bluuebunny/crossref_metadata_2025_split huggingface dataset:
VAX014 for instillation in subjects with nonmuscle-invasive bladder cancer.
Authors: Lerner Seth P. , Karsh Lawrence Ivan , O'Donnell Michael A. , Shore Neal D. , Lotan Yair , Tsuji Shingo , Giacalone Matthew 
Published: February 2022

488 Background: VAX014 is a novel tumor targeted oncolytic agent for intravesical administration. It is comprised of recombinant bacterial minicells, that actively target a3b1 and a5b1 integrins expressed on NMIBC and deliver an active cytotoxic/oncolytic protein payload, perfringolysin O. VAX014 is being investigated for the intravesical treatment of NMIBC in an ongoing multi-center Phase 1 marker lesion trial in subjects with low grade Ta disease (NCT 03854721). Methods: Subjects with up to 5 pathologically confirmed TaG1 lesions ≥ 5mm but ≤ 15mm are eligible to receive six (6) weekly intravesical instillations of VAX014. Subjects with presence or history of high-grade bladder cancer are ineligible. Phase 1a will establish the MTD using a 3+3 design. After the DSMB establishes the RP2D, a Phase 1b expansion will use this dose to treat an additional 10 patients. Results: No serious adverse events or dose limiting toxicities have been recorded through two dose cohorts (3 + 3 design) and evidence of clinical response has been observed. Treatment related adverse events have been limited to Grade 1/2 hematuria, dysuria, and urgency. Preclinical studies indicate the pharmacodynamic activity of VAX014 following weekly intravesical administration to immune competent mice bearing bladder tumors is immune dependent and synergizes with systemic PD-L1 blockade to eliminate organ confined tumors and extravesical tumors. Surviving mice are capable of rejecting tumor rechallenge due to development of protective antitumor immunologic memory in response to therapy. Exploratory immunohistochemical target validation studies in bladder tumor biopsy specimens from subjects with more advanced stage tumors (T1-T3), indicate overexpression of VAX014’s target integrins, a3b1 and a5b1, in most samples tested. Conclusions: These clinical and preclinical data support the further development of VAX014 for the intravesical treatment of NMIBC and set a foundation for combination therapy with systemically administered immune checkpoint blockade in subjects with advanced disease. Clinical trial information: NCT03854721.
Analysis of disease-free survival in CheckMate 274 by PD-L1 combined positive score and tumor proportion score.
Authors: Galsky Matt D. , Bajorin Dean F. , Witjes J. Alfred , Gschwend Jürgen E. , Tomita Yoshihiko , Nasroulah Federico , Li Jun , Collette Sandra , Pérez-Valderrama Begoña , Grimm Marc-Oliver , Appleman Leonard Joseph , Gravis Gwenaelle , Necchi Andrea , Ye Dingwei , Stenner Frank , Wind-Rotolo Megan , Zhang Joshua , Unsal-Kacmaz Keziban 
Published: February 2022

491 Background: CheckMate 274 demonstrated a significant improvement in disease-free survival (DFS) with nivolumab (NIVO) versus placebo (PBO) both in the intent-to-treat population (hazard ratio [HR], 0.70; 98.22% confidence interval [CI], 0.55–0.90; P < 0.001) and in patients (pts) with tumor programmed death ligand 1 (PD-L1) expression ≥ 1% assessed by the tumor proportion score (TPS) (HR, 0.55; 98.72% CI, 0.35–0.85; P < 0.001). An exploratory subgroup analysis showed a trend toward a DFS benefit with NIVO in pts with TPS < 1% (0.82; 95% CI, 0.63–1.06). To further characterize the relationship between PD-L1 expression and NIVO efficacy, we report an analysis of DFS based on PD-L1 expression in both tumor and immune cells using the combined positive score (CPS). Methods: CheckMate 274 is a phase 3, randomized, double-blind, multicenter trial of NIVO versus PBO in pts with high-risk muscle-invasive urothelial carcinoma after radical surgery. Pts were randomized 1:1 to NIVO 240 mg or PBO every 2 weeks intravenously for 1 year of adjuvant treatment. The primary endpoints of the study are DFS in the intent-to-treat population and in pts with TPS ≥ 1%. The Dako PD-L1 IHC 28-8 pharmDx assay was used to evaluate TPS. CPS was determined retrospectively from previously stained immunohistochemistry slides using the CPS algorithm. CPS was calculated as the number of both PD-L1 positive tumor and immune cells divided by the number of viable tumor cells in the evaluable tumor area, multiplied by 100; TPS was similarly calculated