bluuebunny/crossref_metadata_2025 huggingface dataset:
Adjuvant radiation therapy to induce a transitory adaptive up-regulation of programmed death ligand 1 (PD-L1) on circulating epithelial tumor cells (CETCs) to affect the anti-tumor immune response in primary breast cancer patients.
Authors: Schott Dorothea , Pizon Monika , Pachmann Katharina , Pachmann Ulrich A. , Maeurer Matthias
Published: September 2018

11558

Background: Radiation therapy (RT) is an integral part of the treatment of breast carcinoma but unfortunately many patients experience local recurrence. During the inflammatory response that accompanies radiation tumor cells may develop multiple resistance mechanisms for example the up-regulation of PD-L1 on tumor cells which leads to immune evasion. Since CETCs arise from the tumor it is conceivable that under evolutionary pressure they might share some of the immune escape mechanism inherent to tumor cells. In this study we demonstrate that RT leads to a transitory adaptive up-regulation of PD-L1 expression on CETCs. Methods: CETCs and the expression of PD-L1 and Ki-67 were analyzed from 25 patients with primary non-metastatic breast cancer using the maintrac method. The fraction of PD-L1 and Ki-67 positive CETCs were assessed at baseline, 3 and 6 weeks after start of RT and 6 weeks after end of therapy. Additionally, copy number status of PD-L1 was determined using FISH. Results: Fractionated-dose RT leads to a significant increase in PD-L1 expression on CETCs with the highest expression level midterm of irradiation as compared to baseline (49% vs. 74%, p < 0.01). 6 weeks after end of RT the number of PD-L1 positive CETCs returned to baseline value. The up-regulation of PD-L1 was dose dependent. Patients who received higher total dose had significantly more PD-L1 positive CETCs as compared to patients treated with lower total dose midterm of RT (64% vs. 43, p < 0.05). Before start of therapy there was a correlation between the fraction of PD-L1 and Ki-67 positive CETCs (r = 0.6, p < 0.01). PD-L1 copy number gains were significantly associated with PD-L1 expression (r = 0.6, P < 0.05). Conclusions: RTleads to an up-regulation of PD-L1 expression on CETCs, which could be a possible mechanism of acquired radioresistance. Combining immunomodulatory agents with radiation might have the potential to overcome this resistance and could improve clinical outcome in breast cancer.
Genetic variants in CCL5 and CCR5 genes and serum VEGF-A levels to predict efficacy of bevacizumab in metastatic colorectal cancer patients receiving first-line chemotherapy.
Authors: Suenaga Mitsukuni , Cao Shu , Zhang Wu , Ning Yan , Okazaki Satoshi , Berger Martin D. , Miyamoto Yuji , Schirripa Marta , Gopez Roel , Melendez Elizabeth , Soni Shivani , Barzi Afsaneh , Yamaguchi Toshiharu , Lenz Heinz-Josef
Published: September 2018

11564

Background: Early VEGF-A reduction by targeting abundant VEGF-A is a potential predictive marker of bevacizumab (BV). CCL5/CCR5 axis modulates VEGF-A production via endothelial progenitor cells migration. We tested whether genetic polymorphisms in CCL5/CCR5 pathway will predict outcomes in metastatic colorectal cancer (mCRC) patients (pts) receiving BV in first-line setting. Methods: Genomic DNA was extracted from 215 samples of three independent cohorts: 61 pts receiving FOLFOX+BV (median age 60 yrs, median follow-up 39.2 mos); 83 pts receiving FOLFOX (median age 61 yrs, median follow-up 57.6 mos); 71 pts receiving FOLFOX/XELOX+BV as exploratory for serum biochemistry assay (median age 60 yrs, median follow-up 28.9 mos). Single nucleotide polymorphisms of genes in CCL5/CCR5 pathway were analyzed by PCR-based direct sequencing. Serum VEGF-A levels at baseline and day 14 were measured using ELISA. Results: In univariate analysis for the FOLFOX cohort, pts with the CCL5 rs2280789 G/G variant or any CCR5 rs1799988 T allele had shorter overall survival (OS) compared to the those with any A allele or the C/C variant (18.7 vs. 29.4 mos, HR 1.93, 95%CI: 1.05−3.53 P= 0.025; 22.0 vs. 31.2 mos, HR 1.74, 95%CI: 0.98-3.90, P= 0.055). The trend remained in multivariable analysis ( P= 0.090 and P= 0.026). The differences were not confirmed in the FOLFOX+BV cohort. Pts with any CCL5 rs2280789 G allele had longer progression-free survival (PFS) and OS when receiving FOLFOX+BV than FOLFOX (PFS: 19.8 vs. 11.0 mos, HR: 0.44, 95%CI: 0.25-0.78, P= 0.002; OS: 41.8 vs. 21.1 mos, HR: 0.43, 95%CI: 0.24-0.77, P= 0.002); pts carrying any CCR5 rs1799988 T allele had longer PFS and OS ( P= 0.025 and P= 0.008, respectively). No significant difference was shown in pts with either A/A or C/C variant. In the exploratory cohort, any CCL5 rs2280789 G allele was associated with higher VEGF-A levels at baseline and greater decrease of VEGF-A levels at day 14 compared with the A/A variant. Conclusions: CCL5 and CCR5 impact the angiogenic environment. Our data suggest the genotypes may identify specific populations who benefit from BV-based chemotherapy in first-line treatment for mCRC.
Computer extracted measurements of vessel tortuosity on baseline CT scans to predict response to nivolumab immunotherapy for non-small cell lung cancer.
Authors: Khunger Monica , Alilou Mehdi , Thawani Rajat , Madabhushi Anant , Velcheti Vamsidhar
Published: September 2018

