bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic correlates of response and resistance to immune checkpoint inhibitors (ICI) in patients with metastatic urothelial carcinoma (mUC) in a real-world setting.
Authors: Pramod Nikhil , Makarov Vladimir , Dawsey Scott , Pavicic Paul G. , Patgunarajah Ubenthira , Nair Monica , Ornstein Moshe Chaim , Gilligan Timothy D. , Wee Christopher Eing , Nizam Amanda , Mian Omar Y. , Nguyen Jane , Diaz-Montero C. Marcela , Gupta Shilpa 
Published: January 2024

670 Background: Response rates with ICI are only about 20% in mUC and we lack validated biomarkers to select patients who are most likely to derive benefit from ICI. Programmed cell death ligand 1 (PD-L1) has not proven to be a useful biomarker. We need biomarkers of response and resistance to avoid nonbeneficial treatment (Tx) and spare the majority of pts who will not respond to ICI both physical and financial toxicity. Here we report tumor genomic correlates of response and resistance to ICI in pts with mUC. Methods: We identified 335 adult pts with mUC at the Cleveland Clinic treated who received > / = 2 cycles of ICI with pembrolizumab (P) or atezolizumab (A) between 2015 and 2023. Of the 335 pts, 49 had pre-Tx archival formalin fixed paraffin-embedded (FFPE) tissues available. Pts were categorized by their response to ICI as responders (R) (Complete Response (CR), Partial Response (PR), and Stable Disease (SD)) (N = 23) or non-responders (NR) (Progressive Disease (PD)) (N = 26). Whole exome sequencing was performed from macro dissected tumors. Raw data in FASTQ format was aligned to GRCh38 human reference genome, somatic mutations were called by Mutect2 (part of GATK4) and allele-specific copy-number analysis was performed by applying the Facets and Gistic2 package. Results: Comparison of our cohort Tumor Mutation Burden (TMB) with mutation burden of 33 the cancer genome atlas (TCGA) cohorts shows close similarity to TCGA bladder urothelial carcinoma (BCLA). Median TMB in our cohort was 6.46 muts/Mb. In our cohort, TP53 hotspot mutations were found in 52% of the (R) cohort compared to 31% in the (NR) cohort. Additionally, mutations in KMT2C and KMT2A were found in 26% and 22% of the (R) cohort compared to 8% and 12 % of the (NR) cohort. (R) also had increased mutations in the ARID1A (17% vs 4%) and ERBB2 (17% vs 4%) compared to (NR). FGFR3 missense mutations were seen in only 4% of (R) cohort compared to 15% in (NR). In our complete cohort, 49% of patients had ERBB2 copy number amplifications and 92% of patient had CREBP2 deletions. Conclusions: In our real-world cohort of mUC pts treated with ICI, we identified differential genomic alterations between (R) and (NR). High frequency of ERBB2 mutations and alterations in overall cohort and higher frequency in (R) suggests potential role for anti-HER2 therapies alone or in combination with ICI. Ongoing genomic and immunologic correlative studies in our cohort will further help understand biomarkers of response and resistance to ICI in pts with mUC.
Blood-based liquid biopsy: A promising non-invasive test in diagnosis, surveillance, and prognosis of patients with upper tract urothelial carcinoma.
Authors: Ghoreifi Alireza , Shishido Stephanie , Courcoubetis George , Sayeed Salmaan , Huang Amy , Schuckman Anne K. , Aron Monish , Desai Mihir , Daneshmand Siamak , Gill Inderbir , Kuhn Peter , Mason Jeremy , Djaladat Hooman 
Published: January 2024

677 Background: Blood-based liquid biopsy has emerged as a novel biomarker to improve the diagnosis and monitoring of urothelial tumors while enabling individualized risk stratification. The aim of this study was to assess the efficacy of these novel biomarkers in the diagnosis, surveillance, and prognosis of patients with primary upper tract urothelial carcinoma (UTUC). Methods: In this prospective study, peripheral blood samples were collected from patients with primary UTUC before surgery with curative intent and follow-up visits between May 2021 and September 2022. The samples were analyzed using the third-generation comprehensive high-definition single-cell assay (HDSCA3.0) to detect rare events, including circulating tumor cells (CTCs) and oncosomes, based on the immunofluorescent signals of DAPI (D), cytokeratin (CK), CD45/CD31 (CD), and vimentin (V). The findings of pre-surgery liquid biopsies were compared to the blood samples of normal donors (NDs) and matched follow-up liquid biopsy samples. The association between liquid biopsy findings and clinical data elements, including progression-free survival (PFS), was also assessed. Results: Twenty-eight patients with a median (range) age of 67.5 (43-88) years were included, of whom 21 had follow-up samples. Pathologic staging revealed 15 pT<2 and 13 pT≥2 tumors, and most cases (23/28) were high-grade.Significant differences in specific rare analytes were detected in pre-op samples as compared to NDs. On the post- vs. pre-surgery matched analysis, a significant decrease was detected in total-, CK-, and CK|V oncosomes as well as D-, D|V-, and D|V|CD cells. Correlation between pre-surgery liquid biopsy findings and clinical data is shown in Table 1. With a median follow-up of 11 months, seven patients had disease recurrence. Survival analysis demonstrated that patients with greater than 1.95 preoperative CK|V oncosomes as well as those with greater than 4.18 D|CK|V cells had worse PFS compared to other patients ( p=0.02 and p=0.05, respectively). Conclusions: This study demonstrates promising initial evidence for biomarker role of CTCs and oncosomes in diagnosis and surveillance of patients with UTUC.[Table: see text]
Describing the genomic landscape of bladder cancer histologic subtypes.