with the number of PD-L1 positive tumor cells as the numerator. This analysis only included pts with both quantifiable CPS and TPS. Results: Of the 629 pts with quantifiable TPS and CPS, 249 (40%) had TPS ≥ 1% (NIVO, n = 124; PBO, n = 125), 380 (60%) had TPS < 1% (NIVO, n = 191; PBO, n = 189), 557 (89%) had CPS ≥ 1 (NIVO, n = 281; PBO, n = 276), and 72 (11%) had CPS < 1 (NIVO, n = 34; PBO, n = 38). Within TPS < 1% pts, 81% (n = 309) had CPS ≥ 1. The number of pts and the DFS outcomes in pts with TPS ≥ 1% and CPS ≥ 1 are shown in the Table. In pts with TPS < 1% who also had CPS ≥ 1, median DFS (95% CI) was 19.2 (15.6–33.4) months with NIVO versus 10.1 (8.2–19.4) months with PBO. The HR for NIVO versus PBO in these pts was 0.73 (95% CI, 0.54–0.99). Conclusions: This exploratory analysis of PD-L1 expression by CPS showed a higher proportion of pts with CPS ≥ 1 than TPS ≥ 1%, and that most pts with TPS < 1% had CPS ≥ 1. In the CPS ≥ 1 subgroup, median DFS with NIVO was more than double that with placebo. These results support the conclusion that pts with TPS < 1% also benefit from adjuvant NIVO. Clinical trial information: NCT02632409. [Table: see text]
Defining innate immune training potential as a predictor of Bacillus Calmette-Guérin immunotherapy response in nonmuscle-invasive bladder cancer.
Authors: Jiang Song , Redelman-Sidi Gil , Pietzak Eugene J. , Bochner Bernard H. , Glickman Michael S 
Published: February 2022

522 Background: Intravesical instillation of the live attenuated mycobacterium Bacillus Calmette-Guerin (BCG) remains the most effective therapy for the treatment of non-muscle invasive bladder cancer. The precise mechanism of BCG is thought to involve phagocytosis, induction of inflammation, activation of the innate immune apparatus, and an effective cell-mediated T cell response. An increasing body of evidence suggests that the innate immune system has characteristics that involve a heterologous memory of past insults through a process thought to involve epigenetic reprogramming, termed trained immunity. We seek to investigate the potential for innate immune training as a predictor of the anti-tumor effects of BCG. Methods: A prospective biospecimen collection was performed on venous blood from non-muscle invasive bladder cancer patients prior to receiving intravesical BCG therapy. To investigate the role of trained immunity in primary monocytes, cells were isolated from peripheral blood mononuclear cells (PBMC) by plate adhesion. 2-5 x 105 cells/well were assayed in 96-well format, cultured in RPMI 1640 supplemented with 10% Fetal Bovine Serum and 2mM L-glutamine and stimulated with 10:1 MOI BCG for 24 hours. Cells were then washed in media and allowed to rest 6 days. Media was changed on day 3 of rest. Subsequently, cells were stimulated with 25 ng/ml lipopolysaccharide (a TLR4 agonist) for 24 hours. Cell free supernatant was measured for TNF-alpha production by enzyme-linked immunosorbent assay. Results: In vitro training of primary monocytes induced an increase in proinflammatory cytokine production upon re-stimulation. This phenotype was dose dependent on stimulation with LPS, however, the relative change between trained and untrained cells was diminished at higher concentrations of agonist. In our in vitro training experiments, there was demonstrable interpatient variability seen pre-BCG exposure in a cohort of NMIBC patients. These results will be correlated with future long term BCG response in this prospective cohort. Conclusions: We present data on a trained innate immune phenotype on primary monocytes collected from patient samples. These data serve as proof of principle for the ability to induce a trained phenotype in vitro. These findings will be correlated with prospective clinical data on BCG responsiveness and recurrence free survival to allow us to garner further insight into the role of trained immunity in BCG immunotherapy. Such insight will have potential clinical impact on the development of biomarkers and clinical assays that could predict immune responsiveness to BCG a priori, as well as identify possible immunological adjuvants that could enhance the effect of intravesical BCG.
Actionable genomic landscapes from a real-world cohort of localized urothelial carcinoma patients.
Authors: Gerald Thomas , Margulis Vitaly , Meng Xiaosong , Cole Suzanne , Qin Qian , Call Greg , Mauer Elizabeth , Lotan Yair , Woldu Solomon L. 