11566

Background: Immune-checkpoint blockade treatments, particularly drugs targeting the programmed death-1 (PD-1) receptor, demonstrate promising clinical efficacy in patients with non-small cell lung cancer (NSCLC). We sought to evaluate whether computer extracted measurements of tortuosity of vessels in lung nodules on baseline CT scans in NSCLC patients(pts) treated with a PD-1 inhibitor, nivolumab could distinguish responders and non-responders. Methods: A total of 61 NSCLC pts who underwent treatment with nivolumab were included in this study. Pts who did not receive nivolumab after 2 cycles due to lack of response or progression per RECIST were classified as ‘non-responders’, patients who had radiological response per RECIST or had clinical benefit (defined as stable disease >10 cycles) were classified as ‘responders’. A total of 35 quantitative tortuosity features of the vessels associated with lung nodule were investigated. In the training cohort (N=33), the features were ranked in their ability to identify responders to nivolumab using a support vector machine (SVM) classifier. The three most informative features were then used for training the SVM, which was then validated on a cohort of N=28 pts. Results: The maximum curvature ( f1), standard deviation of the torsion ( f2) and mean curvature ( f3) were identified as the most discriminating features. The area under Receiver operating characteristic (ROC) curve (AUC) of the SVM was 0.84 for the training and 0.72 for the validation cohort. Conclusions: Vessel tortuosity features were able to distinguish responders from non-responders for patients with NSCLC treated with nivolumab. Large scale multi-site validation will need to be done to establish vessel tortuosity as a predictive biomarker for immunotherapy. [Table: see text]
Pathogenic variants in DNA damage response (DDR) genes in patients with advanced solid tumors.
Authors: Ileana Dumbrava Ecaterina Elena , Brusco Lauren , Daniels Molly S , Wathoo Chetna , Shaw Kenna Rael , Lu Karen H. , Zheng Xiaofeng , Strong Louise C. , Litton Jennifer Keating , Arun Banu , Eterovic Agda Karina , Piha-Paul Sarina Anne , Subbiah Vivek , Hong David S. , Woodman Scott Eric , Mendelsohn John , Yap Timothy Anthony , Mills Gordon B. , Chen Ken , Meric-Bernstam Funda
Published: September 2018

11567

Background: Deleterious mutations in DDR genes are frequently associated with response to poly(ADP-ribose) polymerase (PARP) inhibitors and platinum chemotherapy. However, much remains unknown about their association with specific molecular signaling pathways. We report the prevalence of pathogenic variants in DDR genes and their co-alteration with other somatic variants. Methods: Targeted exome sequencing of 201 genes was performed in 1,189 patients (pts) with advanced solid tumors enrolled in a molecular testing protocol (NCT01772771), using matched normal and tumor DNA. We assessed germline and somatic alterations in 15 cancer-related DDR genes, their co-occuring genomic alterations and the tumor mutation burden (TMB), defined as number of somatic non-synonymous mutations. Results: A total of 124 pathogenic or likely pathogenic variants in DDR genes were identified in 111/1189 (9%) pts with 57% of these alterations being somatic. These variants were found in the following genes: ATM 17 pts (1.4%); BAP1 5 pts (0.4%); BRCA1 18 pts (1.5%); BRCA2 17pts (1.4%); CHEK1 8 pts (0.7%); CHEK2 16 pts (1.3%); ERCC3 4 pts (0.3%); ERCC4 2 pts (0.2%); ERCC5 3 pts (0.2%); MLH1 4pts (0.3%); MSH2 8 pts (0.7%); MSH6 6 pts (0.5%); PALB2 3 pts (0.2%) and RAD51 1pt (0.1%). DDR alterations were found more frequently in the following tumor types tested: breast 14%, colorectal 12%, melanoma 8%, glioblastoma 6% and ovarian 6%. The most relevant somatic co-alterations with DDR mutations were activation of the PI3K/AKT/mTOR pathway through mutations or copy-number variations in AKT1, MTOR, NF1, PIK3CA, PIK3R1, PTEN, TSC1 and TSC2 (p = 0.008). Patients with deleterious variants in mismatch excision repair genes (MLH1, MSH2 or MSH6) had a significantly higher TMB than all other patients enrolled (median TMB = 62 vs 5, p = 0.002). Patients with somatic pathogenic DDR variants had a significantly higher TMB (median = 13) compared to patients with germline DDR variants (median = 5) (p = 0.004). Conclusions: The association of DNA repair mutations with alterations in signaling pathways provide rationale for novel therapeutic combinations. Variations in TMB based on distinct types of DDR gene alterations may have implications for immunotherapy.
Molecular profiling comparison of breast cancer subtypes in young women and older women.
Authors: Tan Antoinette R. , Feldman Rebecca , Symanowski James Thomas , Fisher Julie Gottlieb , Hadzikadic-Gusic Lejla , White Richard L. , Kim Edward S.
Published: September 2018