Authors: Talukder Rafee , Berg Rachel , Huang Minxuan , Nepomucino Vanessa M. , Stoppler Melissa Conrad , Makrakis Dimitrios , Yen Aihua Edward , Mims Martha P. , Lerner Seth P. , Woldu Solomon L. , Lotan Yair , Yu Evan Y. , Khaki Ali Raza , Aragon-Ching Jeanny B. , Grivas Petros 
Published: January 2024

680 Background: Histologic subtypes of bladder cancer are associated with poor prognosis and therapy resistance; understanding of their biology can help identify therapies to improve outcomes. We aimed to describe the genomic alteration (GA) landscape of pure urothelial (UC) and histologic subtypes: plasmacytoid (PC), micropapillary (MP), sarcomatoid (SA), small cell/neuroendocrine (SC), squamous cell differentiation (SQ), adenocarcinoma (AD). Methods: Approximately 2165 patients (pts) were selected from the Tempus multimodal database. Selection criteria included diagnosis of bladder cancer (UC or histologic subtypes: PC, MP, SA, SC, SQ, AD) and sequencing via the Tempus xT assay. Genomic and immunotherapy biomarkers, including mutations, fusions, copy number variants, tumor mutation burden (TMB-high defined as ≥10 mutations/Mb) and MSI status were determined for each subtype and compared using Fisher’s Exact and Kruskal-Wallis tests. Results: Among 2165 identified pts, 1738 (80%) had UC (84% pure and 16% mixed histology), Table shows genomic alterations per histologic subtype. Median age at diagnosis was 70. The overall cohort included male (73%), white (84%), and ever smokers (71%). Of 1197 pts with staging information available, 71% tumors were stage IV. TMB-H and MSI-high status were noted in 17% and 1.1% of the overall cohort, respectively, and were relatively similar across histologies. PD-L1 positive status by IHC was noted in 30% in the overall cohort, and statistically lower in PC (7.7%), SC (10%) and AD (8.8%) vs UC (32%), SA (46%) and SQ (45%) (p<0.001). Compared to UC, FGFR3 was significantly lower in SC (9% vs 1%, p=0.003) and AD (9% vs 1%, p=0.001). We noted FGFR2/3 fusions in 2.6% of the entire cohort and all cases were UC. Compared to UC, ERBB2 was significantly higher in MP (13% vs 45%, p<0.001) and lower in SQ (13% vs 2%, p<0.001). ERBB2 amplification was more common in MP (16%) vs 8% in PC, 6.2% in UC, and 1.6% in SC. Conclusions: Distinct genomic alteration patterns were found among different histologic subtypes of bladder cancer and conventional UC. Assessing the genomic landscape of bladder cancer can help identify potential ‘actionable’ targets and biomarkers, and better inform clinical trial designs. Limitations include lack of clinical data annotation, tumor heterogeneity and retrospective study nature. [Table: see text]
Identification and characterization of prognostic isoforms associated with bladder cancer outcomes.
