bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiregion sequencing of penile cancer to reveal distinct patterns of heterogeneous actionable mutations.
Authors: Rodney Simon , Tanic Miljana , Barrett James , Amy Webster Philomena , de Winter Patricia , Tan Wei Shen , Khetrapal Pramit , Dong Liqin , Rezaee Sheida , Freeman Alex , Nigam Raj , Malone Peter , Muneer Asif , Beck Stephan , Feber Andrew , Kelly John D 
Published: September 2018

4518 Background: Penile cancer is a rare but mutilating disease. Due to its rarity few studies have investigated the molecular oncogenic changes. There is a huge need to improve the poor outcome of metastatic disease by advancing the standard practice of platinum based therapies. Treatment based on actionable mutations and the potential of immunotherapies may improve clinical outcomes. We present the first analysis of intra-tumour heterogeneity within penile cancer. Methods: Tissue samples, greater than 80% purity, were collected from four spatially distinct tumor regions together with matched normal and metastatic tissue. Deep whole exome sequencing was performed on the resulting 48 samples from eight patients. Mutations were called by using Mutect2 and annotated with Annovar. Copy number changes were estimated using Sequenza and phylogenetic trees created using pyclone. Results: A mean of 650 single nucleotide variants and insertion/deletion events were discovered per tumor sample. Extensive intra-tumor heterogeneity was found with a wide range of different predicted subclonal architectures. Two distinct patterns were noted: either the acquisition of mutations by the lymph node metastasis was an early event with a lower mutational load, or it was a later event with a high mutational load. In the two instances where patients were negative for human papillomavirus infection, the lymph node metastasis evolved at a later date. However in 5/6 cases of HPV infection, an early subclone developed which potentially led to the lymph node metastasis. Driver mutations in p53, cMET or FAT1 were found to be truncal early events in 80% of cases. Actionable mutations in PIK3CA and EGFR were found to be subclonal in two further samples. Conclusions: There is extensive intra- and inter-tumour heterogeneity within penile cancer. The main truncal drivers in penile cancer are cMET, FAT1 and p53. Samples infected with human papillomavirus appeared to have a distinct signature in terms of both copy number changes and clonal architecture. Actionable mutations PIK3CA and EGFR were found to be subclonal in origin. This may have profound effects on the clinical utility of targetable treatments such as tyrosine kinase inhibitors.
Phase II trial of pembrolizumab in patients (pts) with incurable platinum refractory germ cell tumors (GCT).
Authors: Adra Nabil , Althouse Sandra K. , Ammakkanavar Natraj Reddy , Radovich Milan , Albany Costantine , Vaughn David J. , Einhorn Lawrence H. , Hanna Nasser H. 
Published: September 2018

4520 Background: Despite remarkable results with salvage standard-dose (SDCT) or high-dose chemotherapy (HDCT), about 15% of pts with relapsed GCT are incurable. Immune therapy with Pembrolizumab is a novel approach for salvage in pts with metastatic GCT. Methods: Single arm phase 2 trial investigating pembrolizumab 200mg IV Q3weeks until disease progression in pts with relapsed GCT and no curable options. Pts age≥18 with metastatic GCT who progressed after first line cisplatin-based chemotherapy and after at least 1 salvage regimen (HDCT or SDCT) were eligible. Centrally assessed PD-L1 on tumor infiltrating immune cells using PD-L1 (22C3) assay was scored as 0, 1, 2, 3 along with PD-L1 expression score (H-score) incorporating intensity of staining. Pts were eligible irrespective of PD-L1 expression status. The primary endpoint was overall response rate using immune-related response criteria. Simon’s 2-stage design required response in ≥ 1/12 pts to proceed to stage 2 enrolling 8 more pts for a total of 20. Results: 12 male pts were enrolled. Median age 38 (range, 27-55). All pts had non-seminoma. Primary tumor site was testis in 11 pts and mediastinum in 1. Median AFP 615 (range, 1-32,760) and hCG 4 (range, 0.6-37,096). 5 pts had late relapse ( > 2years). Median number of previous chemotherapy regimens was 3 (range, 1-6). 6 pts received prior HDCT. 2 pts had positive PD-L1 staining (H-score 90 and 170). Median number of deliverable pembrolizumab doses was 2 (range, 1-8). There were 5 grade 3 adverse events, with 3 events possibly related to study treatment (chest pain, hyperglycemia, abdominal pain). No partial or complete responses were observed. 2 pts achieved stable disease for 12 and 9 weeks respectively; 10 pts had progression of disease as their best response. The 2 pts with stable disease had continued rising AFP level despite radiographic stability; both had negative PD-L1 staining. Conclusions: This is the first reported trial evaluating immune checkpoint inhibitors in GCT. Although 2 pts had stable disease, each had rising tumor markers suggesting continued treatment resistance. Pembrolizumab is well tolerated but does not appear to have clinically meaningful single-agent activity in refractory GCT. Clinical trial information: NCT02499952.
Molecular profiling of small cell bladder cancer (SCBC) to reveal gene expression determinants of an aggressive phenotype.
Authors: Koshkin Vadim S. , Reynolds Jordan , Elson Paul , Magi-Galluzzi Cristina , McKenney Jesse , Smith Karen Streator , Shadrach Bonnie , Isse Kumiko , Saunders Laura R. , Hu Ming , Tendulkar Rahul D. , Stephenson Andrew J. , Fergany Amr Farouk , Abazeed Mohamed , Rini Brian I. , Garcia Jorge A. , Lee Byron , Mian Omar Y , Grivas Petros 
Published: September 2018