11581

Background: Young women with breast cancer (YWBC; ≤40 years) have a more aggressive clinical course and is associated with a poorer prognosis. In this analysis, we explore molecular features in tumors of YWBC and older women with breast cancer (OWBC; ≥65 years) by subtype. Methods: Somatic genomic profiles of 1879 breast tumors collected from 2013-2017 were assessed retrospectively and included in a de-identified data analysis if ER, PR and HER2 (immunohistochemistry [IHC] and/or in situ hybridization [ISH]) were available. Testing included IHC, ISH and massively parallel sequencing assays (next-generation sequencing [NGS]) at a CLIA-certified laboratory (Caris Life Sciences, Phoenix, AZ). Pearson’s chi-square was utilized for comparisons and significance defined as p < 0.05. Results: Frequency of subtypes in YWBC (n = 536) and OWBC (n = 1343) were 45% and 55% HR+HER2-, 38% and 36% triple-negative (TN), 7% and 5% HER2+HR-, and 10% and 4% in HER2+HR+, respectively. Specimens tested were breast (53%, 43%) and a metastatic site (43%, 57%) in YWBC and OWBC, respectively. HR+HER2- YWBC exhibited higher rates of pathogenic mutations in TP53 (34%, 24.4%; n = 748; p = 0.008), BRCA1 (9%, 4.5%; n = 503; p = 0.047), BRCA2 (14.8%, 8.4%; n = 501; p = 0.032), gene amplifications in FGF3 (26.7%, 10.4%; n = 107; p = 0.034), FGF4 (26.7%, 9.1%; n = 107; p = 0.019), FGF19 (29.6%, 11.6%; n = 96; p = 0.033), CCND1 (36.7%, 18.2%; n = 107; p = 0.042), and overexpression of EGFR (18.6%, 8%; n = 364; p = 0.004). TN YWBC had higher rates of alterations in TP53 (80.2%, 67.4%; n = 577; p = 0.002) and BRCA1 (13.3%, 5.9%, n = 375; p = 0.015). YWBC that was HER2+HR+ exhibited a higher rate of APC mutations (10%, 0%; n = 84; p = 0.03). In OWBC, there were higher rates of PD-L1 expression in HER2+HR- (22.7%, 0%; n = 70; p = 0.009) and TN (13%, 6.3%; n = 458; p = 0.035). There were also higher PIK3CA mutations in HER2+HR+ (43.4%, 18.8%; n = 101; p = 0.008) and CDH1 mutations (12.8%, 0%; n = 85; p = 0.022) in TN. Conclusions: There were distinct molecular aberrations and significantly different frequency of alterations in subtypes of YWBC compared to OWBC. These molecular changes may contribute to increased understanding of breast cancer tumor biology and refinement of treatment strategies in YWBC and OWBC.
Alterations in the Β-catenin pathway in non-small cell lung cancer to define a distinct molecular subtype with prognostic and therapeutic implications.
Authors: Bhattacharya Saveri , Somasundaram Aswin , Ding Fei , Gaither-Davis Autumn , Pennathur Arjun , LaFramboise William A , Dacic Sanja , Kurland Brenda F , Stabile Laura P. , Burns Timothy Francis
Published: September 2018

11584

Background: The treatment of non-small cell lung cancer (NSCLC) has been revolutionized by the development of targeted therapy for distinct molecular subsets. Activation of the β-catenin pathway is essential for colorectal carcinoma tumorigenesis and has been implicated in hepatocellular, thyroid and ovarian cancer. The β-catenin pathway is involved in the cell adhesion complex and Wnt signaling. While mutations in this pathway have been reported in NSCLC and β-catenin overexpression correlates with worse survival, its role in lung tumorigenesis is poorly understood. Methods: We performed targeted next generation sequencing using the Ion Torrent Hotspot Cancer Panel v.2 on tumor tissue from 244 NSCLC patients in which we have defined key demographic and clinical parameters including stage and survival. This cohort contained 91 Stage I cases with mRNA expression data using an Illumina platform. Co-occurrence of genes in the β-catenin pathway and 27 other genes in the panel were assessed by Fisher’s exact test, with Benjamini-Hochberg adjustment for multiple comparisons. Results: Seventeen of 244 tumors had mutations in the β-catenin pathway (APC, CTNNB1, and NOTCH1): 10/170 non-squamous NSCLC (6%, 95% CI 3%-10%), and 7/70 squamous NSCLC (10%, 95% CI 5%-19%). The rate of EGFR and RB1 mutations was higher in tumors with b-catenin pathway mutation (5/17 and 2/17) than in those without (13/227 and 0/227, adjusted p = 0.06 for both). The presence of an APC mutation was also associated with higher mRNA expression of the pro-survival protein, BCL2 (n = 91; 5/41 vs. 0/50, unadjusted p = 0.022, adjusted p = 0.3). Furthermore, APC mutations were more frequently observed in tumors with higher levels of EMT markers (high VIM 8% vs. low VIM 0%, unadjusted p = 0.16) and EMT transcription factors (10% vs. low expression 2%, unadjusted p = 0.16). Finally, we observed a trend toward worse overall survival in non-squamous tumors with mutations in the β-catenin pathway (n = 170, log rank test p = 0.07). Conclusions: These studies suggest that tumors with b-catenin pathway alterations are defined by a more mesenchymal and potentially drug resistant subtype which portends a poor prognosis.
Induction of a BRCAness state by oncometabolites and exploitation by PARP inhibitors.
Authors: Bindra Ranjit , Sulkowski Parker L , Corso Christopher D. , Glazer Peter , Shuch Brian M.
Published: September 2018

11586

Background: 2-Hydroxyglutarate (2HG) exists as two enantiomers, R-2HG and S-2HG, and both are implicated in tumor progression via their inhibitory effects on α-ketoglutarate (aKG)-dependent dioxygenases. The former is an oncometabolite induced by isocitrate dehydrogenase-1 and -2 (IDH1/2) mutations, while the latter is produced under pathologic processes such as hypoxia. Recurring IDH1/2 mutations were first identified in gliomas and acute myeloid leukemia (AML). Methods: Our group recently reported that IDH1/2 mutations induce a homologous recombination (HR) defect which renders tumor cells exquisitely sensitive to Poly (ADP-Ribose) polymerase (PARP) inhibitors. Remarkably, this “BRCAness” phenotype can be completely reversed by mutant IDH1/2 inhibitors, and it can be entirely recapitulated by treatment with either 2HG enantiomer in cells with intact IDH1/2. We performed a comprehensive series of studies that directly implicate two aKG-dependent dioxygenases, KDM4A and KDM4B, as key mediators of the observed phenotype. Results: Using the methodology and preliminary data obtained above as a basis for further inquiry, here we have extended these findings to several related gene mutations, which similarly induce profound synthetic lethality with PARP inhibitors in these tumors, and our data suggest a similar mechanism of action via which HR is suppressed. Finally, we provide additional evidence that suppression of 2HG production with small molecule inhibitors of mutant IDH1/2 function does not lead to any detectable decreases in cell growth or viability in several unique models. Conclusions: Small molecule inhibition of oncogenic kinases is a pillar of precision medicine in modern oncology, and this approach has been extrapolated to treat IDH1/2-mutant and other oncometabolite-producing cancers with inhibitors blocking the neomorphic activity of the mutant proteins. The findings present here directly challenge this therapeutic strategy, and they instead provide a novel approach to treat these tumors with DNA repair inhibitors. Based on these findings, we are planning a multi-center Phase II trial testing the efficacy of olaparib for the treatment of recurrent IDH1/2-mutant tumors later this year.
Phosphopeptide mapping of DLC1 in ER+ breast cancer reveals AMOTL2, a key hippo pathway component, as an important target.
Authors: Gokmen-Polar Yesim , True Jason D , Vieth Edyta , Qi Guihong D , Mosley Amber L , Badve Sunil S.
Published: September 2018