Published: February 2022

525 Background: Recent targeted therapies for advanced and metastatic urothelial cancer have generated enthusiasm, but the actionable genomic landscape of early-stage disease remains largely unknown. Here, we used real-world evidence to investigate differences between somatic and germline mutations in localized, early-stage urothelial cancers and advanced urothelial cancers. Methods: We retrospectively analyzed de-identified NGS data from 1,146 bladder cancer patients (stages I-IV) with formalin-fixed, paraffin-embedded tumor biopsies sequenced using the Tempus|xT solid tumor assay (DNA-seq of 595-648 genes at 500x coverage; whole-exome capture RNA-seq). For the subset of patients with tumor-normal match sequencing (n=758), additional incidental germline alterations in 46 different genes were assessed. Results: A total of 1,146 bladder cancer tumors were investigated: stage I-II (n=124), stage III (n=159), and stage IV (n=863)—summarized in Table. Tumor mutational burden (TMB) was calculated for 1,126 tumors, and TMB-high (TMB-H; ≥10 mutations per megabase) was similar across tumor stages. PD-L1 immunohistochemical staining was performed on 698 tumors, and no significant differences were observed. Microsatellite instability high (MSI-H) status was detected in only 2 (1.6%) stage I-II tumors and 8 (0.9%) stage IV tumors. Alterations—single nucleotide variants, insertions/deletions, and copy number variants—in FGFR2/3, homologous recombination repair genes (18 genes including BRCA1/2 and ATM), additional DNA repair gene mutations ( ERCC2, RB1, FANCC) and NTRK fusions were detected at similar frequencies across disease stages. In 758 patients with tumor/normal matched sequencing, we identified a low rate of incidental germline mutations in MUTYH (stage III, 1%; stage IV, 1.9%), BRCA2 (stages I-II, 1.2%; stage III, 1%; stage IV, 0.5%), BRIP1 (stages I-II, 1.2%), ATM (stage III, 1%; stage IV, 0.7%), MSH6 (stage III, 1%; stage IV, 0.2%), and TP53 (stage III, 1%; stage IV, 0.2%). Conclusions: Patients with bladder cancer have similar rates of potentially actionable mutations and genomic landscapes regardless of clinical disease stage. These findings provide a rationale for further investigating targeted therapies among early-stage bladder cancer patients.[Table: see text]
Expression of Nectin-4 and PD-L1 in bladder cancer with variant histology.
Authors: Case Katherine , Martini Dylan J. , Dababneh Melad , Nazha Bassel , Brown Jacqueline T , Joshi Shreyas S. , Narayan Vikram M. , Ogan Kenneth , Master Viraj A. , Carthon Bradley Curtis , Kucuk Omer , Harik Lara , Bilen Mehmet Asim 
Published: February 2022

529 Background: Nectin-4, a cell adhesion molecule found in a frequently amplified region of the bladder cancer (BC) genome, has been recently used as target for the systemic treatment of locally advanced or metastatic BC. BC with variant histology (BCVH) is associated with poor clinical outcomes, and there is an unmet need for novel treatments in this population. Little is known about Nectin-4 expression and other targets. We investigated Nectin-4 and programmed death-ligand 1 (PD-L1) expression in BCVH. Methods: We performed a retrospective analysis of 117 patients with BCVH whose samples were collected at Winship Cancer Institute of Emory University from 2011-2021. Immunohistochemistry (IHC) was performed for Nectin-4 and PD-L1 expression on formalin-fixed, paraffin-embedded (FFPE) tissue. Nectin-4 staining was performed by Q2 Solutions using non-commercially available anti-Nectin-4 antibody (clone M22-312B41.1). Expression was measured using the H-score method (H-score = [% of strong positive tumor cells × 3] + [% of moderate positive tumor cells × 2] + [% of weak positive tumor cells × 1]). PD-L1 levels were assessed in tumor-infiltrating immune cells using DAKO 22C3 IHC to determine PD-L1 high, defined by a Combined Positive Score (CPS) of ≥10. Results: Median age was 70 years (mean=67.2, range 22-91), with 61.5% male, 54.7% white, and 32.5% black. Nearly all samples were taken from the bladder (95.7%), with 4.3% from sites of metastasis. The most common histologic variant was squamous cell carcinoma (26.5%), and the distribution of variants is summarized in table. Nectin-4 staining was successfully performed on 111 samples, and PD-L1 staining on 116. Nectin-4 expression was seen across different histological subtypes (mean H-score: 153.1, median [range]: 157 [0-300]), with highest expression in plasmacytoid and squamous, and lowest expression in small cell and sarcomatoid (Table). More than one-third (35.3%) were PD-L1 high, and greater in sarcomatoid and squamous cell histology (70.8% and 50% positivity, respectively). Only 5% of plasmacytoid samples were PD-L1 high. Conclusions: Although there is heterogeneity, our results showed expression of Nectin-4 and PD-L1 in this cohort of patients with BCVH. These findings highlight the therapeutic potential of antibody-drug conjugates against Nectin-4- and anti PD1/PD-L1-based therapy in this population. Additional analysis including clinical outcomes and genomic analyses are ongoing, and a prospective clinical trial is planned.[Table: see text]
Prognostic value and therapeutic implications of an integrative molecular subtype and immune content classifier in localized muscle-invasive bladder cancer.