4529 Background: SCBC is rare and its underlying biology poorly understood. Molecular profiling can shed light on the biology and identify treatment targets and biomarkers. Methods: A retrospective review of 63 patients (pts) with biopsy-confirmed SCBC at Cleveland Clinic (1994-2015) was performed. Percentage of small cell component (SC%) was defined by independent pathology review. DLL3 and PD-L1 protein expression were measured by IHC in 53 pts. Gene expression analysis was done in 38 primary SCBC tumor samples, 1 metastatic sample, and 5 normal bladder tissue samples (44 total) from the same cohort using HTG EdgeSeq OBP Assay with probes for 2568 genes. Analysis was performed via the RNAseq workflow (Partek Genomics Suite). Results: Among 63 identified pts, median age was 71 (39-90), 83% were men, median SC% was 100% (range 5-100%), median follow-up was 16.6 months and estimated median overall survival (OS) was 22.8 months. Unsupervised hierarchical clustering of gene expression patterns from 44 samples produced 4 distinct clusters. Pts with tumors in cluster 1 (that also included normal samples) did not have metastasis at diagnosis or distant recurrence, both of which were over-represented in the other 3 clusters. Kaplan-Meier analysis revealed a trend towards longer OS in cluster 1 patients (log rank p = 0.065). Higher gene expression of PRC1, NCAM1 (CD56) and DLL3 correlated with higher SC%, as did lower gene expression of ERBB2, PD-L1 and HPGD (p < 0.01). PD-L1 protein expression (≥1% cells) was noted in 30% of pts but did not correlate with outcome, SC%, DLL3 protein expression, or PD-L1 gene expression. DLL3 protein expression (≥1% cells) was noted in 68% of pts and DLL3 > 10% correlated with decreased OS (p = .03). Higher DLL3 protein expression correlated with DLL3 gene expression (Spearman r = 0.70, p < .01) and with SC% (r = .33, p = .01). Conclusions: This is the first study to reveal distinct gene expression patterns that define aggressive behavior, metastatic potential and outcomes in SCBC. The prognostic value of differential gene expression networks and the presence of underlying genomic and epigenetic alterations is the subject of ongoing prospective validation in a larger cohort.
Incidence of secondary malignancies (SM) in patients (pts) with germ cell tumors (GCT) who received high-dose chemotherapy (HDCT): A retrospective study from the European Society for Blood and Marrow Transplantation (EBMT) database.
Authors: Secondino Simona , Necchi Andrea , Rosti Giovanni , Badoglio Manuela , Raggi Daniele , Giannatempo Patrizia , Lanza Francesco , Pedrazzoli Paolo 
Published: September 2018