11592

Background: Metastases suppressor genes are believed to control tumor progression and metastases. Deleted in Liver Cancer 1 (DLC1) acts as a gatekeeper for tumor and metastasis suppression. Low expression of DLC1 correlates with poor prognosis in patients with ER+ breast cancer. It is essential to understand the impact of DLC1 and its functional network in preventing tumor and metastasis suppression. Methods: T47D cells with stable DLC1-Full-Length (DLC1-FL) were generated using mammalian expression cloning vector, pcDNA3.1+/C-(K)-DYK, and CloneEZ™ technology. Growth rate of control and DLC1-FL knock-in cells was assessed for 2 weeks using clonogenic assay. Proteomic and phosphopeptide enrichment assays (Pierce TiO2 enrichment kit) were performed in triplicates to examine the basis of altered growth phenotype. The PeakJuggler node in Proteome Discoverer was utilized for label-free quantitation of both protein and peptide MS peak areas. In addition, GO term enrichment analysis was performed in DAVID for the significantly changed phosphopeptides. Results: Stable knock-in of T47D-DLC1-FL inhibits cell growth significantly in vitro compared to T47D-control in clonogenic assay. The phosphopeptide enrichment proteomic analyses showed 199 phosphopeptides were identified only in T47D-DLC1-FL and 182 peptides were identified only in T47D-control cells. Pathway analysis using DAVID showed 3 main clusters of significantly differently identified phosphopeptides (p-values ≤ 0.01) involving cadherin binding (p = 4.9e-12), cell-cell adherens junction (p = 3.9e-10), and cell-cell adhesion (p = 9.4e-7). Analysis of specific phosphopeptides showed canonical pathways such as CTNNB1 (Thr552), and BCL2L13 (370-385). More importantly, phosphorylation of HIPPO-pathway component AMOTL2 at S766, critical for promoting YAP signaling and invasion was only identified in T47D-control but not T47D-DLC1-FL (p = 5.78e-5). Conclusions: This data suggest that the absence of DLC1 promotes phosphorylation of AMOTL2, and thereby activating YAP-TAZ signaling leading to invasiveness. This data provides mechanistic basis for targeting this pathway to prevent recurrence in ER+ breast cancer.
Programmed cell death ligands expression in pheochromocytomas (PCC) and paragangliomas (PGL): Relationship with the hypoxic response and malignant behaviour.
Authors: Pinato David James , Black James M , Trousil Sebastian , Dina Roberto , Trivedi Pritesh , Mauri Francesco A , Sharma Rohini
Published: September 2018

11597

Background: The hypoxic response underlies the pathogenesis and malignant behaviour of PCC/PGL. Regulation of PD-1 receptor-ligand signalling, a therapeutically actionable driver of the anti-tumour immune response, is a hypoxic-driven trait across malignancies. We evaluated the prognostic role of PD ligands in association with biomarkers of hypoxia and angiogenesis in patients with PCC/PGL. Methods: Tissue microarrays sections including consecutive cases of PCC/PGL diagnosed between 1983-2011 were stained for PD-L1 & 2, Ki-67, hypoxia inducible factor 1a (Hif-1a), Carbonic Anhydrase IX (CaIX), Vascular Endothelial Growth Factor-A (VEGF-A). Candidate biomarkers were assessed for correlation with clinical variables including overall survival. Results: In total, 100 patients, 10% malignant, 64% PCC, 29% familial with a median tumour size of 4.7 cm (range 1-14) were included. Median follow-up was 4.7 years. PD-L1 expression was observed in 18% of cases and was independent of adverse pathological features including capsular (CI), vascular invasion (VI), necrosis (N) and expression of biomarkers of hypoxia. We observed a trend towards association with malignancy (p = 0.08). PD-L2 expression was found in 16% of tumors. PD-L2 overexpression strongly correlated with CI, VI, N (p < 0.01) and malignant behaviour (p = 0.009) and was associated with stronger Hif-1a and CaIX immunolabeling (p < 0.01). PD-L2 but not PD-L1 expression was predictive of shorter survival (162 versus 309 months, HR 3.1 95%CI 1.1-9.2, Log-rank p = 0.03). Gene set enrichment analysis on the TGCA PCC/PGL RNA-seq dataset (n = 184) revealed a positive correlation between PD-L2 and a number of transcripts involved in angiogenesis and immunity including Interleukin-6 (Pearson R = 0.57) and CD-8a (R = 0.56). Conclusions: We report for the first time PD-1 ligands expression in PCC/PGL with a distinctive prognostic and clinicopathologic role. These findings support a potential therapeutic role for PD-1/PD-L1 targeted checkpoint inhibitors in these tumors.
Selecting patients with metastatic colorectal cancer for treatment with temozolomide using proteomic analysis of MGMT.
Authors: Schwartz Sarit , Cecchi Fabiola , Tian Yuan , Scott Kerry , Di Bartolomeo Maria , Morano Federica , Fucà Giovanni , Martinetti Antonia , De Braud Filippo G. , Dominoni Francesca , Milione Massimo , Calegari Maria Alessandra , Orlandi Armando , Barone Carlo , Pietrantonio Filippo , Hembrough Todd A.
Published: September 2018

