID1A (50%) followed by PBRM1 (16%), ARID2 (12%), SMARCA4 (12%), and SMARCB1 (10%). All mutations were predicted to be inactivating. Actionable co-occurring pathway alterations were found in 58% of patients, most commonly PI3K (26%), FGFR(16%), and NOTCH1/2 (10%). The majority of patients (62%) were enrolled on a clinical trial. Best responses on other targeted agents included 1 CR (BRAFV600E colon), 4 PR (transformed teratoma, skin SCC, ovarian, NSCLC), 12 SD. Exceptional responders included BRAFV600E colon cancer on BRAFi based therapy for 66 cycles, NSCLC on Nivolumab for 34 cycles, and MSI-H colon cancer on regorafenib/cetuximab for 27 cycles. Conclusions: The role of SWI/SNF in patients with extended clinical benefit from other targeted agents should be explored. Co-occurring genetic alterations are observed in PI3K, FGFR, and NOTCH pathways. Future pre-clinical and/or clinical studies could target these pathways in combination with EZH2/EED inhibitors.

EphA2 gene targeting using neutral liposomal small interfering RNA (EPHARNA) delivery: A phase I clinical trial

TPS2604

Background: EphA2 is a member of the largest subfamily of receptor tyrosine kinases, with over 14 receptors and 8 ligands. EphA2 overexpression is common in many human cancers, including lung, breast, prostate, colorectal, pancreatic, melanoma, esophageal and endometrial cancers. EphA2 can function as an oncoprotein when introduced into cells with low expression. In addition, downregulation of constitutive expression reduces tumorigenicity in breast, endometrial, ovarian and pancreatic cancers in vitro and in vivo models. EphA2 is a desirable target because of its selective expression in cancer (vs. adult normal tissue), and its important role in promoting tumor growth and metastasis. It has kinase-dependent and independent functions, making it an ideal target for RNAi-based targeting. We have previously reported that EphA2 siRNA incorporated in DOPC nanoliposomes (EPHARNA) was highly effective in reducing EphA2 protein levels after a single dose. In addition, three weeks of treatment with EPHARNA (150 μg/kg twice weekly) in an orthotopic mouse model of ovarian cancer (HeyA8 or SKOV3ip1) significantly reduced tumor growth compared with non-silencing siRNA, and demonstrated synergistic anti-tumor activity when combined with conventional chemotherapy. EPHARNA underwent GLP development in 2 animal models (murine and primate) at M.D. Anderson to support the IND (#72924). The first-in-human trial (NCT01591356) is ongoing and recruiting study subjects. Methods: Adult Patients > 18 years of age with histologic proof of advanced recurrent solid tumors, who are not candidates for known regimens or protocol treatments of higher efficacy or priority. All patients (dose escalation and dose expansion phases) must be willing to undergo pre- and post-treatment biopsies. For dose expansion phase, patients must have EphA2 overexpression by IHC evaluation. Enrollment is ongoing for the dose escalation with the plan for dose expansion. A total of 16 patients have been enrolled and treated in the dose escalation phase. Clinical trial information: NCT01591356.

Phase II study for the evaluation of efficacy of pembrolizumab (MK-3475) in patients with cancer of unknown primary

TPS3103

Background: Cancer of unknown primary is a biopsy proven malignancy for which an anatomic primary remains unidentified after a focused search. It accounts for 3-4 % of all solid cancers and most investigators limit it to epithelial and undifferentiated cancers. Patients with metastatic melanoma and sarcoma are excluded. Sophisticated imaging, robust pathologic evaluation including immunostains, and genomic and proteomic characterization of these cancers have challenged the management of CUP. The paradigm has shifted from empiric platinum based combination doublets to a personalized approach. Nevertheless, without an anatomic primary, clinical trial opportunities are limited. There remains an unmet research need to evaluate the role of immunotherapy, specifically checkpoint blockade drugs in specific subsets of CUP patients. Methods: Adult Patients ≥ 18 years of age with ECOG PS 0-1, must meet the definition of a CUP cancer. Patients must be intolerant and/or refractory to at least one line of established therapy known to provide clinical benefit for their condition within the last 6 months (often, a platinum based therapy for carcinomas). Patients must have either measurable (RECIST 1.1) or evaluable disease. Although not limited to subtypes, there is a signficant interest in enrolling patients with isolated disseminated lymphadenopathy, HPV (+) CUP and those who have an IHC profile of those known cancers for which anti-PD therapy has been approved (lung, renal, others) The primary objective of this trial is to evaluate efficacy by evaluation of non-progression rate (NPR) at 27 weeks (9 cycles) as defined as the percentage of CUP patients who are alive and progression-free at 27 weeks (9 cycles) as assessed by RECIST 1.1. Secondary objectives include evaluating safety and tolerability of pembrolizumab (MK-3475); correlating efficacy, non-progression rate (NPR) at 27 weeks (9 cycles), objective response (CR or PR), progression-free survival (PFS), overall survival (OS) and duration of response (DOR) to PD-L1 status; and identifying imaging characteristics associated with immunological changes in tumor following treatment with pembrolizumab. Enrollment is ongoing. Clinical trial information: NCT02721732.