Authors: Farha Mark , Cotta Brittney , Vince Randy , Nallandhighal Srinivas , Kaffenberger Samuel D. , Palmbos Philip , Alva Ajjai Shivaram , Morgan Todd Matthew , Palapattu Ganesh S. , Salami Simpa , Udager Aaron M. 
Published: February 2022

530 Background: Localized muscle-invasive bladder cancer (MIBC) exhibits heterogeneous molecular features and outcomes, with a 5-year mortality rate of approximately 30%. Immune checkpoint blockade (ICB) has the potential to improve oncological outcomes but molecular tools are needed to identify those most likely to benefit. Here, we integrate transcriptomically derived tumor immune microenvironment (TIME) data with molecular subtypes to create a novel integrative classifier with prognostic and therapeutic implications. Methods: RNAseq data from patients with localized muscle-invasive bladder cancer (MIBC) from the Cancer Genome Atlas BLCA (TCGA-BLCA) project was utilized (n = 187). CIBERSORT was used for immune cell deconvolution, and unsupervised hierarchical clustering divided the cohort based on similar immune profiles. Consensus molecular clustering information for the cohort was obtained from Kamoun et al. Overall survival (OS) of each cluster were analyzed. The tumor immune dysfunction and exclusion (TIDE) tool, which uses a genomic signature validated on immunotherapy treated melanoma patients to model tumor immune evasion, was then used to predict response to ICB. Results: In the TCGA-BLCA cohort, there were two distinct clusters enriched with macrophages, CL1-M0Hi (n = 18) and CL5-M2Hi (n = 35). Compared to the rest of the cohort, these two macrophage enriched clusters combined exhibited a decreased OS (33.1 mo vs. NR, p = 0.01). TIDE tool predicted ICB response was lowest in CL1 (6/18, 33%; p = 0.09), CL5 (12/35, 34%; p = 0.02), and the Ba/Sq molecular cluster (16/57, 28%; p = 1.3x10-5). Patients designated as CL1 or CL5 by immune clustering and Ba/Sq by molecular consensus were combined into a subgroup (n = 20). Compared to the rest of the cohort, this Ba/Sq_MacrophageHi subgroup had a higher body mass index (31.0 vs. 25.8 BMI, p = 0.0004), more whites (95% vs. 64%, p = 0.03), and had a higher stage (80% Stage III/IV vs. 20% Stage I/II, p = 0.05). The Ba/Sq_MacrophageHi cluster demonstrated higher PD-L1 expression (mean Z score 0.15 vs. -0.09; p = 0.008), there was a higher degree of T cell exclusion (mean Z score 0.16 vs. -0.06; p = 0.003) and cancer-associated fibroblasts (mean Z score 0.03 vs. -0.02; p = 3.4x10-5). Overall, the predicted response to ICB by TIDE in the Ba/Sq_MacrophageHi was lower (OR 0.15, 0.03-0.55 p = 0.002) and OS was significantly shorter (median 16.7 mos vs. 54.9 mo, p = 0.04). Conclusions: We demonstrated the prognostic significance of the Basal/Squamous subtype with macrophage enrichment in patients with localized MIBC. Pending further prospective validation, this sub-population may be less amenable to ICB treatment.
Development and clinical application of PredicineBEACON next-generation minimal residual disease assay for genitourinary cancers.