11601

Background: Temozolomide (TMZ) is a standard treatment for melanoma and glioblastoma and it has shown limited but encouraging activity in patients with metastatic colorectal cancer (mCRC). In multiple cancer types, the DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) is a resistance marker for TMZ; MGMT promoter methylation is associated with loss of MGMT expression and response to TMZ. We hypothesized that mCRC patients whose tumors expressed quantities of MGMT protein below a pre-defined cutoff would have better outcomes on TMZ than patients with MGMT expression above the cutoff. To test our hypothesis, we assessed MGMT by mass spectrometry in the tumor samples of patients with refractory mCRC and MGMT promoter methylation receiving TMZ. Methods: Archived formalin-fixed, paraffin-embedded tissue sections were obtained from 24 patients from two phase 2 trials. A pathologist marked the tumor areas, which were microdissected and solubilized. In each tumor sample, multiple protein biomarkers including MGMT were quantified with selected reaction monitoring mass spectrometry. An MGMT cutoff of 200 amol/ug was based on the limit of quantitation from a concentration curve. The Mantel-Cox log-rank and the Fisher’s exact tests were used for survival comparisons. Results: MGMT protein was detected in 13 of 24 (54.2%) colorectal tumor samples (range: 229.3-784.8 amol/µg). The overall response rate was 29%. Patients with MGMT protein levels below a cutoff of 200 amol/ug (n = 11) had a notably higher response rate than patients with MGMT levels above the cutoff (64% vs. 0%; p = 0.001 Fisher’s test). Also a longer progression-free survival was observed (4.3 vs. 1.6 months, HR = 0.36, 95% CI = 0.13-1.10, p = 0.054). Results for overall survival were consistent but not statistically significant (8.9 vs 6.9 months, HR = 0.55, p = 0.221). Conclusions: Patients with mCRC whose tumors expressed low or undetectable levels of MGMT protein had a better outcomes following TMZ treatment than their counterparts. Quantitative proteomic analysis of MGMT could potentially be used to select CRC patients for TMZ treatment. The results of validation studies are forthcoming.
Preliminary correlative analysis of PD-L1 expression from the SUNRISE study.
Authors: Kallinteris Nikoletta Lea , Sanborn Rachel E. , Horn Leora , Gerber David E. , Natale Ronald B. , Tang Min , Downing Sean , Clement Amanda , Guennel Tobias , Shan Joseph , Hoyt Cliff
Published: September 2018

11603

Background: SUNRISE, a global, double-bind, Phase III trial of docetaxel (D) plus bavituximab (B) or D plus placebo (P) in previously treated non-squamous non-small cell lung cancer, demonstrated similar overall survival (OS) in both treatment arms. Biomarkers including pre-treatment PD-L1 expression are being retrospectively assessed in on-going exploratory analyses. Methods: Archival tissue obtained at the time of diagnosis was requested but not required in the SUNRISE trial. FFPE slides were stained with a panel of lymphoid cell markers: CD3+, CD8+, FoxP3+, PD-L1+, CD163+, CK+ and DAPI using a 6-plex quantitative immunohistochemistry (IHC) assay (OPAL, PerkinElmer, Hopkinton, MA, USA). Baseline PD-L1 expression was retrospectively scored on tumor cells (TC) as a percentage of PD-L1 expressing tumor cells: TC3≥50%, TC2≥5% and < 50%, TC1≥1% and < 5%, and TC0 < 1%. Cox regression models for PD-L1 IHC subgroup populations were used for correlation with OS. Results: In the subset of patients with available diagnostic biopsies (110 out of 597 randomized patients), the prevalence of PD-L1 expression was 5% for TC3, 18% for TC2/3, 35% for TC1/2/3, 65% for TC0. Median OS (mOS) of the D+B arm is 11.5 months (TC0, < 1%) and 6.0 months (TC1/2/3, ≥1%) with HR 0.38 (95% CI, 0.19-0.76); p-value = 0.004. mOS of the D+P arm is 11.1 months (TC0, < 1%) and 10.4 months (TC1/2/3, ≥1%) with HR 0.93 (95% CI, 0.47-1.87); p value = 0.844. Conclusions: Baseline PD-L1 expression in a subset of SUNRISE patients demonstrated that PD-L1 expression (TC0) was associated with a significantly prolonged OS compared to positive PD-L1 expression (TC1/2/3) in patients receiving D+B. No difference in OS was observed in the D+P group by PD-L1 expression. These observations are consistent with the hypothesis that bavituximab may demonstrate more effect in PD-L1 negative or low expressing “immune cold” tumors. Clinical trial information: NCT01999673.
Comprehensive analysis of potential immunotherapy genomic biomarkers by profiling paired tumor/normal exome of 1,000 Chinese cancer patients.
Authors: Xu Qiang , Wang Guan , Dai Chun , Xu Xiaoman , Wei Jinwang , Xu Jiayue , Wu Angela , Wang Jiping
Published: September 2018

11605

Background: With the broadening landscape of immunotherapy use, it is important to identify patients who are likely to benefit from the therapy. We reported the comprehensive analyses of potential predictive biomarkers for PD1/PD-L1 inhibitors based on Chinese patients’ exome profiling data. Methods: Over 1,000 cancer patients from 70 hospitals across 20 provinces in China were recruited and the whole exome of tumor/normal samples of each patient were sequenced. Four potential genomic biomarkers: tumor mutation burden (TMB), mismatch repair deficiency (MMR), microsatellite instability (MSI), and PD-L1 (CD274) amplification (PD-L1 AMP) were analyzed in this Chinese cohort and compared with the mainly Caucasian cohort in TCGA database. Results: At least one of the four preselected genomic biomarkers was identified in 40.8% of this Chinese cancer patient cohort by clinical whole exome sequencing (CWES) analysis. Similar to TCGA cohort, the top 3 high TMB tumor types are lung, esophagus and colorectal cancer. Chinese hepatocellular carcinoma (HCC) patients showed higher TMB than the TCGA cohort (Median: 106 vs. 65 non-synonymous mutations per tumor NMT), which might be due to different etiologies. Five late stage cancer patients (3 lung, 1 melanoma and 1 gallbladder) using PD1/PD-L1 blockade with high TMB showed durable clinical benefit (SD≥6months/PR/CR). Comparing with TCGA data, Chinese colorectal cancer cohort (252 patients) had relative lower MSI-high or MMR related mutations (8.33% vs. 12.5%, and 3.97% vs. 10.0% respectively). PD-L1 AMP most frequently occurred in lung squamous (14.3% VS 9.8% TCGA), HER2-positive breast cancer (8.8% VS 6.8% TCGA with unknown HER2 status) and sarcoma (6.0% VS 9.4%TCGA). One Chinese renal cell carcinoma patient with PD-L1 AMP received anti-PD-1 treatment and on-going PFS is 7 months by far. Conclusions: Our CWES analysis and limited clinical follow-up observations suggested that about 40% Chinese cancer patients had at least one of the 4 potential immunotherapy predictive biomarker mutations. Long-term follow-up is needed to verify the validity of those markers.
Case-control study of PD-1, PD-L1 and B7-H3 expression in lung cancer (CA) patients (pts) with and without human immunodeficiency virus (HIV) infection.
Authors: Scilla Katherine Ann , Zandberg Dan Paul , Bentzen Soren , Heath Jonathon , Ioffe Olga B. , Cellini Ashley L , Mainor Candace Barette , Edelman Martin J. , Riedel David , Feliciano Josephine Louella
Published: September 2018