Authors: Patsalis Christopher , Bankhead Armand , Palmbos Phillip Lee 
Published: January 2024

683 Background: Alternative splicing events can represent driver aberrations in cancer the same way as mutations, copy number changes, and gene fusions. We previously identified TP63 isoforms that were associated with prognosis in patients with bladder cancer and other tumor types. However, little is known about how isoform expression heterogeneity in other genes contributes to outcomes in bladder cancer. We hypothesized that expression of alternative isoforms in bladder cancer would be associated with clinical outcomes in a manner distinct from previously seen gene level associations. Methods: To examine this, we developed a high-throughput approach to identify and characterize prognostic gene isoforms that are associated with worse prognosis using RNA-sequencing data from The Cancer Genome Atlas (TCGA) bladder cancer cohort (BLCA). To identify gene isoforms that associate with bladder cancer outcomes, we aligned patient reads using HISAT2 and quantified expression for 69,272 isoforms using the Refseq isoform definitions from NCBI and the Stringtie algorithm. We filtered our quantifications to isoforms that belong to a gene with two or more isoforms, and those that had >0.1 Log2 TPM expression. The remaining 42,798 isoforms were tested for association with overall survival using cox regression and based on the following criteria: an isoform had to have a Hazard Ratio greater than 1 with a p-value < 0.05, an FDR adjusted p-value < 0.2 for a log-rank survival statistic using 3 quantile expression thresholds (25, 50 and 75th), and no significant gene-level association with disease prognosis. We validated our quantifications by confirming read coverage at the unique splice junctions for each isoform and by RT-PCR. We then performed differential expression and pathway enrichment analyses for tumors with or without expression of each pathogenic isoform. Results: 34 individual isoforms (from 30 genes) fit the criteria for association with survival. Several isoforms identified by our screen, such as FLNB, AXL, and COL6A3 isoforms, were previously shown to be associated with cancer outcomes in other tumor types. Expression of 7 isoforms were confirmed in human bladder cancer (2 isoforms of COL6A1, APLP2, TIAL1, and 1 isoform of FLNB) using RT-PCR. Expression of 21 of these prognostic isoforms were enriched in the aggressive basal squamous molecular subtype. Pathway analysis of TCGA BLCA tumors expressing these isoforms revealed enrichment of gene pathways associated with invasive cancer phenotypes, such as epithelial to mesenchymal transition and MYC targets. Conclusions: Specific isoforms are significantly associated with bladder cancer patient survival and suggest that splicing events in certain genes may act as driver aberrations in bladder cancer. Further work will need to be done to establish the regulatory mechanisms as well as how these isoforms contribute to cancer progression.
Peripheral biomarker analysis in patients with advanced urothelial carcinoma (UC) after platinum chemotherapy treated with cabozantinib (CABO) plus durvalumab (DURVA): Preliminary analysis from the phase 2 ARCADIA trial.
Authors: Giannatempo Patrizia , Sgambelluri Francesco , Stellato Marco , Guadalupi Valentina , Raggi Daniele , Rametta Alessandro , Bottiglieri Achille , Claps Melanie , Walter Ferrari Bravo , Oldani Simone , Zimatore Matteo , Calareso Giuseppina , Alessi Alessandra , Cattaneo Laura , Verzoni Elena , De Braud Filippo G. , Procopio Giuseppe , Necchi Andrea , Anichini Andrea , Mortarini Roberta 
Published: January 2024

684 Background: Preliminary results of the interim analysis of the ARCADIA trial have shown that combining multitargeted receptor tyrosine kinase inhibitor CABO with the checkpoint inhibitor DURVA has promising activity and a manageable safety profile in patients (pts) affected by UC recurred or progressed after failure of at least one line of platinum-based chemotherapy for metastatic disease in a phase II study (NCT03824691). To identify peripheral blood biomarkers potentially associated with clinical response, we carried out a quantitative profiling of innate and adaptive immune subsets from a subset of treated pts. Methods: From 09/2019 and 08/2023 blood samples from 65 pts were collected at baseline and before the third treatment cycle. Absolute cell counts for 29 innate and adaptive immune subsets were determined by multiparametric flow cytometry. Results: In pre-therapy samples a significant higher counts for all CD45+ leukocytes were found in non-responders compared to responders (p=0.0053, Mann Whitney test, n= 27 patients). This was, explained by higher counts for CD16+CD15+ neutrophils (p=0.0005), classical CD14+CD16- (p=0.0119) and CD14++CD16+ intermediate (p=0.0186) monocytes, CD56dim CD16+ NK cells (p=0.0365) and Lin-HLA-DR-/LoCD33+CD14+CD15- M-MDSCs (p=0.0281). At baseline, higher neutrophils counts were associated with worse PFS (p=0.0117, log rank test), while higher eosinophils counts were associated with improved PFS (p=0.0158). Compared to responders, non-responders underwent a significant reduction in post-treatment counts for all CD45+ leukocytes (p=0,0024, Wilcoxon matched pair test), due to reduction of neutrophils (p=0.0068), CD15+CD16- eosinophils (p=0.0068), CD3+ T cells (p=0.0425) CD19+ B cells (p=0.0068), classical monocytes (p=0.0034), activated (HLA-DR+) CD56dim CD16- NK cells (p=0.0068), M-MDSCs (p=0.0161), Lin- HLA-DR-/Lo CD33+ CD14- CD15+ PMN-MDSCs (p=0.001), Lin- HLA-DR+ CD33- pDCs (p=0.0269) and Lin- HLA-DR+ CD33+ mDCs (p=0.0005). Conclusions: These preliminary findings suggest that high baseline counts for granulocytes, monocytes and MDSCs may negatively impact on response in pts treated with CABO+DURVA. Moreover, baseline neutrophils and eosinophils counts show opposite impact on PFS. Grant support: NET-2016-02361632 from Italian Health Ministry to A. Anichini. Clinical trial information: NCT03824691 .