Authors: Xie Feng , Zang Jingyu , Zhang Yue , Zhang Ruiyun , Huang Yong , Zhuang Guanglei , Chen Haige , Du Pan , Jia Shidong 
Published: February 2022

539 Background: Tumor-informed minimal residual disease (MRD) assay has been studied in muscle invasive bladder cancer (MIBC) in IMvigor010 study. However, the current methods require the use of tumor tissue and lacking actionable insights. In this study, a tumor-agnostic and actionable MRD assay (PredicineBEACON) is developed with high sensitivity and capability to detect actionable mutations in blood- or urine-based circulating tumor DNA. Methods: PredicineBEACON tumor-agnostic MRD assay includes three components, i.e., baseline mutation identification, personalized panel design, and ultra-deep next generation sequencing of cancer variants. Step 1: whole exon sequencing with boosted depth in 600 cancer-related genes is performed using baseline tumor tissue or liquid biopsy (blood or urine) to identify somatic mutations. Step 2: Up to fifty somatic mutations are selected for personalized MRD panel design, in combination with the use of a fixed core panel of 500 actionable/hotspot variants. Step 3: MRD and actionable mutations were called from ultra-deep sequencing (100,000X). A companion low-pass whole-genome sequencing (LP-WGS) is performed to monitoring copy number variation (CNV). In the current study of patients with MIBC, urine samples at baseline were used for personalized variant generation. Urine samples under neoadjuvant immunotherapy and blood samples after radical cystectomy were collected and tested with the PredicineBEACON MRD assay. Results: PredicineBEACON MRD assay demonstrated a sensitivity of 0.005% tumor fraction. In patients of MIBC, urine-based MRD assay detected the dynamic changing of disease evolution under neoadjuvant therapy and preceded the radiographic response. Actionable mutations, including FGFR3, TERT and PIK3CA mutations, were detected. Copy number burden revealed by LP-WGS correlated with disease evolution. Plasma-based MRD assay on the patients after radical cystectomy is currently ongoing. Conclusions: PredicineBEACON tumor-agnostic MRD assay provides an ultra-sensitive and actionable MRD detection with high sensitivity and specificity. Assessment of MRD could potentially be leveraged, for example, to avoid overtreatment of early stage of genitourinary cancers such as non-metastatic prostate cancer, non-muscle invasive bladder cancer and muscle invasive bladder cancer.
Characterization and functional analysis of microbiome in bladder cancer.
Authors: Bukavina Laura , Calaway Adam C. , Isali Ilaha , Prunty Megan , Ghannoum Mahmoud , Retuerto Mauricio , Mishra Kirtishri , Sindhani Mohit , Castro Bigalli Alberto , MacLennan Gregory , Ponsky Lee Evan , Markt Sarah C. , Abbosh Phillip 
Published: February 2022

541 Background: The role of microbiome in genitourinary cancer is an emerging field, with evidence implicating the important role of microbiome as causative factors or cofactors in tumorigenesis and drug metabolism. Our study aims to characterize healthy and bladder cancer enterotypes in the gut and identify functional alterations through the use of metagenomics data. Methods: After prospective collection of 29 rectal swab samples of bladder cancer (BCa) patients undergoing cystectomy, and 32 healthy volunteers, we perform 16S rRNA amplicon sequencing on 61 samples (29 with bladder cancer, 32 without cancer). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to infer functional categories associated with taxonomic composition. The p values were adjusted using the false discovery rate. The a- and b-diversity analyses were performed using QIIME. The Mann-Whitney U test was employed to evaluate the statistical significance of b-diversity distances within and between groups of interest. Results: Across all the bladder cancer stool samples, estimation of relative abundance revealed of the five most dominant bacterial populations was Bacteroidales ( 46.21%), Clostridiales ( 32.29%), Burkholderiales (9.07%), Erysipelotrichales (3.20%) and Lactobacillales ( 2.20%). In contrast, healthy controls exhibited an increased relative abundance of Enterobacteriales ( 10.75% vs 0.52%) and Pseudomonadales (8.33% vs 0.18%) as compared to tumor samples. The microbial diversity differences between Bca and normal samples showed no differences across alpha diversity metrics (Shannon diversity p>0.05) as compared to normal tissue. However, there was significant difference in clustering of organisms as determined by principal coordinate analysis ( PCoA) ordination of unweighted UniFrac Distances, (p=0.002). Furthermore, upon stratification of patients on smoking status (all healthy=nonsmokers), clustering persisted, albeit non smokers with bladder cancer displayed an intermediate across PCoA. Bca samples exhibited higher LDA score Campylobacterales (log change 8.0, p<0.001, padj <0.001) ,Fusobacteriales (log change 6.11, p<0.001/ padj<0.01), Epysipelotrichales (log 2.55, p<0.001/ padj <0.001 ), Actinomycetales (log change 1.86, p=0.001/ padj<0.001), Verrucomicrobiales (log change 1.78, p=0.017/padj=0.031) and Enterobacteriales (log change -1.54,p=0.017/ padj= 0.132). Conclusions: In conclusion, our study provides preliminary evidence that the GI microbiota is different in bladder cancer patients. Collectively, our study highlights distinct microbial overexpression of Campylobacter and Fusobacterium in Bca cohort not previously reported, both implicated in tumorigenesis, and could serve as a target that could be modulated to enhance treatment response.