11606

Background: PD-1, PD-L1 and B7-H3 are co-signaling molecules involved in CA immunology. There are limited data on expression of these molecules in HIV-infected (HIV+) lung CA pts and these pts are routinely excluded from immunotherapy trials. Methods: We reviewed archived lung CA tissue samples from HIV+ cases (n = 13) and HIV-uninfected controls (n = 13) from 2001-2015. Cases and controls were matched by histology and stage. Baseline demographics were collected for all pts. CD4 count and HIV RNA viral load (VL) were collected for HIV+ pts. Immunostained tumor sections were analyzed for percent of tumor cells expressing PD-L1 and B7-H3 (Abcam), and percent of tumor-infiltrating lymphocytes (TIL) expressing PD-1 and PD-L1 (Abcam). Positive expression was defined as > 5%. Statistical analysis was performed using the non-parametric Mann-Whitney test and the chi-square test. Proportions are specified as percentage with 95% confidence limits in parentheses. Results: Lung CA HIV+ case pts were predominantly male (62%), black race (100%), adenocarcinoma histology (77%), stage 4 disease (62%), and had a median age of 48 years. Of case pts with available data, mean CD4 count was 307 (range 37-617) and mean HIV VL was 29,400 (range 0-100,000). PD-L1 expression on tumor cells was positive in 23% (8%, 50%) of cases and 46% (23%, 71%) of controls. B7-H3 expression on tumor cells was positive in 92% (67%, 99%) of cases and 69% (42%, 87%) of controls. PD-1 expression on TIL was positive in 69% (42%, 87%) of cases and 54% (29%, 77%) of controls. PD-L1 expression on TIL was positive in 31% (13%, 58%) of cases and 69% (42%, 87%) of controls (p = 0.05). B7-H3 percent expression on tumor cells was significantly higher in cases vs controls (median 90% vs 20%, p = 0.005), but there were no significant differences in percent expression of PD-L1 on tumor cells, PD-1 on TIL or PD-L1 on TIL. Conclusions: HIV+ lung CA pts had significantly higher B7-H3 tumor percent expression compared to HIV-uninfected controls, with similar rates of PD-L1 tumor percent expression, PD-1 TIL percent expression and PD-L1 TIL percent expression. These results support inclusion of HIV+ lung CA pts in future immunotherapy trials.
Development of a pan-cancer 15 gene expression signature to detect a subgroup driven by EMT/MAPK signalling.
Authors: McCabe Nuala , Knight Laura A , Price Bethanie , McCavigan Andrena , El-Helali Aya , Harkin Denis P , Gourley Charlie , Kennedy Richard D.
Published: September 2018

11616

Background: Epithelial–mesenchymal transition (EMT) is the conversion of epithelial cells to mesenchymal cells and involves loss of cell–cell adhesion and cell polarity and increased motility, invasiveness and metastases. The EMT process has therefore been under investigation as a new target for anticancer drug discovery. The aim of this work was to develop an EMT biomarker suitable for formalin-fixed paraffin embedded (FFPE) tissue that could be used for patient treatment selection. Methods: Unsupervised hierarchical clustering of ovarian cancer gene expression data (TCGA. 2011) previously identified an EMT subgroup. We confirmed this EMT subgroup in FFPE tissue using 265 high grade serous ovarian cancer (HGSOC) FFPE samples. The analysis was extended to show existence of an EMT subgroup across a range of solid tumours including colon, lung, melanoma and prostate cancer. Further to this, a common gene list was generated to include only transcripts with high variability and expression across diseases, and used as a starting list for development of a 15 transcript assay which can be used to prospectively identify the EMT subgroup from archived tissue. Results: The 15 gene expression assay was a poor prognostic marker in Colorectal, (Relapse free survival: HR = 1.46 [95% CI:1.07-1.98]); Lung, (Relapse free survival: HR = 2.18 [95% CI:1.33-3.56]); Prostate cancer, (Biochemical recurrence: HR 2.49 CI: 1.43-4.34) and was associated with activated MAPK (phospho-MAPK) in preclinical models and clinical samples (p < 0.05). The assay score was reduced by MEK inhibition (p < 0.05) and elevated by KRAS, NRAS and MEK1 overexpression (p < 0.05). The assay predicted response to the MEK inhibitors Trametinib and Selumetinib in cell line models (p < 0.001). Conclusions: A 15 gene expression assay has been developed from FFPE samples across multiple diseases to detect an EMT molecular subgroup associated with MAPK signalling. The assay predicted sensitivity to MEK inhibitors in pre-clinical model systems. Further work aims to validate the assay as a predictive biomarker in clinical samples from patients treated with EMT or MEK targeted therapies.
Parallel VENTANA IHC and RT-PCR of ALK status in non-small cell lung cancer and response to crizotinib.
Authors: Xu Chunwei , Wang Wen-xian , Fang Meiyu , Chen Yan-ping , Chen Yu , Zhong Li-hua , Chen Fang-fang , Zhuang Wu , Lin Gen , Chen Xiao-hui , Xu Hai-peng , Huang Yun-jian , Guan Yan-Fang , Yi Xin , Lv Tangfeng , Wang Xiao-jiang , Shi Yi , Lin Xian-dong , Chen Gang , Song Yong
Published: September 2018