EIF2S1 as a novel diagnostic marker for bladder cancer in urinary extracellular vesicles.
Authors: Tomiyama Eisuke , Fujita Kazutoshi , Kato Taigo , Hatano Koji , Kawashima Atsunari , Nonomura Norio 
Published: January 2024

692 Background: Urinary extracellular vesicles (uEVs) secreted directly from BCa are considered a promising tool for diagnosing BCa, as they contain cancer-specific molecules. Among them, proteins in uEVs have attracted considerable attention, and several membrane EV proteins have been reported as urinary markers for BCa. However, few studies have focused on non-membranous (cytoplasmic) EV proteins. This study aimed to explore and validate a uEV-based diagnostic marker for BCa, focusing on cytoplasmic EV proteins. In addition, the functions of the identified protein were assessed. Methods: uEVs were isolated by ultracentrifugation with a sucrose cushion. Shotgun proteomics (TMT-labeled LC-MS/MS) was performed on uEVs from seven patients with BCa and four healthy individuals. Diagnostic marker candidates were selected from the identified cytoplasmic EV proteins and validated with targeted proteomics (SRM/MRM) of uEVs from 49 patients with BCa and 48 individuals without BCa, including patients with hematuria. The functional analysis of the identified EV protein was conducted in vitro. Results: Shotgun proteomics identified 1960 proteins, of which 17 cytoplasmic EV proteins were significantly elevated in the uEVs from patients with BCa (Fold change >1.5, p-value < 0.05). Of these, all ten measurable EV proteins were confirmed to be significantly elevated in urine from patients with BCa, of which EV-EIF2S1 showed the best diagnostic performance (ROCAUC: 0.83, sensitivity: 80%, specificity: 77%) in the validation cohort. Additionally, EV-EIF2S1 distinguished patients with BCa from non-BCa hematuria patients in a suitable manner (ROCAUC: 0.92, sensitivity: 82%, specificity: 83%). In the functional analysis of EIF2S1 in BCa cell lines T24 and 5637, the knockdown of EIF2S1 markedly inhibited cell proliferation. Cell cycle studies showed that the knockdown of EIF2S1 resulted in cell cycle arrest and induction of apoptosis. Therefore, EIF2S1 was considered an essential protein for the growth and survival of BCa cells. Conclusions: We identified EIF2S1 in uEVs as a novel diagnostic marker for BCa, enabling accurate and non-invasive diagnosis for BCa in a hematuria setting.
ABC transporter expression to predict therapeutic effect of enfortumab vedotin in urothelial cancer.