A phase I study of PT-112 in advanced solid tumors

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Background: PT-112 is a novel platinum-pyrophosphate agent designed to avoid the toxicity and drug resistance mechanisms of conventional chemotherapy. Pre-clinical models show effects on multiple cell signaling components: p16 mediated G1/S cell cycle arrest; modulation of MDM2/p53 expression; extrinsic apoptosis initiation; and immunogenic cell death (ICD) induction. This Phase I first-in-human, multicenter, open label study assesses PT-112’s safety and pharmacokinetic (PK) profile in advanced solid tumor patients (pts), to determine the RP2D and signals of activity. Methods: Pts with advanced solid tumors and acceptable marrow / organ function received PT-112 IV over 1-hr on days 1, 8, and 15 every 4 wks in a 3+3 dose escalation design. Intra-subject escalation was allowed. PK samples from cycles 1-2 were analyzed by ICP-MS and LC-MS/MS. Results: 44 pts have been treated across dose levels (DL) from 12-300mg/m2. Cumulative dosing ranged from 1 to 60 infusions, and cumulative exposure from 96 to 5,244 mg/m2. PK parameters were dose proportional. Target Cmax and AUC levels were achieved, with constant VD. DLTs were observed at 150mg/m2 (G3 pancytopenia); 250mg/m2 (G2 renal injury in a cervical ca pt with hydro-nephrosis); and 300mg/m2 (G3 rash). The most common treatment-related AEs were G1-2 fatigue (26% pts), nausea (23%), vomiting (14%), constipation (12%), and diarrhea (12%). Numerous signals of activity were observed at DLs ≥ 125mg/m2. These include a confirmed PR in a NSCLC pt with 6 prior lines of therapy and no response to TKI inhibition or PD-1 blockade; PFS > 6 months (7-18 months) in 3 pts; metabolic response via PET scan in bone and liver mets (basal cell and pancreatic ca.); biomarker responses in ovarian and prostate ca.; and nodal/metastatic volumetric reduction in 3 pts. Conclusions: PT-112 is a well-tolerated novel agent with a pleiotropic mode of action and feasibility for long-term and combination treatment. Numerous signals of anti-cancer efficacy in heavily pre-treated pts suggest lack of cross-resistance with conventional agents. MTD has not yet been reached. PT-112’s profile makes it an attractive candidate for further development, including in combination with immunotherapy. Clinical trial information: NCT02266745.

Phase I study of nab-paclitaxel, gemcitabine, and bevacizumab in advanced cancers