11623

Background: Advanced NSCLC patients who harbor (ALK) rearrangement were sensitive to crizotinib. However, not all ALK-positive patients benefit equally from crizotinib. A method for determining ALK rearrangement is RT-PCR, the Chinese FDA has approved RT-PCR to detect ALK rearrangement. In this regard, VENTANA IHC is a standard method to identify ALK protein overexpression in NSCLC. However, up to now, it is still largely unknown about the response to crizotinib for Chinese NSCLC patients having ALK overexpress detected by VENTANA IHC. To better clarify the clinical implication of VENTANA IHC to detect ALK rearrangement, we compared the curative effect and survival by the two methods in advanced NSCLC patients and analysis VENTNA IHC and RT-PCR inconsistent cases. Methods: A total of 1720 patients with NSCLC who had their ALK rearrangement detected by IHC and/or RT-PCR were included in this analysis. And we compared the efficacy and survival of patients with ALK positive detected by IHC and RT-PCR. We used next-generation sequencing (NGS) to detect patients whom two methods were not consistent. Results: 187/1720 patients were identified as ALK-positive by IHC and/or RT-PCR and 66 patient received crizotinib. We identified 172/1674 patients had ALK positive by IHC method, 41/322 patients had ALK rearrangements by RT-PCR method. And 29/276 patients with ALK positive were simultaneously analyzed by IHC and RT-PCR. The overall response rates (ORR) were 65.90% by IHC and 55.88% by RT-PCR, respectively. And the disease control rates (DCR) were 86.36% by IHC and 76.47% by RT-PCR. The median PFS of IHC was 8.5 months and RT-PCR was 9.2 months Targeted next-generation sequencing in the special type: Among 6 cases of 17 cases ALK positive patients were inconsistent by IHC and RT-PCR performed with NGS, 4 cases were identified to have EML4-ALK fusions, and 2 cases were KCL1-ALK(ND) and FBXO36-ALK (PFS 21.2 months). Conclusions: VENTANA IHC is a reliable and rapid screening tool in routine pathologic laboratories for the identification of suitable candidates for targeted therapy. It has a moderate sensitivity and a slightly higher curative effect, and some VENTANA IHC positive but RT-PCR negative cases may benefit from crizotinib.
KRAS in non-small cell lung cancer: Single institution experience—What factors are involved?
Authors: Amanam Idoroenyi Usua , Gupta Rohan , Mambetsariev Isa , Koczywas Marianna , Cristea Mihaela C. , Massarelli Erminia , Reckamp Karen L. , Salgia Ravi
Published: September 2018

11624

Background: Disease heterogeneity with variable molecular mutations is one of the main contributory factors in non-small cell lung cancer (NSCLC). The goal of this study was to better understand the KRAS patients with co-occurring mutations. Methods: We identified 60 patients with a diagnosis of NSCLC and a KRAS mutation in the COH Cancer Registry from 2009 to 2016. Next generation sequencing was performed. Results: Of the 60 patients identified, 42 (70%) were Stage IV at diagnosis, 7 (12%) Stage I and 7 (12%) stage II and 4 (6%) Stage III. 47 (78) patients were smokers. Caucasian was the most common (n = 44, 73%) racial group, followed by Asians (n = 9, 15%), African-Americans (n = 3, 5%), other (n = 3, 5%) and Pacific Islander (n = 1, 1.7%). The average age at diagnosis was 67 (median 69.50) years; 30 patients (50%) were over 70 years, 23 (38%) patients were 51-69 years, and 7 (12%) 50 years or below. Majority of the patients had metastatic disease (n = 52, 87%) with 20% (n = 12) having brain metastasis with average metastatic sites 1.6. An average of 1.97 (range = 0-5) lines of therapy including chemotherapy, biologic agents or immunotherapy were received. 12 (20%) patients received immunotherapy, radiation in 28 (47%) and surgery in 22 (37%) with a median overall survival at 15 months. The most frequent molecular alteration was codon 12 mutation (n = 47, 78%), followed by codon 13 (n = 7, 12%) and codon 61 (n = 6, 10%) mutations. The most common co-occurring mutations in this cohort were TP53 (n = 15, 25%), ATM (n = 9, 15%), LRP1B (n = 9, 15%), ARID1A (n = 8, 13%), STK11 (n = 8, 13%), ARID1B (n = 7, 12%), TERT (n = 7, 12%), EGFR (n = 6, 10%), RBM10 (n = 6, 10%), SPTA1 (n = 6, 10%). We are currently evaluating the relevance of the Circos plot analysis for these mutations, clinical response to immunotherapy and potential biomarkers. Conclusions: KRAS mutations are among the most common molecular alterations identified in NSCLC. Effective treatments targeting KRAS mutations have represented a challenge so far. Understanding the significance of co-mutations and their therapeutic implications, especially in response to immunotherapy and other agents represents an important step to develop better treatment options for KRAS mutated lung cancers.
High risk genetic screening program in a community hospital breast imaging center.
Authors: Kushwaha Anne C. , Sweeney Lilian E , Ghosh Madhumita , Arun Banu
Published: September 2018