Authors: Shimoda Hiroki , Takada-Owada Atsuko , Kijima Toshiki , Kokubun Hidetoshi , Uematsu Toshitaka , Takei Kohei , Nakazato Yoshimasa , Yashi Masahiro , Ishida Kazuyuki , Kamai Takao 
Published: January 2024

693 Background: Enfortumab vedotin (EV) is an antibody-drug conjugate consisting of anti-Nectin-4 antibody and is approved for metastatic urothelial cancer. Predictors of therapeutic benefit of EV have not been established since nectin-4 expression varies widely with the course of treatment. ATP Binding Cassette (ABC) transporters which export the administered anti-cancer drugs out of the cells have been postulated as one of the mechanisms of therapeutic resistance to EV. In this study, we evaluated the expression of Nectin-4 and ABC transporters in primary biopsy tissues, primary radical resection tissues, and metastatic sites from urothelial cancer patients and evaluated their association with prognosis after EV therapy. Methods: We studied 16 patients who received enfortumab vedotin for metastatic urothelial cancer. Biopsy of primary tissue, radical surgery of primary tumor, and resection of metastatic sites was performed in 16, 7, and 4 patients, respectively. In these specimens, the expression of nectin-4 and ABC transporters was evaluated by immunostaining. Among ABC transporters, we evaluated MDR1 (ABCB1), MRP1 (ABCC1), and BCRP (ABCG2) since they have been reported to be associated with anticancer drug resistance. Staining intensity on the cell membrane was classified into 0 to 3 according to the evaluation criteria of HER2. We investigated the relationship between the expression of nectin-4 and ABC transporters and survival after EV therapy. Results: Nectin-4 was positive in all patients (score 3 in 12 patients, score 1 in 4 patients) in primary biopsy. All patients tested negative for MDR1. MRP1 was positive in 11 (score 2 in 2 patients and score 1 in 9 patients), and BCRP was positive in 14 (score 2 in 10 patients, score 1 in 4 patients). Nectin-4 expression decreased in radical surgery tissues and metastatic sites. On the other hand, ABC transporter expression remained unchanged or rather increased in radical surgery tissues and metastatic sites (Table). Patients with both MRP1 and BCRP expression in the primary biopsy specimen (n=8) had significantly worse PFS and OS after EV therapy while nectin-4 expression in the primary biopsy specimen was not associated with survival. Conclusions: Patients with ABC transporter expression had a poor prognosis after EV therapy, although nectin-4 expression in primary biopsies was not associated with prognosis. Nectin-4 expression tended to decrease, while the ABC transporter remained unchanged or enhanced as the disease progressed. [Table: see text]
Population based trends in intravesical gemcitabine use among patients with high-risk non-muscle invasive bladder cancer.
Authors: Williams Stephen B. , He Jinghua , Jackson Aeja , Ireland Andrea , Balaji Hiremagalur Parthasarathy , Huang Wenxi , Shi Qian , Ellis Lorie , Singhal Mukul 
Published: January 2024

699 Background: Intravesical gemcitabine (iGEM) use among patients with high-risk non-muscle invasive bladder cancer (HR NMIBC) has shown effectiveness towards preventing or delaying tumor recurrence, although Bacillus Calmette-Guérin (BCG) remains the standard of care for newly diagnosed HR NMIBC. This retrospective cohort study investigated iGEM users and reported their treatment patterns among SEER-Medicare enrollees newly diagnosed with HR NMIBC patients naïve (BCG-N) or exposed (BCG-Exp) to BCG therapy. Methods: Patients enrolled inMedicare Part A & B fee-for-service enrolled, with HR NMIBC, defined by Tis, Ta, T1, N0, M0 and ≥65 years with iGEM use between 2008-2020 were evaluated. Patients with missing TNM stage, low/ intermediate risk NMIBC, or other primary cancers were excluded. Index date was defined as the first claim of iGEM after HR NMIBC diagnosis, regardless of their prior BCG use. Patients were followed until the earliest event of death, end of Medicare advantage enrollment, or data availability end (12/31/2020). Demographic and clinical characteristics were reported in the baseline period (12-month pre-index) and treatment patterns were reported calendar year post-index date for BCG-N and BCG-Exp cohorts. Results: The analysis included 277 BCG-N and 402 BCG-Exp patients receiving iGEM. In both cohorts, mean age was >75 years, ≥80% were male, and >90% were White. The mean (SD) national cancer index comorbidity index score was 0.85 (0.7) for BCG-N and 0.63 (0.7) for BCG-Exp. Intravesical therapy use beyond a perioperative instillation during the baseline period was observed in 27% of BCG-N and 14% of BCG-Exp patients; docetaxel (17% BCG-N, <1% BCG-Exp) and mitomycin (12% BCG-N, 14% BCG-Exp) were most common. The median number of iGEM doses in the BCG-N group was 6 (IQR 1,8) with mean (SD) of 28 (43) days of retreatment interval. In BCG-Exp, the median number of iGEM doses was 6 (IQR 2,9) with mean (SD) of 23 (26) days of retreatment interval. The table shows increasing iGEM use in both BCG-N and BCG-Exp groups, with 70% of BCG-N in years 2019 through 2020, and 22-30% of BCG-Exp patients receiving iGEM in years 2017 through 2020. Conclusions: Recent BCG shortages may have played a significant role in recent increased uptake of iGEM in both BCG-N and BCG-Exp cohort among HR NMIBC patients. Further information on the efficacy and safety outcomes of iGEM vs BCG in various HR NMIBC populations are needed. [Table: see text]