4549 Background: Little is still known about the incidence of SM in young adult pts with GCT after HDCT, owing to the rarity of the disease, and the need for registries with long term follow-up (FUP) data. In Europe, the EBMT may provide a suitable platform for such retrospective analyses. Methods: Criteria for patient selection included diagnosis of GCT, adult male gender, ≥2yr of FUP after the administration of HDCT. Summary statistics were used to describe pt characteristics and outcomes. χ2 tests were used to compare groups according to the length of FUP. Kaplan-Meier estimates were used to estimate overall survival (OS). Univariable Cox regression analyses examined clinical factors potentially associated with OS. Survival times were calculated from the HDCT administration date. To estimate the probability of developing SM, the cumulative incidence of SM was calculated for all pts. Results: From 1981 to 2014, 9,153 autografts, accounting for 5,100 pts, have been registered. Of them, 1,855 had ≥2yr of FUP. Among the latter, a total of 56 cases of SM were identified (3.0%). 28 (50%) had solid SM, 22 (39.3%) hematologic (hem) SM (5 had uncoded SM). Median age at first HDCT was 34 years (IQR: 30-42), median age at development of SM was 42 (37-51). 26 pts (46.4%) received single HDCT cycle, 22 (39.3%) multiple HDCT cycles (8 unknown). 31 pts had ≥5 yr FUP, 25 pts 2-5 yr FUP. The median latency of SM was 3.3yrs (IQR: 1.8-6.1) for hem SM and 5.6yrs (IQR: 1.2-10.8) for solid SM. Median FUP was 6.4yrs. Univariably, the type of SM (solid vs. hem) was significantly associated with OS. Hem vs solid SM: HR: 2.17 (95%CI: 1.19-4.97, p = 0.020). Median OS of pts who developed solid SM was 13.3yrs compared to 4.1yrs of those with hem SM. The retrospective nature of the data is the major limitation. Conclusions: In the largest European database of SM in GCT pts, we observed different trends for SM development according to the SM type. This information may be important for FUP guidelines of these pts. Dataset implementation is ongoing and we will compare the SM incidence from EBMT database with SM rates in the general EU population.
Genomic comparison of matched primary and metastatic germ cell tumors (GCT).
Authors: Audenet Francois , Donoghue Mark , Pietzak Eugene J. , Isharwal Sumit , Cheng Michael L. , Iyer Gopa , Funt Samuel , Bajorin Dean F. , Al-Ahmadie Hikmat , Reuter Victor E. , Eng Jana , Reichel Jonathan B , Arcila Maria E. , Tsui Dana , Shady Maha , Berger Michael F. , Bosl George J. , Sheinfeld Joel , Solit David B. , Feldman Darren R. 
Published: September 2018

4556 Background: Tumor genomic analysis may be useful in patients with GCT as a means of identifying potentially actionable genomic alterations or mutations such as TP53 that confer resistance to chemotherapy. As GCTs often exhibit significant morphologic heterogeneity, we evaluated the level of concordance between genomic alterations in matched primary and metastatic GCT samples. Methods: GCT patients enrolled on an institutional prospective sequencing protocol with available primary and metastatic tumor tissue were eligible. Each tumor was subjected to MSK-IMPACT, an exon capture sequencing assay, which detects copy number alterations (CNAs) and mutations in 410 cancer-related genes. For each primary-metastasis pair, concordance and clonality was assessed using the FACETS algorithm. Results: Matched primary-metastasis tumor pairs were available for 36 patients (78% nonseminoma, 22% seminoma, median age 33.5 years). All patients received chemotherapy, with 25 (69%) receiving treatment prior to analysis of the metastatic samples. The frequency of genetic alterations was low with a median of 3 mutations (1-7), 7 amplifications (1-26) and 1 deletion (1-9) detected per sample, with no significant difference in mutational/CNA burden between primaries and metastases. Of 109 unique mutations across patients, only 44 (40%) were concordant between the primary and matched metastasis, including 5 of 9 hotspot mutations. For CNAs, 184 (81%) of 226 were concordant. Only 24 of 109 (22%) mutations were clonal (defined as predicted to be present in all cancer cells) in either the primary or metastatic matched samples; of these, only 4 were clonal in both the primary and metastatic samples, including 2 hotspots. However, 4 of 5 alterations in TP53/MDM2 were shared by both the primary and metastasis pairs. In a separate exploratory cohort, 4 TP53 mutations were identified in 3 primary tumors and 1 metastasis, and all 4 mutations were also detected by cell-free DNA profiling. Conclusions: Genomic concordance, particularly for mutations, is poor between primary and metastatic GCT samples. Cell-free DNA analysis may help overcome this limitation by identifying alterations in progressive tumors without need for a new biopsy.
Intermediate prognosis in metastatic germ cell tumors (IPGCT): Outcome and prognostic factors.
Authors: Seidel Christoph Alexander , Daugaard Gedske , Tryakin Alexey , Necchi Andrea , Hentrich Marcus , Cohn-Cedermark Gabriella Elisabeth , Stahl Olof , Goncalves Margarida Brito , Gerl Arthur , Oechsle Karin , Bokemeyer Carsten 
Published: September 2018