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Background: Gemcitabine (gem) with nab-paclitaxel (nab-p) is known to have antitumor activity and a favorable toxicity profile. The addition of bevacizumab (bev) to nab-paclitaxel has also been found to enhance nab-paclitaxel cytotoxicity. Methods: We therefore performed a modified 3+3 dose escalation study with 15 dose levels of fixed dose gem 1000 mg/m2IV (day 1, 8, 15) and escalating doses of nab-p IV (day 1,8, 15) and bev IV (day 1,15) every 28 days. The study design allowed for the possibility of multiple MTDs. Correlative studies on VEGF polymorphism and response were planned. (NCT01113476). Results: 103 patients (45 male) with advanced cancers were enrolled (19 ovarian, 18 pancreatic, and 18 gastroesophageal (GE) cancers among the most common). All patients were ECOG PS 0-2, median age was 60 years (range 17-85), and 51 patients (50%) were gem refractory with a median of 3 prior lines of therapy. 3 DLTs were observed during dose escalation - one with nab-p 50 mg/m2 and bev 10 mg/m2 (grade 3 dysphagia, dehydration), one with nab-p 75 mg/m2 and bev 10 mg/m2 (grade 3 cellulitis) and one with nab-p 150 mg/m2 and bev 5 mg/m2 (grade 3 bacteremia, hypotension). 2 DLTs were observed among the 13 patients in the nab-p 100 mg/m2 and bev 5 mg/m2 expansion cohort (one grade 3 diarrhea, one grade 3 fatigue) and 1 DLT among the 12 patients in the nab-p 75 mg/m2 and bev 10 mg/m2 expansion cohort (grade 3 rectal bleed). Dose escalation up to nab-p 125 mg/m2 and bev 15 mg/m2was well tolerated with no MTD. One patient with gem refractory peritoneal papillary carcinoma achieved a complete response, 13 patients (13%) had partial responses (PR), and 54 patients (52%) had prolonged stable disease (pSD) ≥ 12 weeks. 4 patients achieving PR and 26 patients with pSD were previously gem refractory. 3/6 (50%) small cell cancers achieved PR and all 6 of these patients had tumor shrinkage of at least 25%. 4/19 (21%) ovarian cancers achieved PR, 3/18 (17%) GE cancers achieved PR, and 1/18 (6%) pancreatic cancers achieved PR. Conclusions: The combination of gem 1000 mg/m2, nab-p 125 mg/m2 and bev 15 mg/m2 is safe, well-tolerated, and has activity even at lower doses in advanced malignancies, including gem refractory tumors. Correlative VEGF polymorphism studies are ongoing. Clinical trial information: NCT01113476.

Proof-of concept phase I study of everolimus, letrozole and trastuzumab in hormone receptor-positive, HER2-positive/amplified or mutant metastatic breast cancer or other solid tumors: Evaluating synergy and overcoming resistance

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Background: Preclinical models suggested synergistic antineoplastic activity of anti-estrogen therapy with HER2 and mTOR inhibitors. Methods: We designed a 3+3 dose escalation phase I study of the aromatase inhibitor letrozole 2.5mg PO daily, mTOR inhibitor everolimus 2.5-10mg PO daily and HER2 antibody trastuzumab 4-8mg loading dose followed by 2-4mg maintenance dose IV on day 1 of 21-day cycle in patients with hormone-receptor positive, HER2-positive/amplified or mutant advanced cancers (confirmed by immunohistochemistry and/or FISH and/or next-generation sequencing). The primary objectives were to determine maximum tolerated dose (MTD), dose limiting toxicities (DLT), overall safety and response. Results: A total of 18 patients (men, 1; women, 17; HER2 amplification, 14; HER2 mutation, 4; breast cancer, 15; ovarian cancer, 1; cervical cancer, 1; gastroesophageal junction cancer, 1), median age 56 years, median of 6 prior therapies (including letrozole [9] or other aromatase inhibitor [8]; everolimus [3]; trastuzumab [14] or other HER2 targeted therapy [1]) were enrolled in the planned 6 dose levels. The MTD has not been reached and grade 3 (G3) mucositis at the dose level 4 was the only DLT. Other G3 or G4 drug-related toxicities included G4 hyperglycemia in 1 patient, G3 hyperglycemia in 3 patients, G3 thrombocytopenia in 1 patient, G3 anemia in 1 patient and G3 headache in 1 patient. Of 18 patients, 3 (17%) had a partial response (all with heavily-pretreated breast cancer with HER2 amplification [2] or HER2A775_G776insYVMA mutation [1]), 11 (61%) stable disease (SD) including 7 (39%) patients with SD > 6 months (all with heavily-pretreated breast cancer), 3 (17%) progressed and 1 had pending evaluation. The median change in size of target lesions per RECIST 1.1. was -11% (-68% to +47%). Median progression-free survival was 9 months (95% CI 5.8-12.2). Conclusions: The combination of letrozole, everolimus and trastuzumab is well tolerated with encouraging activity in heavily-pretreated patients with HER2-amplified or mutant advanced breast cancer. Clinical trial information: NCT02152943.