1507

Background: The NCCN has published guidelines for screening and testing of Hereditary Breast and Ovarian Cancer (HBOC) that is typically used by the primary physician or oncologist. Little data exists on the value of genetic screening at a major health care access point: the breast imaging center (BIC). Using BICs as potential clinics to identify high risk women could increase the number of appropriate referrals for genetic risk assessment. Therefore, at our hospital-based BIC serving mostly low to middle income patients in a major metropolitan center, we developed a practical screening tool based on the HBOC guidelines and prospectively screened women receiving screening and diagnostic mammography. Methods: A questionnaire based on the NCCN HBOC genetic referral guidelines was added to the intake forms of all patients (pts) obtaining breast imaging at our BIC from 2012 to 2015. Forms were reviewed by the radiologists and flagged if the patient met the guidelines of the tool. Identified pts were contacted by letter and/or telephone and a nurse navigator or genetic counselor verified data, and provided information about genetic counseling to the patient prior to scheduling genetic counseling appointments. Results: Almost 35, 000 pts were seen during the study period. 1214 pts (3.5%) were flagged as possibly high risk, of which 189 pts. had received prior genetic testing. Of the 1025 remaining pts identified as candidates for genetic counseling, 258 (25%) made a genetic counseling appointment and 163 (16%) received genetic counseling. 106 pts. were tested for BRCA1/2. 9 pts (8.5%) tested positive for a BRCA1/2 pathogenic mutation and 8 pts (7.5%) had a Variant of Unknown Significance. Conclusions: Screening for HBOC syndromes at the time of annual breast imaging in a community-based middle to low income metropolitan breast imaging center is practical. Our screening tool identified women with BRCA mutations who would have been otherwise missed. This will have immediate implications for the patient and their family members in regards to increased surveillance and risk reductive surgery discussions.
Multi-gene panel testing of patients with multiple primary malignancies suspected with hereditary cancer syndrome.
Authors: Chan Gloria HJ , Ong Pei Yi , Low Jeffrey JH , Kong Hwai L. , Ow Samuel Guan Wei , Tan David SP , Lim Yi Wan , Eng Lim Siew , Lee Soo Chin
Published: September 2018

1512

Background: Developing multiple primary cancers is an indicator of underlying hereditary cancer predisposition, but there is a paucity of data regarding the characteristics and clinical genetic testing outcome of these patients. Methods: We compared cancer index patients with 1 vs > 1 primary malignancy who underwent evaluation and clinical testing with multi-gene panels comprising up to 49 genes in a cancer genetics clinic in a tertiary cancer centre in Asia from 1998-2016. Results: Among 1191 cancer index patients, 960 (80.6%), 205 (17.2%), and 26 (2.2%) respectively had 1, 2, and ≥3 primary malignancies. Among patients with > 1 primary cancers (n = 231), the most common cancer pairs were breast-breast (35.4%), breast-ovary (12.1%), endometrium-ovary (8.2%), colon-colon (2.4%) and, colon-endometrium (2.4%). The mean age at diagnosis of the first, second and third cancers were 46.0 (21 to 87), 52.1 (21 to 89) and 57.7 (41 to 83) respectively. The mean duration between first and second cancers is 6.0 years (0 to 32). The most commonly suspected syndromes in patients with 1 vs > 1 primary cancer were hereditary breast and ovarian cancer 63.8% vs 53.6%, Lynch 24.8% vs 31.1%, Li-Fraumeni syndromes 1.8% vs 1.7%, and others 9.3% vs 13.4% (p = 0.03). Patients with > 1 primary cancer were more likely to have > 20% a priori risk of suspected hereditary cancer syndrome (42.8% vs. 26.5%; p < 0.001). 504/1191 (42.3%) patients underwent gene testing, including 394/960 (41.0%) and 110/231 (47.6%) patients with 1 vs > 1 cancer. Deleterious mutations were more likely to be identified in patients with > 1 vs 1 cancer (34.5% vs. 25.8%; p = 0.073), with causative genes being BRCA1 38.5%, BRCA2 17.9%, MLH1/MSH2/MSH6 20.5%, TP53 7.7%, and others (ATM [n = 2], MUTYH, APC, PALB2, RAD51 [n = 1 each]) for patients with > 1 cancer. VUS rates were 31.7% vs.31.8% in patients with 1 vs > 1 cancer, and were identified in genes including BRIP1, CHEK2, PALLD, POLE, PTEN, STK11, SMARCA4, and VHL. Conclusions: Patients with > 1 primary cancer comprised one-fifth of cancer index patients evaluated at a cancer genetics clinic, and were more likely to be found with deleterious mutations than patients with only 1 cancer on multi-gene panel testing.
Optimizing somatic genomic reporting and physician interpretation with web-based, interactive technologies.
Authors: Gray Stacy W. , Cronin Angel M. , Sholl Lynette M. , Cerami Ethan , Gagan Jeffrey , Uno Hajime , Oliver Nelly , Lowenstein Carol , Lederman Ruth , Revette Anna , Suarez Aaron , Lee Charlotte , Byran Jordan , Van Allen Eliezer Mendel
Published: September 2018

1517

Background: The increased availability of tumor genomic profiling is revolutionizing oncology. However, the promise of precision care will not be realized if providers misinterpret complex genomic data. Methods: We created web-based, interactive reports with enhanced data visualization elements and embedded decision support for > 300 gene panels. We conducted a randomized vignette-based survey study to determine whether exposure to the interactive reports, as compared to static reports, improves physicians’ genomic understanding and report-based satisfaction. Overall comprehension and satisfaction scores were calculated across three vignettes (possible range 0-18 and 1-4 respectively, higher score correspond to improved endpoints). Results: 105 physicians at a major cancer center participated (29% participation rate); 67% medical, 20% pediatric, 7% radiation and 7% surgical oncology; 37% female. Prior to viewing the case-based vignette reports, 34% of physicians reported that they found it difficult to make treatment recommendations based on the standard report in their routine practice. After viewing the case-based vignettes, physicians’ overall comprehension scores did not differ significantly by report type (mean score interactive 11.6 vs. static 10.5, difference = 1.1, 95% CI -0.3, 2.5, p = 0.13). However, physicians who viewed the interactive report were more likely to correctly assess sequencing quality (p < 0.001) and understand when reports needed to be interpreted with caution (e.g., if low tumor purity, p = 0.02). Overall satisfaction scores were significantly higher in the interactive group than the static group (mean score 2.5 vs. 2.1, difference = 0.4, 95% CI 0.2, 0.7, p = 0.001). Of the 92 physicians who endorsed the need for additional genomic support for providers, 66% reported that interactive genomic reports would be helpful. Conclusions: Interactive, genomic reports may improve physicians’ ability to accurately assess genomic data and increase physician satisfaction. To advance the field, further research in representative provider populations is warranted and efforts to integrate interactive genomic reports into electronic health records are needed.