4560 Background: The IGCCCG classification published in 1997 is based on data from the 1970-80s. Approximately 25% of metastatic GCT patients belong to the intermediate prognosis category, that was associated with a 5-year overall survival (OS) rate of 79%. However, more recent data suggest significant changes. We have thus performed an international registry of IPGCT patients to analyze current treatment, outcome, and potential prognostic factors. Methods: Data of IPGCT patients, diagnosed between 1979-2012, were retrospectively collected from 14 centers. Treatment and outcome before and after implementation of IGCCCG were analyzed. For patients diagnosed since 1997 prognostic factors were investigated by uni- and multivariate analysis to test whether current patients or subgroups may require less intensive treatment. Results: This registry includes 637 patients: group 1 diagnosed prior 1997 (n = 237), and group 2 since 1997 (n = 400). Mean follow-up duration was 128.4 months (IQR: 168.9). Patients in group 1 and 2 received first-line treatment with BEP (median 4 cycles; range 1 - 6) in 98% and 97%, respectively. Response to chemotherapy (CR and marker negative PR) was similar: 91% group 1; 94% group 2; (p = 0.233), but survival curves were significantly superior in group 2 associated with a 5-year OS rate of 87% (group 2) and 81% (group 1), respectively (p = 0.011; 95%CI 294-317). Recurrence rates were higher in group 1 (36% versus 24%; p = 0.001). Patients treated with 3 cycles BEP (n = 58) in both groups had a similar outcome concerning OS compared to patients treated with 4 cycles (n = 489) (p = 0.415). Uni- and multivariate analysis revealed LDH levels < 2.0 UNL prior chemotherapy (p = 0.018; HR 0.35) and an adequate tumor marker decline at days 18-21 (half-life) of first cycle (p = 0.025; HR 2.58) as independent prognosticators, both associated with 5-year OS rates of 94%, respectively. Conclusions: Outcome of intermediate patients seems improved after implementation of the IGCCCG classification and less intensive regimes may also be sufficient. Here, patients treated with 3xBEP had a non-inferior outcome. A baseline LDH < 2.0 UNL and an adequate tumor marker decline after first treatment cycle can be used for further stratification.
Differential expression of c-Met between primary and metastatic sites in clear-cell renal cell carcinoma (ccRCC) and its association with PD-L1 expression.
Authors: Lalani Aly-Khan A. , Albiges Laurence , Gray Kathryn P. , Pal Soumitro , Pignon Jean-Christophe , Gupta Mamta , Bhatt Rupal Satish , McDermott David F. , Atkins Michael B. , Vande Woude George Franklin , Signoretti Sabina , Choueiri Toni K. 
Published: September 2018

4573 Background: Preclinical models show that c-Met promotes survival of renal cancer cells through the regulation of programmed death-ligand 1 (PD-L1). The relationship between c-Met and PD-L1 in human ccRCC is not well characterized. We compared c-Met expression between primary and metastatic sites in ccRCC tissues and evaluated the association with PD-L1 expression. Methods: Pairedprimary and metastatic samples from 45 ccRCC patients were included. Areas with predominant and highest Fuhrman nuclear grade (FNG) were selected. c-Met expression was evaluated by IHC using an anti-Met monoclonal antibody (MET4 Ab, VARI) and calculated by a combined score (CS, 0-300) as: intensity of c-Met staining (0-3) x % of positive cells (0-100). PD-L1 expression was previously assessed by IHC (PMID: 26014095). c-Met expression (average c-Met CS) between paired primary and metastatic samples were compared using Wilcoxon signed-rank test. Associations of c-Met expression with PD-L1 expression (+/-) and other clinical features were assessed with Wilcoxon rank-sum tests. Results: Our cohort included 45 primary ccRCCs and 54 corresponding metastases. c-Met expression was higher in metastatic sites compared to primary (c-Met CS: 55 vs. 28, p=0.0003) and was numerically-greater in PD-L1+ vs. PD-L1- tumors. Higher c-Met expression was associated with higher FNG and T-stage in both primary and metastatic sites (Table). Conclusions: Higher c-Met expression in metastases compared to paired primary tumors in our cohort of ccRCC suggests that testing for biomarkers of response to c-Met inhibitors should be conducted in metastases. Although the observation of higher c-Met expression in PD-L1+ tumors requires further investigation, it supports exploring these targets in combination trials. [Table: see text]
Genomic instability and DNA damage repair in clear cell renal cell carcinoma.
Authors: Pilie Patrick Glen , Zhou Lijun , Tong Pan , Matin Surena F. , Sircar Kanishka , Tamboli Pheroze , Karam Jose A. , Wood Christopher G. , Hoang Anh , Jonasch Eric 
Published: September 2018

4581 Background: Kidney cancer accounts for 2-3% of all new cancers with clear cell renal cell carcinoma (ccRCC) the most common subtype. ccRCC is characterized by a high level of genomic instability, suggesting defective DNA damage repair (DDR). The most frequent genomic alteration in ccRCC involves loss of the 3p chromosomal arm which harbors the von Hippel Lindau gene ( VHL), in addition to nearby genes SETD2, BAP1, and PBRM. We hypothesized that VHL loss leads to defective DDR as an early event in ccRCC carcinogenesis, giving way to a mutator phenotype. We posited that assessment of very early ccRCC tumors would inform us regarding the core mutations required to drive tumorigenesis in ccRCC, and that we could confirm these findings in appropriate model systems. Methods: We performed whole-exome (WES) DNA sequencing on 11 early-stage ccRCC tumors from 5 individuals, along with their matched normal DNA. We then analyzed ccRCC samples with and without somatic VHL mutations from the Cancer Genome Atlas (TCGA) for mutational load. Finally we assessed DDR signaling activity in renal proximal tubular cell lines (RPTEC) with VHL/SETD2 knockdown and in murine embryo fibroblasts (MEFs) from Vhl and Setd2knockout mice treated with etoposide via γH2AX expression and direct repeat-green fluorescent protein reporter assay. Results: All 11 samples revealed loss of 3p with pathogenic germline or somatic mutation in remaining VHL allele. No mutations were found in genes frequently mutated in larger ccRCC, including PBRM1, BAP1 or SETD2. WES revealed ~100 mutations/tumor, with no shared mutations across samples, even within the same individual. TCGA analysis showed similar mutational loads across ccRCC samples. MEFs with biallelic loss of Vhl and monoallelic loss of Setd2 and RPTEC with VHL and SETD2knockdown displayed increased DNA damage with impaired homologous repair and increased non-homologous end joining (NHEJ). Conclusions: Early stage ccRCC tumors with loss of VHL and chr 3p demonstrate genomic instability and a mutator phenotype similar to more advanced ccRCC. Cell line models of early ccRCC show increased DNA damage with a greater reliance on error-prone NHEJ machinery. These defects could be targeted for synthetic lethal treatment strategies.
The aggressive variant prostate carcinoma (AVPC) molecular signature (-MS) and platinum-sensitivity in castration resistant prostate cancer (CRPC).
Authors: Aparicio Ana , Xiao Lianchun , Tapia Elsa Li Ning , Hoang Anh , Ramesh Naveen , Wu Wenhui , Chancoco Haidee , Heath Elisabeth I. , Efstathiou Eleni , Thompson Timothy C. , Troncoso Patricia , Broom Bradley McIntosh , Zurita Amado J. , Navin Nicholas , Logothetis Christopher , Corn Paul Gettys 
Published: September 2018

5013 Background: The AVPC are a subset of prostate cancers that share the clinical, therapy response and molecular profiles of the small cell prostate carcinomas, a histological variant of the disease that responds poorly to androgen receptor directed therapies. The AVPC are characterized by a molecular signature of combined tumor suppressor defects (≥ 2 alterations in Tp53, RB1 and/or PTEN by immunohistochemistry or genomic analyses). We conducted a randomized phase II study of cabazitaxel (CAB) plus or minus carboplatin (CARB) in men with CRPC and asked whether the AVPC-MS predicted for platinum benefit. Methods: 160 men with metastatic CRPC were randomized 1:1 to receive IV CAB (25 mg/m2) or CAB/CARB (25 mg/m2; AUC4) Q21 days with growth factor support until disease progression, unacceptable toxicity or for up to 10 cycles. Imaging occurred every 2 cycles. The primary endpoint was progression free survival (PFS). 73 tumor samples obtained within 1 year of registration from 65 of the 160 patients (pts) were stained for Tp53, RB1, PTEN, AR-N terminus, AR-C terminus and Ki67. DNA of sufficient quantity for sequencing was extracted from 27 tumors and 70 plasma samples. Results: At a median follow up of 21.6 months (mo), median PFS (mPFS) in the overall population (n = 160) is 4.6 mo (95%CI 3.5, 5.8) with CAB vs 7.4 mo (95% CI 5.6, 8.3) with CAB/CARB (p = 0.004). Men with AVPC-MS-positive tumors had a mPFS of 4.5 mo (95%CI 1.5, NA) with CAB [n = 9] vs 8.0mo (95%CI 6.11-9.7) with CAB/CARB [n = 23] (p = 0.0036) whereas men with AVPC-MS-negative tumors had a mPFS of 6.8mo (95%CI 5.2, NA) with CAB [n = 12] vs 5.4mo (95%CI 3.72, NA) with CAB/CARB [n = 12] (p = 0.1445). Analysis of plasma DNA samples is ongoing and will be presented at the meeting. Conclusions: The AVPC-MS identifies a subset of men platinum-sensitive CRPC tumors. These findings should serve as the foundation for a therapeutically relevant classification of prostate cancer. Clinical trial information: NCT01505868.